CHEETAH Center Publications
CHEETAH Center Publications
Funding Cycle I (66 papers published)
Funding Cycle II (93 papers published)
2007
1. Wright ER, Schooler JB, Ding HJ, Kieffer C, Fillmore C, Sundquist WI, Jensen GJ. (2007). Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells. EMBO J. 26(8):2218-26. PMCID: PMC1852790.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852790/
Cores: EM Tomography, Virology
2. Morita E, Sandrin V, Alam SL, Eckert DM, Gygi SP, Sundquist WI. (2007). Identification of human MVB12 proteins as ESCRT-I subunits that function in HIV budding. Cell Host Microb. 2(1):41-53. PMCID: PMC2034311.
http://www.ncbi.nlm.nih.gov/pubmed/18005716
Cores: Virology, Hydrodynamics, Eukaryotic Protein Expression
3. Welch BD, VanDemark AP, Heroux A, Hill CP, Kay MS. (2007). Potent D-peptide inhibitors of HIV-1 entry. Proc Natl Acad Sci USA. 104(43):16828-33. PMCID: PMC2040420.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2040420/
Core: Hydrodynamics, X-ray Crystallography
4. Kelly BN, Kyere S, Kinde I, Tang C, Howard BR, Robinson H, Sundquist WI, Summers MF, Hill CP. (2007). Structure of the antiviral assembly inhibitor CAP-1 complex with the HIV-1 CA protein. J Mol Biol. 373(2):355-66. PMCID: PMC2066180.
http://www.ncbi.nlm.nih.gov/pubmed/17826792
Cores: X-ray Crystallography, Virology
5. Neil SJ, Sandrin V, Sundquist WI, Bieniasz PD. (2007). An interferon-alpha-induced tethering mechanism inhibits HIV-1 and Ebola virus particle release but is counteracted by the HIV-1 Vpu protein. Cell Host Microb. 2(3):193-203. PMCID: PMC3793644.
http://www.ncbi.nlm.nih.gov/pubmed/18005734
Core: Virology
6. Fisher RD, Chung HY, Zhai Q, Robinson H, Sundquist WI, Hill CP. (2007). Structural and Biochemical Studies of ALIX/AIP1 and Its Role in Retrovirus Budding. Cell. 128(5):841-52. PMID: 17350572.
http://www.ncbi.nlm.nih.gov/pubmed/17350572
Cores: X-ray Crystallography, Virology, Bacterial Protein Expression
7. Higa MM, Alam SL, Sundquist WI, Ullman KS. (2007). Molecular characterization of the Ran-binding zinc finger domain of Nup153. J Biol Chem. 282(23):17090-100. PMID:17426026.
http://www.ncbi.nlm.nih.gov/pubmed/17426026
Core: Protein NMR Spectroscopy
8. Sundquist WI, Hill CP. (2007). How to assemble a capsid. Cell. 131(1):17-9. PMID: 17923081.
https://www.ncbi.nlm.nih.gov/pubmed/?term=17923081
Cores: Virology, X-ray Crystallography
9. Ganser-Pornillos BK, Cheng A, Yeager M. (2007). Structure of full-length HIV-1 CA: a model for the mature capsid lattice. Cell. 131(1):70-9. PMID: 17923088.
http://www.ncbi.nlm.nih.gov/pubmed/17923088
Core: EM Crystallography
10. Stuchell-Brereton MD, Skalicky JJ, Kieffer C, Karren MA, Ghaffarian S, Sundquist WI. (2007). ESCRT-III recognition by VPS4 ATPases. Nature. 449(7163):740-4. PMID: 17928862.
http://www.ncbi.nlm.nih.gov/pubmed/17928862
Cores: Protein NMR Spectroscopy, Virology, Protein Interactions
2008
11. Campbell EM, Perez O, Anderson JL, Hope TJ. (2008). Visualization of a proteasome-independent intermediate during restriction of HIV-1 by rhesus TRIM5alpha. J Cell Biol. 180(3):549-61. PMCID: PMC2234241.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2234241/
Core: Virus Imaging
12. Edgcomb SP, Aschrafi A, Kompfner E, Williamson JR, Gerace L, Hennig M. (2008). Protein structure and oligomerization are important for the formation of export-competent HIV-1 Rev-RRE complexes. Protein Sci. 17(3)420-30. PMCID: PMC2248316.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248316/
Cores: Cell Biology/Imaging, Biochemistry
13. Leblanc JJ, Perez O, Hope TJ. (2008). Probing the structural states of human immunodeficiency virus type 1 pr55gag by using monoclonal antibodies. J. Virol. 82(5):2570-74. PMCID: PMC2258915.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2258915
Cores: Virus Imaging
14. Kim S, Pang HB, Kay MS. (2008). Peptide mimic of the HIV envelope gp120-gp41 interface. J Mol Biol. 376(3):786-9. PMCID: PMC2265733.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265733/
Core: Hydrodynamics
15. Yu Z, Gonciarz MD, Sundquist WI, Hill CP, Jensen GJ. (2008). Cryo-EM structure of dodecameric Vps4p and its 2:1 complex with Vta1p. J Mol Biol. 377(2):364-77. PMCID: PMC2279015.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2279015
Cores: EM Tomography, X-ray Crystallography, Virology, Bacterial Protein Expression
16. McCullough J, Fisher RD, Whitby FG, Sundquist WI, Hill CP. (2008). ALIX-CHMP4 interactions in the human ESCRT pathway. Proc Natl Acad Sci USA. 105(22):7687-91. PMCID: PMC2409388.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2409388
Cores: X-ray Crystallography, Virology
17. Langelier CR, Sandrin V, Eckert DM, Christensen DE, Chandrasekaran V, Alam SL, Aiken C, Olsen JC, Kar AK, Sodroski JG, Sundquist WI. (2008). Biochemical characterization of a recombinant TRIM5alpha protein that restricts human immunodeficiency virus type 1 replication. J Virol. 82(23):11682-94. PMCID: PMC2583683.
http://jvi.asm.org/content/82/23/11682.long
Cores: Eukaryotic Protein Expression, Hydrodynamics, Virology
18. Kieffer C, Skalicky JJ, Morita E, De Dominico I, Ward DM, Kaplan J, Sundquist WI. (2008). Two distinct modes of ESCRT-III recognition are required for VPS4 functions in lysosomal protein targeting and HIV-1 budding. Dev Cell. 15(1):62-73. PMCID: PMC2586299.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2586299
Cores: Protein NMR Spectroscopy, Protein Interactions
19. Eckert DM, Shi Y, Kim S, Welch BD, Kang E, Poff ES, Kay MS. (2008). Characterization of the steric defense of the HIV-1 gp41 N-trimer region. Protein Sci. 17(12):2091-100. PMCID: PMC2590922.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2590922
Core: Hydrodynamics
20. Gonciarz MD, Whitby FG, Eckert DM, Kieffer C, Heroux A, Sundquist WI, Hill CP. (2008). Biochemical and structural studies of yeast Vps4 oligomerization. J Mol Biol. 384(4):878-95. PMCID: PMC2632936.
http://www.ncbi.nlm.nih.gov/pubmed/18929572
Cores: X-ray Crystallography, Virology, Bacterial Protein Expression
21. Ganser-Pornillos BK, Yeager M, Sundquist WI. (2008). The structural biology of HIV assembly. Curr Opin Struct Biol. 18(2):203-17. PMCID: PMC2819415.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2819415
Cores: Virology, EM Crystallography
22. Lee E, Fahimian BP, Iancu CV, Suloway C, Murphy GE, Wright ER, Castano-Diez D, Jensen GJ, Miao J. (2008). Radiation dose reduction and image enhancement in biological imaging through equally sloped tomography. J Struct Biol. 16(2):221-7. PMCID: PMC3099251.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099251/
Core: EM Tomography
23. Natarajan S, Katsamba PS, Miles A, Eckman J, Papalia GA, Rich RL, Gale BK, Myszka DG. (2008). Continuous-flow microfluidic printing of proteins for array-based applications including surface plasmon resonance imaging. Anal Biochem. 373(2):141-6. PMID: 17868635.
http://www.ncbi.nlm.nih.gov/pubmed/17868635
Core: Protein Interactions
24. Zhai Q, Fisher RD, Chung H-Y, Myszka DG, Sundquist WI, Hill CP. (2008). Structural and functional studies of ALIX interactions with YPX(n)L late domains of HIV-1 and EIAV. Nature Struct Mol Biol. 15(1):43-9. PMID: 18066081.
http://www.ncbi.nlm.nih.gov/pubmed/18066081
Core: X-ray Crystallography, Virology, Protein Interactions
2009
25. Pond SJ, Ridgeway WK, Robertson R, Wang J, Millar DP. (2009). HIV-1 Rev protein assembles on viral RNA one molecule at a time. Proc Natl Acad Sci. 106(5):1404-8. PMCID: PMC2635779.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2635779
Cores: Fluorescence Spectroscopy, Biochemistry
26. Szymczyna BR, Taurog RE, Young MJ, Snyder JC, Johnson JE, Williamson JR. (2009). Synergy of NMR, computation, and x-ray crystallography for structural biology. Structure. 17(4):499-507. PMCID: PMC2705668.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705668/
Core: Biochemistry
27. Bajorek M, Schubert HL, McCullough J, Langelier C, Eckert DM, Stubblefiel W-M B, Uter NT, Myszka DG, Hill CP, Sundquist WI. (2009). Structural basis for ESCRT-III protein autoinhibition. Nature Struct Mol Biol. 16(7):754-62. PMCID: PMC2712734.
http://www.ncbi.nlm.nih.gov/pubmed/?term=pmc2712734
Cores: Virology, X-ray Crystallography, Bacterial Protein Expression
28. Suloway C, Shi J, Cheng A, Pulokas J, Carragher B, Potter CS, Zheng SQ, Agard DA, Jensen GJ. (2009). Fully automated, sequential tilt-series acquisition with Leginon. J Struct Biol. 167(1):11-8. PMCID: PMC2724967.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2724967/
Core: EM Tomography
29. Pornillos O, Ganser-Pornillos BK, Kelly BN, Hua Y, Whitby FG, Stout CD, Sundquist WI, Hill CP, Yeager M. (2009). X-ray structures of the hexameric building block of the HIV capsid. Cell. 137(7):1282-92. PMCID: PMC2840706.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2840706
Cores: EM Crystallography, X-ray Crystallography, Virology
30. Tivol WF, Briegel A, Jensen GJ. (2009). An improved cryogen for plunge freezing. Microscopy and Microanalysis. 14(5):375-9. PMCID: PMC3058946.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058946/
Core: EM Tomography
31. Eddings MA, Eckman JW, Arana CA, Connolly JE, Papalia GA, Gale BK, Myszka DG. (2009). Spot and Hop – Internal referencing for surface plasmon resonance imaging using a three-dimensional microfluidic flow cell array. Anal Biochem. 385(2):309-13. PMID: 19059374.
http://www.ncbi.nlm.nih.gov/pubmed/?term=19059374
Core: Protein Interactions
2010
32. Krishna V, Ayton GS, Voth GA. (2010). Role of protein interactions in defining HIV-1 capsid shape and stability: A coarse-grained analysis. J Biophys. 98(1):18-26. PMCID: PMC2800964.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800964/
Core: Computation
33. Chow JYH, Jeffries CM, Kwan AH, Guss JM, Trewhella J. (2010). Calmodulin disrupts the structure of the HIV-1 MA protein. J Mol Biol. 400(4):702-14. PMCID: PMC2902600.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2902600
Core: Small Angle Scattering
34. Rich RL, Quinn JG, Morton T, Stepp JD, Myszka DG. (2010). Biosensor-based fragment screening using FastStep injections. Analytical Biochemistry. 407(2):270-7. PMCID: PMC2949542.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2949542
Core: Protein Interactions
35. Welch BD, Francis JN, Redman JS, Paul S, Weinstock MT, Whitby FG, Eckert DM, Hill CP, Root MJ, Kay MS. (2010). Design of a potent D-peptide HIV-1 entry inhibitor with a strong barrier to resistance. J Virol. 84(21):11235-44. PMCID: PMC2953169.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2953169
Core: Hydrodynamics, X-ray Crystallography
36. Schubert HL, Zhai Q, Sandrin V, Eckert DM, Garcia-Maya M, Saul L, Sundquist WI, Steiner RA, Hill CP. (2010). Structural and functional studies on the extracellular domain of BST2/Tetherin in its reduced and oxidized conformations. Proc Natl Acad Sci. 107(42):17951-6. PMCID: PMC2964199.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2964199
Cores: X-ray Crystallography, Virology, Bacterial Protein Expression
37. Ayton GS, Voth GA. (2010). Multiscale computer simulation of the immature HIV-1 virion. Biophys J. 99(9):2757-65. PMCID: PMC2966041.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2966041
Core: Computation
38. Koirala S, Bui HT, Schubert HL, Eckert DM, Hill CP, Kay MS, Shaw JM. (2010). Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes. J Cell Biol. 191(6):1127-39. PMCID: PMC3002026.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3002026
Cores: Hydrodynamics, X-ray Crystallography
39. Fu CY, Wang K, Gan L, Lanman J, Khayat R, Young MJ, Jensen GJ, Doerschuk PC, Johnson JE. (2010). In vivo assembly of an archaeal virus studied with whole-cell electron cryotomography. Structure. 18(12):1579-85. PMCID: PMC3042139.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3042139
Core: EM Tomography
40. Pornillos OW, Ganser-Pornillos BK, Banumathi S, Hua Y, Yeager M. (2010). Disulfide bond stabilization of the hexameric capsomer of human immunodeficiency virus. J Mol Biol. 401(5):985-95. PMCID: PMC3050670.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3050670
Core: EM Crystallography
41. Briegel A, Chen S, Koster AJ, Plitzko JM, Schwartz CL, Jensen GJ. (2010). Correlated light and electron microscopy. Meth Enzymol. 481:317-41. PMID: 20887863.
http://www.ncbi.nlm.nih.gov/pubmed/?term=20887863
Core: EM Tomography
2011
42. Zhai Q, Landesman MB, Robinson H, Sundquist WI, Hill CP. (2011). Identification and structural characterization of the ALIX-binding late domains of simian immunodeficiency virus SIVmac239 and SIVagmTan-1. J Virol. 85(1):632-7. PMCID: PMC3014167.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3014167
Cores: X-ray Crystallography, Virology, Protein Interactions
43. Ganser-Pornillos BK, Chandrasekaran V, Pornillos OW, Sodroski JG, Sundquist WI, Yeager M. (2011). Hexagonal assembly of a restricting TRIM5a protein. Proc Natl Acad Sci. 108(2):534-9. PMCID: PMC3021009.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3021009
Cores: EM Crystallography, Eukaryotic Expression, Hydrodynamics, Virology
44. Pornillos O, Ganser-Pornillos BK, Yeager M. (2011). Atomic-level modeling of the HIV capsid. Nature. 469(7330):424-7. PMCID: PMC3075868.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3075868
Core: EM Crystallography
45. Swulius MT, Chen S, Ding JH, Li Z, Briegel A, Pilhofer M, Tocheva EI, Lybarger SR, Johnson TL, Sandkvist M, Jensen GJ. (2011). Long helical filaments are not seen encircling cells in electron cryotomograms of rod-shaped bacteria. Biochem Biophys Res Commun. 407(4):650-5. PMCID: PMC3093302.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3093302
Core: EM Tomography
46. Guerrero-Ferreira R, Viollier P, Ely B, Poindexter J, Goergieva M, Jensen GJ, Wright E. (2011). Alternative mechanism for bacteriophage adsorption to the motile bacterium Caulobacter crescentus. Proc Natl Acad Sci. 108(24):9963-8. PMCID: PMC3116389.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3116389
Core: EM Tomography
47. Hulme A, Perez O, Hope TJ. (2011). Complementary assays reveal a relationship between HIV-1 uncoating and reverse transcription. Proc Natl Acad Sci. 108(24):9975-80. PMCID: PMC3116424.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3116424
Core: Virus Imaging
48. Diaz-Griffero F, Gallo DE, Hope TJ, Sodroski J. (2011). Trafficking of some old world primate TRIM5a proteins through the nucleus. Retrovirology. 8:38. PMCID: PMC3120760.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120760/
Core: Virus Imaging
49. Schultheisz HL, Szymczyna BR, Scott LG, Williamson JR. (2011). Enzymatic de Novo Pyrimidine Nucleotide Synthesis. J Am Chem Soc. 133(2):297-304. PMCID: PMC3134529.
http://www.ncbi.nlm.nih.gov/pubmed/21166398
Core: Biochemistry
50. Robertson-Anderson R, Wang J, Edgcomb S, Carmel A, Williamson JR, Millar DP. (2011). Single-molecule studies reveal that DEAD-Box protein DDX1 promotes oligomerization of HIV-1 Rev on the Rev Response Element. J Mol Biol. 410(5):959. PMCID: PMC3140434.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3140434
Cores: Fluorescence Spectroscopy, Biochemistry
51. Zhai Q, Landesman MB, Chung H-Y, Dierkers A, Jeffries CM, Trewhella J, Hill CP, Sundquist WI. (2011). Activation of the retroviral budding factor ALIX. J Virol. 85(17):9222-6. PMCID: PMC3165844.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3165844
Cores: X-ray Crystallography, Virology, Protein Interactions
52. Yeager M. (2011). Design of in vitro Symmetric Complexes and Analysis by Hybrid Methods Reveal Mechanisms of HIV Capsid Assembly. J Mol Biol. 410(4):534-52. PMCID: PMC3166646.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166646/
Core: EM Crystallography
53. Zhai Q, Landesman M, Robinson H, Sundquist WI, Hill CP. (2011). Structure of the Bro1 domain containing protein BROX and functional analyses of the ALIX Bro1 domain in HIV-1 budding. PLoS One. 6(12):e27466. PMCID: PMC3230590.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3230590
Cores: X-ray Crystallography, Virology, Protein Interactions
54. Gan L, Ladinsky MS, Jensen GJ. (2011). Organization of the smallest eukaryotic spindle. Curr Bio. 21(18):1578-83. PMCID: PMC3234289.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3234289
Core: EM Tomography
55. Puglisi, EV & Puglisi, JD (2011). Secondary structure of the HIV reverse transcription initiation complex by NMR. J. Mol Biol. 410(5):863-74. PMCID: PMC3710119
https://www.ncbi.nlm.nih.gov/pubmed/21763492
Core: RNA Structure and Dynamics
2012 (cont. after Cycle II grant award)
56. Edgcomb SP, Carmel AB, Naji S, Ambrus-Aikelin G, Reyes JR, Thompson J, Saphire AC, Gerace L, Williamson JR. (2012). DDX1 is an RNA-Dependent ATPase Involved in HIV-1 Rev Function and Virus Replication. J Mol Biol. 415(1):61-74. PMCID: PMC3249508.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249508/
Cores: Biochemistry, Cell Biology/Imaging
57. Jägger S, Cimermancic P, Gulbahce N, Johnson J, McGovern K, Clarke SC, Shales M, Mercenne G, Li K, Barry H, Jang GM, Akiva E, Pache L, Marlett J, Shoshannah LR, Stephens M, D’Orso I, Fernandes J, Fahey M, Mahon C, O’Donoghue AJ, Todorovic A, Morris JH, Maltby D, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez R, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. (2012). Global landscape of HIV-human protein complexes. Nature. 481(7381):365-70. PMCID: PMC3310911.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3310911
Core: Virology
58. Naji S, Ambrus G, Cimermančič P, Reyes JR, Johnson J, Filbrandt R, Huber MD, Vesely P, Yates 3rd JR, Krogan NJ, Saphire AC, Gerace L. (2012). Host cell interactome of HIV-1 Rev revealed by comparative proteomics includes RNA helicases that function in multiple steps of virus replication. Mol Cell Proteom. 11(4):M111.015313. PMCID: PMC3322577.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322577/
Core: Cell Biology/Imaging
59. Kräusslich H-G, Sundquist WI. (2012). HIV Assembly, Budding and Maturation. HIV in Cold Spring Harbor Perspectives. 2(7):95-118. PMCID: PMC3385941.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3385941
Core: Virology
60. Lemke CT, Titolo S, von Schwedler U, Goudreau N, Mercier JF, Wardrop E, Faucher AM, Coulombe R, Banik SS, Fader L, Gagnon A, Kawai SH, Rancourt J, Tremblay M, Yoakim C, Simoneau B, Archambault J, Sundquist WI, Mason SW. (2012). Distinct effects of two HIV-1 capsid assembly inhibitor families that bind the same site within the N-terminal domain of the viral CA protein. J Virol. 86(12):6643-55. PMCID: PMC3393593.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3393593/
Core: Virology
61. Grime JMA, Voth GA. (2012). Early Stages of the HIV-1 capsid protein lattice formation. Biophys J. 103(8):1774-83. PMCID: PMC3475334.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3475334
Core: Computation
62. Skalicky JJ, Arii J, Wenzel D, Stubblefield W-MB, Kztsuyama A, Uter NT, Bajorek M, Myszka DG, Sundquist WI. (2012). ESCRT-III interactions of the human LIP5 protein. J Biol Chem. 287(52):43910-26. PMCID: PMC3527974.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527974/
Core: Protein NMR Spectroscopy, Protein Interactions
63. Neves MA, Yeager M, Abagyan R. (2012). Unusual arginine formations in protein function and assembly: rings, stirngs, and stacks. J Phys Chem B. 116(23):7006-13. PMCID: PMC3613333.
http://www.ncbi.nlm.nih.gov/pubmed/?term=22497303
Core: Administration (Administrative supplement)
64. Gallo D., Hope TJ. (2012). Knockdown of MAP4 and DNAL1 produces a post-fusion and pre-nuclear translocation impairment in HIV-1 replication. Virology. 422(1):13-21. PMCID: PMC3732191
http://www.ncbi.nlm.nih.gov/pubmed/?term=22018492
Core: Virus Imaging
65. Pljevaljcic P, Robertson-Anderson R, Millar DP. (2012). Analysis of RNA folding and ribonucleoprotein assembly by single-molecule fluorescence spectroscopy. Meth Mol Bio. 875:271-95. PMCID: PMC3744346.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744346/
Core: Fluorescence Spectroscopy
66. Danielson CM, Cianci GC, Hope TJ. (2012). Recruitment and dynamics of proteasome association with rhTRIM5α cytoplasmic complexes during HIV-1 infection. Traffic. 13(9):1206-17. PMCID: PMC3760259.
http://www.ncbi.nlm.nih.gov/pubmed/22624877
Core: Virus Imaging
67. Effanin G, Dordor A, Sandrin V, Martinelli N, Sundquist WI, Schoehn G, Weissenhorn W. (2012). ESCRT-III CHMP2A and CHMP3 form variable helical polymers in vitro and act synergistically during HIV-1 budding. Cell Microbiol. 15(2): 213-26. PMCID: PMC3783020.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783020/
Core: Virology
68. Gan L, Jensen GJ. (2012). Electron tomography of cells. Quart Rev Biophys. 45(1):27-56. PMID: 22082691.
http://www.ncbi.nlm.nih.gov/pubmed/?term=22082691
Core: EM Tomography
69. Ganser-Pornillos BK, Yeager M, Pornillos O. (2012). Assembly and Architecture of HIV. Adv Exp Med Biol. 726:441-65. PMID: 22297526.
http://www.ncbi.nlm.nih.gov/pubmed/?term=22297526
Core: EM Crystallography
70. Sundquist WI, Krug RM. (2012). Structural Biology: Assemble, replicate, remodel and evade. Curr Opin Virol. 2(2):111-4. PMID: 22482706.
http://www.sciencedirect.com/science/article/pii/S1879625712000351
Core: Virology
2013
71. Hill CP, Sundquist WI. (2013). Building a super elongation complex for HIV. eLIFE. 2:e00577. PMCID: PMC3592195.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3592195
Cores: X-ray Crystallography and Virology
72. Yu Z, Dobro MJ, Woodward CL, Levandoski A, Danielson C, Sandrin V, Shi J, Aiken C, Zandi R, Hope TJ, Jensen GJ. (2013). Unclosed HIV-1 capsids suggest a curled sheet model of assembly. J Mol Biol. 425(1):112-23. PMCID: PMC3597093.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597093/
Cores: EM Tomography, Virus Imaging, Virology
73. Koirala S, Guo Q, Kalia R, Bui HT, Eckert DM, Frost A, Shaw JM. (2013). Interchangeable adaptors regulate mitochondrial dynamin assembly for membrane scission. Proc Natl Acad Sci USA. 110(15):E1342-51. PMCID: PMC3625255.
http://www.ncbi.nlm.nih.gov/pubmed/?term=23530241
Core: Protein Interactions
74. Dobro MJ, Samson RY, Yu Z, McCullough J, Ding HJ, Chong PL, Bell SD, Jensen GJ. (2013). Electron cryotomography of ESCRT assemblies and dividing Sulfolobus cells suggest spiraling filaments are involved in membrane scission. Mol Biol Cell. 24(15), 2319–27. PMCID: PMC3727925.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3727925/
Core: Electron Tomography
75. Kono K, Takeda E, Tsutsui H, Kuroishi A, Hulme AE, Hope TJ, Nakayama EE, Shioda T. (2013). Slower uncoating is associated with impaired replicative capability of simian-tropic HIV-1. PloS One. 8(8):e72531. PMCID: PMC3742594.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3742594/
Core: Virus Imaging
76. Briegel A, Pilhofer M, Mastronarde D, Jensen GJ. (2013). The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards. J Struct Biol. 183(1):95-8. PMCID: PMC3765063.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765063/
Core: Electron Tomography
77. Danielson CM, Hope TJ. (2013). Using anti-ubiquitin antibodies to probe the ubiquitination state within rhTRIM5α cytoplasmic bodies. AIDS Res Hum Retroviruses. 29(10):1373-85. PMCID: PMC3785812.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785812/
Core: Virus Imaging
78. Lamorte L, Titolo S, Lemke CT, Goudreau N, Mercier JF, Wardrop E, Shah VB, von Schwedler UK, Langelier C, Banik SS, Aiken C, Sundquist WI, Mason SW. (2013). Discovery of Novel Small-Molecule HIV-1 Replication Inhibitors That Stabilize Capsid Complexes. Antimicrob Agents Chemother. 57(10):4622-31. PMCID: PMC3811413.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811413/
Core: Virology
79. Votteler J, Sundquist WI. (2013). Virus Budding and the ESCRT Pathway. Cell Host Microbe. 14(3):232-41. PMCID: PMC3819203.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819203/
Core: Virology
80. Brandariz-Nuñez A, Valle-Casuso JC, White TE, Nguyen L, Bhattacharya A, Wang Z, Demeler B, Amie S, Knowlton C, Kim B, Ivanov DN, Diaz-Griffero F. (2013). Contribution of oligomerization to the anti-HIV-1 properties of SAMHD1. Retrovirology. 10(1):131. PMCID: PMC3882887.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3882887/
Core: Administration (Collaborative Development Award)
81. Monroe N, Han H, Gonciarz MD, Eckert DM, Karren MA, Whitby FG, Sundquist WI, Hill CP. (2013). The oligomeric state of the active Vps4 AAA ATPase. J Mol Biol. 426(3):510-25. PMCID: PMC3919030.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919030/
Cores: X-ray Crystallography, Bacterial Protein Expression, Virology, Protein Interactions
82. McCullough J, Colf LA, Sundquist WI. (2013). Membrane fission reactions of the mammalian ESCRT pathway. Annu Rev Biochem. 82:663-92. PMCID: PMC4047973.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4047973/
Core: Virology
83. Yeager M, Dryden KA, Ganser-Pornillos BK. (2013). Lipid monolayer and sparse matrix screening for growing two-dimensional crystals for electron crystallography: methods and examples. Methods Mol. Bio. 955:527-37. PMCID: PMC4127334.
http://www.ncbi.nlm.nih.gov/pubmed/?term=23132079
Cores: Eukaryotic Protein Expression, EM Tomography, Electron Crystallography, Administration (Collaborative Development Award), Virology
84. Biris N, Tomashevski A, Bhattacharya A, Diaz-Griffero F, Ivanov DN. (2013). Rhesus monkey TRIM5α SPRY domain recognizes multiple epitopes that span several capsid monomers on the surface of the HIV-1 mature viral core. J Mol Biol. 425(24):5032-44. PMCID: PMC416666.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116666/
Core: Administration (Collaborative Development Award)
85. Rey FA, Sundquist WI. (2013). Macromolecular assemblies. Curr Opin Struct Biol. 23(2):224-8. PMID:23663961.
https://www.ncbi.nlm.nih.gov/pubmed/?term=23663961
Core: Virology
86. Petrov A, Wu T, Puglisi EV, Puglisi JD. (2013). RNA purification by preparative polyacrylamide gel electrophoresis. Methods Enzymol. 2013;530:315-30. PMID: 24034329.
https://www.ncbi.nlm.nih.gov/pubmed/?term=24034329
Core: RNA Structure and Dynamics
2014
87. Yang Y, Brandariz-Nuñez A, Fricke T, Ivanov DN, Sarnak Z, Diaz-Griffero F. (2014). The binding ability of the rhesus TRIM5α PRYSPRY domain to the capsid is necessary but not sufficient for HIV-1 restriction. Virology. 448:217-28. PMCID: PMC3900861.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3900861
Core: Administration (Collaborative Development Award)
88. Ladinsky MS, Kieffer C, Olson G, Deruaz M, Vrbanac V, Tager AM, Kwon DS, Bjorkman PJ. (2014). Electron tomography of HIV-1 infection in gut-associated lymphoid tissue. PLoS Pathogens. 10(1):e003899. PMCID: PMC3907528.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3907528
Core: Tissue EM
89. Sanchez JG, Okreglicka K, Chandrasekaran V, Welker JM, Sundquist WI, Pornillos O. (2014). The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer. Proc Natl Acad Sci. 111(7):2494-9. PMCID: PMC3932864.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932864/
Cores: Eukaryotic Protein Expression, Protein Interactions
90. Ren J, Pei-Chen LC, Pathak MC, Temple BR, Nile AH, Mousley CJ, Duncan MC, Eckert DM, Leiker TJ, Ivanova PT, Myers DS, Murphy RC, Brown HA, Verdaasdonk J, Bloom KS, Ortlund EA, Neiman AM, Bankaitis VA. (2014). A phosphatidylinositol transfer protein integrates phosphoinositide signaling with lipid droplet metabolism to regulate a developmental program of nutrient stress-induced membrane biogenesis. Mol Biol Cell. 25(5):712-27. PMCID: PMC3937096.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937096/
Core: Protein Interactions
91. Narayan K, Danielson CM, Lagarec K, Lowekamp BC, Coffman P, Laquerre A, Phaneuf MW, Hope TJ, Subramaniam S. (2014). Multi-resolution correlative focused ion beam scanning electron microscopy: applications to cell biology. J Struct Biol. 85(3):278-84. PMCID: PMC3943650.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943650/
Core: Virus Imaging
92. Hulme AE, Hope TJ. (2014). The cyclosporin A washout assay to detect HIV-1 uncoating in infected cells. Methods Mol Biol. 1087:37-46. PMCID: PMC4084958.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084958/
Core: Virus Imaging
93. Kovalskyy DB, Ivanov DN. (2014). Recognition of the HIV capsid by the TRIM5α restriction factor is mediated by a subset of pre-existing conformations of the TRIM5α SPRY domain. Biochemistry. 53(9):1466-76. PMCID: PMC4119003.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119003/
Core: Administration (Collaborative Development Award)
94. Sastri J, Johnsen L, Smolin N, Imam S, Mukherjee S, Lukic Z, Brandariz-Nunez A, Robia SL, Diaz-Griffero F, Wiethoff C, Campbell EM. (2014) Restriction of HIV-1 by rhesus TRIM5alpha is governed by alpha helices in the Linker2 region. J Virol 88, 8911-23. PMCID: PMC4136267.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136267/
Core: Administration (Collaborative Development Award)
95. Fricke T, White TE, Schulte B, de Souza Aranha Vieira DA, Dharan A, Campbell EM, Brandariz-Nunez A, Diaz-Griffero F. (2014) MxB binds to the HIV-1 core and prevents the uncoating process of HIV-1. Retrovirology 11(68). PMCID: PMC4145229.
https://www.ncbi.nlm.nih.gov/pmc/?term=PMC4145229
Core: Administration (Collaborative Development Award)
96. Stieh DJ, Maric D, Kelley ZL, Anderson MR, Hattaway HZ, Beilfuss BA, Rothwangl KB, Veazey RS, Hope TJ. (2014). Vaginal challenge with an SIV-based dual reporter system reveals that infection can occur throughout the upper and lower female reproductive tract. PLoS Pathog. 10(10):e1004440 PMCID: PMC4192600.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4192600
Core: Virus Imaging
97. Lukic Z, Dharan A, Fricke T, Diaz-Griffero F, Campbell EM. (2014) HIV-1 uncoating is facilitated by dynein and kinesin 1. J Virol 88, 13613-25. PMCID: PMC4248982.
https://www.ncbi.nlm.nih.gov/pmc/?term=PMC4248982
Core: Administration (Collaborative Development Award)
98. Chen J, Grünwald D, Sardo L, Galli A, Plisov S, Nikolaitchik OA, Chen D, Lockett S, Larson DR, Pathak VK, Hu WS. (2014). Cytoplasmic HIV-1 RNA is mainly transported by diffusion in the presence or absence of Gag protein. Proc Natl Acad Sci USA. 111(48):E5205-13. PMCID: PMC4260538.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4260538
Core: Administration (Collaborative Development Award)
99. Bhattacharya A, Alam, SL Fricke T, Zadrozny K, Sedzicki J, Taylor AB, Demeler B, Pornillos O, Ganser-Pornillos BK, Diaz-Griffero F, Ivanov DN, Yeager, M. (2014). Structural basis of HIV-1 capsid recognition by PF74 and CPSF6. Proc Natl Acad Sci. 111(52):18625-30. PMCID: PMC4284599.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284599/
Cores: EM Crystallography, Administration (Collaborative Development Award), Eukaryotic Protein Expression
100. Purdy MD, Bennett BC, McIntire WE, Khan AK, Kasson PM, Yeager M. (2014). Function and dynamics of macromolecular complexes explored by integrative structural and computational biology. Curr Opin Struct Biol. 27:138-48. PMID: 25238653.
http://www.ncbi.nlm.nih.gov/pubmed/?term=25238653
Cores: Administration (Administrative supplement) and EM Crystallography
2015
101. Woodward CL, Cheng SN, Jensen GJ. (2015). Electron cryotomography studies of maturing HIV-1 particles reveal the assembly pathway of the viral core. J Virol. 89(2):1267-77. PMCID: PMC4300640.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4300640
Core: Electron Tomography
102. Hulme AE, Kelley Z, Okocha EA, Hope TJ. (2015). Identification of capsid mutations that alter the rate of HIV-1 uncoating in infected cells. J Virol. 89(1):643-51. PMCID: PMC4301138.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4301138
Core: Virus Imaging
103. Mercenne G, Alam SL, Arii J, Lalonde MS, Sundquist WI. (2015). Angiomotin functions in HIV-1 assembly and budding. eLife. 4:e03778. PMCID: PMC4337731.
http://www.ncbi.nlm.nih.gov/pubmed/25633977
Core: Virology
104. VanderLinden RT, Hemmis CW, Schmitt B, Ndoja A, Whitby FG, Robinson H, Cohen RE, Yao T, Hill CP. (2015). Structural basis for the activation and inhibition of the UCH37 deubiquitylase. Mol Cell. 57(5):901-11. PMCID: PMC4355076.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355076/
Cores: X-ray Crystallography, Bacterial Expression
105. Takeda E, Kono K, Hulme AE, Hope TJ, Nakayama EE, Shioda T. (2015). Fluorescent image analysis of HIV-1 and HIV-2 uncoating kinetics in the presence of old world monkey TRIM5α. PLoS One. 10(3):e0121199. PMCID: PMC4372348.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4372348/
Core: Virus Imaging
106. Clinton TR, Weinstock MT, Jacobsen MT, Szabo-Fresnais N, Pandya MJ, Whitby FG, Herbert AS, Prugar LI, McKinnon R, Hill CP, Welch BD, Dye JM, Eckert DM, Kay MS. (2015). Design and characterization of ebolavirus GP prehairpin intermediate mimics as drug targets. Protein Sci. 24(4):446-63. PMCID: PMC4380977.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380977/
Cores: Protein Interactions, X-ray Crystallography
107. Hancks DC, Hartley MK, Hagan C, Clark NL, Elde NC. (2015). Overlapping patterns of rapid evolution in the nucleic acid sensors cGAS and OAS suggest a common mechanism of pathogen antagonism and escape. PLOS Genetics. 11(5): e1005203. PMCID: PMC4420275.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4420275
Core: Administration (Collaborative Development Award)
108. Zhao H, Eckert DM. (2015). A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation. Plos One. 10(5):e0126420. PMCID: PMC4440767.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4440767
Core: Protein Interactions
109. Smith CSS, Preibisch S, Joseph A, Abrahamsson S, Rieger B, Myers E, Singer RHS, Grünwald D. (2015). Nuclear accessibility of beta-actin mRNA is measured by 3D single-molecule real-time tracking. J Cell Biol. 209(4):609-19. PMCID: PMC4442804.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4442804
Core: Administration (Collaborative Development Award)
110. DePaula-Silva AB, Cassiday PA, Chumley J, Bosque A, Monteiro-Filho CM, Mohan CS, Cone KR, Krogan N, Elde NC, Planelles V. (2015). Determinants for degradation of SAMHD1, Mus81 and induction of G2 arrest in HIV-1 Vpr and SIVagm Vpr. Virology 477:10-17. PMCID: PMC4455942.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4455942
Core: Administration (Collaborative Development Award) and Administrative Supplement
111. Han H, Monroe N, Votteler J, Shakya B, Sundquist WI, Hill CP. (2015). Binding of substrates to the central pore of the Vps4 ATPase is autoinhibited by the microtubule interacting and trafficking (MIT) domain and activated by MIT interacting motifs (MIMs). J Biol Chem. 290(21):13490-9. PMCID: PMC4505595.
http://www.ncbi.nlm.nih.gov/pubmed/25833946
Cores: X-ray Crystallography, Protein NMR Spectroscopy.
112. Yudina Z, Roa A, Johnson R, Biris N, de Souza Aranha Vieira DA, Tsiperson V, Reszka N, Taylor AB, Hart PJ, Demeler B, Diaz-Griffero F, Ivanov DN. (2015). RING Dimerization Links Higher-Order Assembly of TRIM5α to Synthesis of K63-Linked Polyubiquitin. Cell Rep. 12(5):788-97. PMCID: PMC4526822.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4526822
Core: Administration (Collaborative Development Award)
113. Fletcher AJ, Christensen DE, Nelson C, Tan CP, Schaller T, Lehner PJ, Sundquist WI, Towers GJ. (2015). TRIM5α requires Ube2W to anchor Lys63-linked ubiquitin chains and restrict reverse transcription. EMBO J. 34(15):2078-95. PMCID: PMC4551353.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4551353
Cores: Virology, Eukaryotic Protein Expression
114. Pickett CL, Corb BW, Matthews CR, Sundquist WI, Berg JM. (2015). Toward a sustainable biomedical research enterprise: Finding consensus and implementing recommendations. Proc Natl Acad Sci. 112(35):10832-6. PMCID: PMC4568264.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4568264 http://www.pnas.org/content/112/35/10832.full
Core: Administration
115. Wong RW, Mamede JI, Hope TJ. (2015). Impact of nucleoporin-mediated chromatin localization and nuclear architecture on HIV integration site selection. J Virol. 89(19):9702-5. PMCID: PMC4577903.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4577903
Core: Virus Imaging
116. Scharf L, Wang H, Gao H, Chen S, McDowall AW, Bjorkman PJ. (2015). Broadly neutralizing antibody 8ANC195 recognizes closed and open States of HIV-1 Env. Cell. 162(6):1379-90. PMCID: PMC4587768.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4587768
Core: Tissue EM
117. Kemble DJ, McCullough LL, Whitby FG, Formosa T, Hill CP. (2015). FACT Disrupts Nucleosome Structure by Binding H2A-H2B with Conserved Peptide Motifs. Molecular Cell. 60(2):294-306. PMCID: PMC4620744.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4620744
Cores: X-ray Crystallography, Bacterial Protein Expression
118. Ding HJ, Oikonomou C, Jensen GJ. (2015). The Caltech Tomography Database and Automatic Processing Pipeline. J Struct Biol. 192(2):279-86. PMCID: PMC4633326.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4633326
Core: Electron Tomography
119. Sewald X, Ladinsky MS, Uchil PD, Beloor J, Pi R, Herrmann C, Motamedi N, Murooka TT, Brehm MA, Greiner DL, Shultz LD, Mempel TR, Bjorkman PJ, Kumar P, Mothes W. (2015). Retroviruses use CD169-mediated trans-infection of permissive lymphocytes to establish infection. Science. 350(6260):563-7. PMCID: PMC4651917.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4651917
Core: Administration (Collaborative Development Award), Tissue EM
120. McCullough J, Clippinger AK, Talledge N, Skowyra ML, Saunders MG, Naismith TV, Colf LA, Afonine P, Arthur C, Sundquist WI, Hanson PI, Frost A. (2015). Structure and membrane remodeling activity of ESCRT-III helical polymers. Science. 350(6267):1548-51. PMCID: PMC4684769.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4684769
Core: Administration (Collaborative Development Award), Virology
121. Smith CS, Lari A, Derrer CP, Ouwehand A, Rossouw A, Huisman M, Dange T, Hopman M, Joseph A, Zenklusen D, Weis K, Grünwald D, Montpetit B. (2015). In vivo single particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p. J Cell Biol. 211(6):1121-30. PMCID: PMC4687877.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4687877
Core: Administration (Collaborative Development Award)
122. Smith CS, Stallinga S, Lidke KA, Rieger B, Grünwald D. (2015). Probability-based particle detection that enables threshold-free and robust in vivo single-molecule tracking. Mol Biol Cell. 26(22):4057-62. PMCID: PMC4710236.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4710236
Core: Administration (Collaborative Development Award)
123. Campbell EM, Weingart J, Sette P, Opp S, Sastri J, O'Connor SK, Talley S, Diaz-Griffero F, Hirsch V, Bouamr F. (2015) TRIM5alpha-Mediated Ubiquitin Chain Conjugation Is Required for Inhibition of HIV-1 Reverse Transcription and Capsid Destabilization. J Virol 90, 1849-57. PMCID: PMC4733990.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733990/
Core: Administration (Collaborative Development Award)
124. Smith CS, Tu LC, Grünwald D. (2015). A 4D view on mRNA. Oncotarget. 6(30):28515-6. PMCID: PMC4745664.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4745664
Core: Administration (Collaborative Development Award)
125. Sundquist WI, Ullman KS. (2015). An ESCRT to seal the envelope. Science. 348(6241):1314-5. PMID: 26089496
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+26089496
Core: Virology
126. Campbell EM, Hope TJ. (2015). HIV-1 capsid: the multifaceted key player in HIV-1 infection. Nat Rev Microbiol. 13(8):471-83. PMCID: PMC4876022.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26179359
Cores: Virus Imaging, Administration (Collaborative Development Award)
127. Forest, KT, Hill CP. (2015) Macromolecular machines and assemblies: rise and fall at the molecular level. Curr Opin Struct Biol. 31:7-8. PMCID: PMC4878820.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878820/
Core: X-ray Crystallography
128. Woodward CL, Mendonca LM, Jensen GJ. (2015). Direct visualization of vaults within intact cells by electron cryo-tomography. Cell Mol Life Sci. 72(17):3401-9. PMCID: PMC4898762.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4898762
Core: Electron Tomography
129. Treweek, JB, Chan KY, Flytzanis NC, Yang B, Deverman BE, Greenbaum A, Lignell A, Xiao C, Cai L, Ladinsky MS, Bjorkman PJ, Fowlkes CC, Gradinaru V. (2015). Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. Nat Protoc. 10(11):1860-96. PMCID: PMC4917295.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26492141
Core: Tissue EM
130. Millar DP, Trewhella, J. (2015). New frontiers of biophysical methods: Tools for structural biology and beyond. Curr Opin Struc Biol. 28:vii-x. PMID: 25292464.
https://www.ncbi.nlm.nih.gov/pubmed/?term=New+frontiers+of+biophysical+methods%3A+Tools+for+structural+biology+and+beyond
Core: Fluorescence Spectroscopy
131. Hope T. (2015). Visualizing trans-infection. Science. 350(6260):511-2. PMID: 26516268.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+26516268
Core: Virus Imaging
2016
132. Imam S, Talley S, Nelson RS, Dharan A, O'Connor C, Hope TJ, Campbell EM. (2016). TRIM5α degradation via autophagy is not required for retroviral restriction. J Virol. 90(7):3400-10. PMCID: PMC4794682.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4794682
Cores: Administration (Collaborative Development Award), Virus Imaging
133. Stieh DJ, Matias E, Xu H, Fought AJ, Blanchard JL, Marx PA, Veazey RS, Hope TJ. (2016). Th17 cells are preferentially infected very early after vaginal transmission of SIV in macaques. Cell Host Microbe. 19(4):529-40. PMCID: PMC4841252.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4841252
Core: Virus Imaging
134. Monroe N, Hill CP. (2016). Meiotic Clade AAA ATPases: Protein Polymer Disassembly Machines. J Mol Biol. 428(9B):1897-1911. PMCID: PMC4860049.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4860049
Core: X-ray Crystallography, Bacterial Protein Expression
135. Ma H, Tu LC, Naseri A, Huiman M, Zhang S, Grünwald D, Pederson T. (2016). Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow Nat Biotechnol. 34(5):528-30. PMCID: PMC4864854.
http://www.ncbi.nlm.nih.gov/pubmed/?term=27088723
Core: Administration (Collaborative Development Award)
136. Grime JMA, Dama JF, Ganser-Pornillos BK, Woodward CL, Jensen GJ, Yeager M, Voth GA. (2016). Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly. Nature Comm. 7:11568. PMCID: PMC4869257.
http://www.ncbi.nlm.nih.gov/pubmed/?term=27174390
Cores: Computation, Electron Crystallography, Electron Tomography, Administration (Collaborative Development Award)
137. Mamede JI, Hope TJ. (2016). Detection and tracking of dual-labeled HIV particles using wide-field live cell imaging to follow viral core integrity. Methods Mol Biol. 1354:49-59. PMCID: PMC4876021.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26714704
Core: Virus Imaging
138. Chuong EB, Elde NC, Feschotte C. (2016). Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science. 351(6277):1083-7. PMCID: PMC4887275.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26941318
Core: Administration (Collaborative Development Award)
139. Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster AS, Young ID, Michels-Clark T, Aquila A, Liang M, Hunter MS, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H. (2016). Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nature Methods. 13(1):59-62. PMCID: PMC4890631.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+26619013
Core: RNA Structure and Dynamics
140. Iwasa JH. (2016). The Scientist as Illustrator. Trends Immunol. 37(4):247-50. PMCID: PMC4900463.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26968491
Core: Administration (Administrative supplement)
141. Musser SM, Grünwald D. (2016). Deciphering the structure and function of nuclear pores using single-molecule fluorescence approaches. J Mol Biol. Epublication ahead of print. 428(10):2091-119. PMCID: PMC4909493.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26944195
Core: Administration (Collaborative Development Award)
142. Dharan A, Talley S, Tripathi A, Mamede JI, Majetschak M, Hope TJ, Campbell EM. (2016). KIF5B and Nup358 Cooperatively Mediate the Nuclear Import of HIV-1 during Infection. PLoS Pathog 12, e1005700. PMCID: PMC4915687.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915687/
Cores: Virus Imaging, Administration (Collaborative Development Award)
143. Wagner JM, Roganowicz MD, Skorupka K, Alam SL, Christensen DE, Doss G, Wan Y, Frank GA, Ganser-Pornillos BK, Sundquist WI, Pornillos O. (2016). Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5α. eLife.5:e16309. PMCID: PMC4936894.
https://www.ncbi.nlm.nih.gov/pubmed/?term=27253059
Cores: Eukaryotic Protein Expression, Administration (Collaborative Development Award), Protein Interactions, Virology
144. Li Y-L, Chandrasekaran V, Carter SD, Woodward CL, Christensen DE, Dryden KA, Pornillos O, Yeager M, Ganser-Pornillos BK, Jensen GJ, Sundquist WI. (2016). Primate TRIM5 proteins form hexagonal nets on HIV-1 capsids. eLife.5:e16269. PMCID: PMC4936896.
http://www.ncbi.nlm.nih.gov/pubmed/?term=27253068
Cores: Eukaryotic Protein Expression, EM Tomography, Electron Crystallography, Administration (Collaborative Development Award), Virology
145. Wagner JM, Zadrozny K, Chrustowicz J, Purdy MD, Yeager M, Ganser-Pornillos BK, Pornillos O. (2016). Crystal structure of an HIV assembly and maturation switch. eLife. 5:e17063. PMCID: PMC4946879.
http://www.ncbi.nlm.nih.gov/pubmed/?term=27416583
Core: Administration (Collaborative Development Award), Electron Crystallography, Collaboration with Owen Pornillos (CRNA).
146. Bhattacharya A, Wang Z, White T, Buffone C, Nguyen LA, Shepard CN, Kim B, Demeler B, Diaz-Griffero F, Ivanov DN. (2016). Effects of T594 phosphomimetic mutations on tetramer stability and dNTPase activity of SAMHD1 cannot explain the retroviral restriction defect. Sci Rep. 6:31353. PMCID: PMC4980677.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980677/#
Core: Administration (Collaborative Development Award)
147. Sewald X, Motamedi N, Mothes W. (2016) Viruses exploit the tissue physiology of the host to spread in vivo. Curr Opin Cell Biol. 41:81-90. PMCID: PMC4983526.
https://www.ncbi.nlm.nih.gov/pubmed/?term=Viruses+exploit+the+tissue+physiology+of+the+host+to+spread+in+vivo
Core: Administration (Collaborative Development Award)
148. Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grünwald D, Pederson T. (2016). CRISPR-Cas9 nuclear dynamics and target recognition in living cells. J Cell Biol. 214(5):529-37. PMCID: PMC5004447.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC5004447
Core: Administration (Collaborative Development Award)
149. Coey A, Larsen K, Puglisi JD, Viani Puglisi E. (2016). Heterogeneous Structures Formed by Conserved Sequences Found in the HIV Reverse Transcription Initiation Site. RNA. 22(10):1-10. PMCID: PMC5066621.
http://www.ncbi.nlm.nih.gov/pubmed/?term=27613581
Core: RNA structure and Dynamics
150. Wang H, Cohen AA, Galimidi RP, Gristick HB, Jensen GJ, Bjorkman PJ. (2016). Cryo-EM structure of a CD4-bound open HIV-1 Envelope trimer reveals structural rearrangements of the gp120 V1V2 loop. Proc Natl Acad Sci USA. 113: E7151-E7158 PMCID: PMC5135367.
https://www.ncbi.nlm.nih.gov/pubmed/?term=Cryo-EM+structure+of+a+CD4-bound+open+HIV-1
Cores: Tissue EM, EM Tomography
151. Smith CS, Huisman M, Siemons M, Grünwald D, Stallinga S. (2016). Simultaneous measurement of emission color and 3D position of single molecules. Optics Express. 24(5):4996-5013. PMCID: 5499633.
https://www.osapublishing.org/oe/abstract.cfm?uri=oe-24-5-4996
Core: Administration (Collaborative Development Award)
152. Bayro MJ, Ganser-Pornillos BK, Zadrozny KK, Yeager M, Tycko R. (2016). Helical Conformation in the CA-SP1 Junction of the Immature HIV-1 Lattice Determined from Solid-State NMR of Virus-like Particles. J Am Chem Soc. 138(37):12029-32. PMID: 27593947.
https://www.ncbi.nlm.nih.gov/pubmed/27593947
Core: Electron Crystallography, Administration (Collaborative Development Award)
153. Votteler J, Ogohara C, Yi S, Hsia Y, Natterman U, Belnap DM, King NP, Sundquist WI. (2016). Designed proteins induce the formation of nanocage-containing extracellular vesicles. Nature. 540(7632):292-5. PMID: 27919066.
https://www.ncbi.nlm.nih.gov/pubmed/27919066
Core: Virology
154. Schommers P, Martrus G, Matschl U, Sirignano M, Lütgehetmann M, Richert L, Hope TJ, Fätkenheuer G, Altfeld M. (2016) Changes in HIV-1 Capsid Stability Induced by Common Cytotoxic-T-Lymphocyte-Driven Viral Sequence Mutations. J Virol. 2016 90(16):7579-86. PMCID: PMC4984629.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4984629
Core: Virus Imaging
2017
155. Schoeneberg J, Lee I, Iwasa JH, Hurley, JH. (2017). Reverse-topology membrane scission by the ESCRT proteins. Nat Rev Mol Cell Biol. 18(1):5-17. PMCID: PMC5198518.
https://www.ncbi.nlm.nih.gov/pubmed/27703243
Core: Administration (Administrative supplement)
156. Hammond JA, Lamichhane R, Millar DP, Williamson JR. (2017) A DEAD-Box helicase mediates an RNA structural transition in the HIV-1 Rev Response Element. J Mol Biol. 429(5):697-714. PMCID: PMC5510989.
https://www.ncbi.nlm.nih.gov/pubmed/28153748
157. Freund NT, Wang H, Scharf L, Noguiera L, Horwitz JA, Sievers SA, Sok D, Cai H, Golijanin J, Lorenzi JC, Halper-Stromber A, Toth I, Piechocka-Torcha A, Gristick HB, Sanders RW, Moore JP, Wang L-X, Seaman MS, Burton D, Gazumyan A, Walker BD, West AP, Bjorkman PJ, Nussenzweig MC. (2016). Co-existence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller. Science Translational Medicine. 9(373). PMCID: PMC5467220.
https://www.ncbi.nlm.nih.gov/pubmed/?term=28100831
Core: Tissue EM
158. Lamichhane, R, Hammond, J.A., Pauszek, R.A. 3rd, Anderson, R.M., Pedron, I., van der Schans, E., Williamson, J.R., Millar, D.P. (2017) A DEAD-Box Protein Acts Through RNA to Promote HIV-1 Rev-RRE Assembly. Nucleic Acids Res, 45(8):4632-4641. PMCID: PMC5416872.
https://www.ncbi.nlm.nih.gov/pubmed/28379444
159. Yang S, Kreutzberger AJB, Kiessling V, Ganser-Pornillos BK, White JV, Tamm LK. (2017). HIV virions sense plasma membrane heterogeneity for cell entry. Sci Adv. 3(6):e1700338. PMCID: PMC5489272.
https://www.ncbi.nlm.nih.gov/pubmed/28782001
160. Mamede JI, Cianci GC , Anderson MR, Hope TJ. (2017). Early cytoplasmic uncoating is associated with infectivity of HIV-1. PNAS. 114(34):e7169-7178. PMCID: PMC5576815.
https://www.ncbi.nlm.nih.gov/pubmed/28784755
161. Pak AJ, Grime JMA, Sengupta P, Chen AK, Durumeric AEP, Srivastava A, Yeager M, Briggs JAG, Lippincott-Schwartz J, Voth GA. (2017). Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane. PNAS. 114(47):e10056-65. PMCID: PMC5703280.
https://www.ncbi.nlm.nih.gov/pubmed/29114055
162. Hammond JA, Zhou L, Lamichhane R, Chu H-Y, Millar DP, Gerace L, Williamson JR. (2017). A survey of DDX21 activity during Rev/RRE complex formation. J Mol Biol. 430(4):537-53. PMCID: 5762417.
https://www.ncbi.nlm.nih.gov/pubmed/28705764
163. Carter SD, Mageswaran SK, Farino ZJ, Mamede JI, Oikonomou CM, Hope TJ, Freyberg Z, and Jensen GJ. (2017). Distinguishing signal from autofluorescence in cryogenic correlated light and electron microscopy of mammalian cells. J Struct Biol. 201(1):15-25. PMCID: PMC5771259.https://www.ncbi.nlm.nih.gov/pubmed/29078993
164. Swulius MT, Nguyen LT, Ladinsky MS, Mishra M, Jensen GJ. (2017). Structure of the actomyosin ring and implications for constriction. PNAS. 115(17):e1455-64. PMCID: PMC5816141.https://www.ncbi.nlm.nih.gov/pubmed/28705764
165. Redman JS, Francis JN, Marquardt R, Papac D, Mueller AL, Eckert DM, Welch BD, Kay MS. (2018). Pharmacokinetic and chemical synthesis optimization of a potent D-peptide HIV entry inhibitor suitable for extended-release delivery. Mol Pharm. 15(3):1169-79. PMCID: PMC5893306.https://www.ncbi.nlm.nih.gov/pubmed/29436835
166. Kieffer C, Ladinsky MS, Ninh A, Galimidi RP, Bjorkman PJ, (2016). Longitudinal imaging of HIV-1 spread in humanized mice with parallel 3D immunofluorescence and electron tomography. Elife.5:e23282. PMCID: PMC5338924.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC5338924
Core: Tissue EM
167. Gu M, Chen OS, LaJoie D, Ladinsky MS, Redd, MJ, Nikolova L, Bjorkman PJ, Ullman KS, Sundquist WI, Frost A. (2016). LEM2 and CHMP7 function in ESCRT-dependent nuclear envelope closure in fission yeast and human cells. BioRxiv. 114(11):E2166-E2175. PMCID: PMC5358359.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC5358359
Cores: Administration (Collaborative Development Award), Virology, Tissue EM
168. Monroe N, Han H, Shen PS, Sundquist WI, Hill C. (2017). Structural Basis of Protein Translocation by the Vps4-Vta1 AAA ATPase. Elife.6:e24487. PMCID: PMC5413351.
https://www.ncbi.nlm.nih.gov/pubmed/28379137
Core: Bacterial Protein Expression, X-ray Crystallography, Virology
169. Wang, H, Gristick, HB, Scharf, L, West, AP, Jr, Galimidi, RP, Seaman, MS, Freund, NT, Nussenzweig, MC, Bjorkman, PJ. (2017). Asymmetric recognition of HIV-1 Env trimer by V1V2 loop-targeting antibodies. eLife 6: e27389. PMCID: PMC5472438.
https://www.ncbi.nlm.nih.gov/pubmed/28994411
170. Sdano, MA, Fulcher, JM, Palani, S, Chandrasekharan, MB, Parnell, TJ, Whitby, FG, Formosa, T, Hill, CP. (2017). A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription. Elife. pii: e28723. PMCID: PMC5599234.
https://www.ncbi.nlm.nih.gov/pubmed/28826505
171. Schneider JR, Carias AM, Bastian AR, Cianci GC, Kiser PF, Veazey RS, Hope TJ. (2017). Long-term direct visualization of passively transferred fluorophore-conjugated antibodies. J Immunol Methods, 450:66-72, PMCID: PMC5603196.
https://www.ncbi.nlm.nih.gov/pubmed/28780040
172. Trettin KD, Sinha NK, Eckert DM, Apple SE, Bass BL (2017). Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA. PNAS 114: E7939-48. PMCID: PMC5617286.
https://www.ncbi.nlm.nih.gov/pubmed/28874570
173. Gristick, HB, Wang, H, Bjorkman, PJ. (2017). X-ray and EM structures of a natively glycosylated HIV-1 envelope trimer. Acta Cryst. D 73: 822-8. PMCID: PMC5633907.
https://www.ncbi.nlm.nih.gov/pubmed/28994411
174. Dawidziak DM, Sanchez JG, Wagner JM, Ganser-Pornillos BK, Pornillos O. (2017). Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase. Proteins. 85(10):1957-1961. PMCID: PMC5638660.
https://www.ncbi.nlm.nih.gov/pubmed/29187540
175. Schaller MD, McDowell G, Porter A, Shippen D, Friedman KL, Gentry MS, Serio TR, Sundquist WI. (2017). What’s in a name? Elife pii: e32437. PMCID: PMC5655148.
https://www.ncbi.nlm.nih.gov/pubmed/29063834
176. Roganowicz MD, Komurlu S, Mukherjee S, Plewka J, Alam SL, Skorupka KA, Wan Y, Dawidowski D, Cafiso DS, Ganser-Pornillos BK, Campbell EM, Pornillos O. (2018). TRIM5α SPRY/coiled-coil interactions optimize avid retroviral capsid recognition. PLoS Pathog. 13(10): e1006686. PMCID: PMC5667893.
https://www.ncbi.nlm.nih.gov/pubmed/29187540
177. Kieffer, C, Ladinsky MS, Bjorkman, PJ. (2017). Multiscale imaging of HIV-1 transmission in humanized mice. AIDS Res Hum Retroviruses. 33(S1):S6-7. PMCID: PMC5685215.
https://www.ncbi.nlm.nih.gov/pubmed/28882056
178. Han H, Monroe N, Sundquist WI, Shen PS, Hill CP. (2017). The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets. Elife pii:e31324. PMCID: PMC5716660.
https://www.ncbi.nlm.nih.gov/pubmed/29165244
2018
179. Wagner JM, Christensen DE, Bhattacharya A, Dawidziak DM, Roganowicz MD, Wan Y, Pumroy RA, Demeler B, Ivanov DN, Ganser-Pornillos BK, Sundquist WI, Pornillos O. (2018). General model for retroviral capsid pattern recognition by TRIM5 proteins. J Virol. 92(4):e01563-17. PMCID: PMC5790955.
https://www.ncbi.nlm.nih.gov/pubmed/29187540
180. Bailey LJ, Sheehy KM, Dominik PK, Liang WG, Rui H, Clark M, Jaskolowski M, Kim Y, Deneka D, Tang WJ, Kossiakoff AA. (2018). Locking the elbow: Improved antibody Fab fragments as chaperones for structure determination. J Mol Biol. 430(3):337-47. PMCID: PMC5800945.
https://www.ncbi.nlm.nih.gov/pubmed/29273204
181. Sheperd JD. (2018). Arc - An endogenous neuronal retrovirus? Semin Cell Dev Biol. 77:73-78. PMCID: PMC5862763.
https://www.ncbi.nlm.nih.gov/pubmed/28941877
182. Barnes, CO, Gristick, HB, Freund, NT, Escolano, A, Lyubimov, AY, Hartweger, H, West Jr, AP, Cohen, AE, Nussenzweig, MC, Bjorkman, PJ. (2018). Structural characterization of a highly potent V3-glycan broadly neutralizing antibody bound to natively-glycosylated HIV-1 envelope. Nat Commun. 9(1):1251-62. PMCID:5871869.
https://www.ncbi.nlm.nih.gov/pubmed/2593217
183. Pastuzyn ED, Day CE, Kearns RB, Kyrke-Smith M, Taibi AV, McCormick J, Yoder N, Belnap DM, Erlendsson S, Morado DR, Briggs JAG, Feschotte C, Shepherd JD. (2018). The neuronal gene Arc encodes a repurposed retrotransposon Gag protein that mediates intercellular RNA transfer. Cell 173(1):275-88. PMCID: PMC 5923900.
https://www.ncbi.nlm.nih.gov/pubmed/29570995
184. Larsen KP, Mathiharan YK, Kappel K, Coey AT, Chen DH, Barrero D, Madigan L, Puglisi JD, Skiniotis G, Puglisi EV. (2018). Architecture of an HIV-1 reverse transcriptase initiation complex. Nature. 557(7703):118-22. PMCID: PMC5934294.
https://www.ncbi.nlm.nih.gov/pubmed/29695867
185. Donaldson, Ladinsky, MS, Yu, KB, Sanders, JG, Yoo, BB, Chou, WC, Conner, ME, Earl, AM, Knight, R, Bjorkman, PJ, Mazmanian, SK. (2018). Gut microbiota utilize immunoglobulin A for mucosal colonization. Science, epublication ahead of print: 03 May, 2018, eaaq0926, DOI:10.1126/science.aaq0926. PMCID in process.
https://www.ncbi.nlm.nih.gov/pubmed/29724905
Funding Cycle I (66 papers published)
Funding Cycle II (93 papers published)
2007
1. Wright ER, Schooler JB, Ding HJ, Kieffer C, Fillmore C, Sundquist WI, Jensen GJ. (2007). Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells. EMBO J. 26(8):2218-26. PMCID: PMC1852790.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852790/
Cores: EM Tomography, Virology
2. Morita E, Sandrin V, Alam SL, Eckert DM, Gygi SP, Sundquist WI. (2007). Identification of human MVB12 proteins as ESCRT-I subunits that function in HIV budding. Cell Host Microb. 2(1):41-53. PMCID: PMC2034311.
http://www.ncbi.nlm.nih.gov/pubmed/18005716
Cores: Virology, Hydrodynamics, Eukaryotic Protein Expression
3. Welch BD, VanDemark AP, Heroux A, Hill CP, Kay MS. (2007). Potent D-peptide inhibitors of HIV-1 entry. Proc Natl Acad Sci USA. 104(43):16828-33. PMCID: PMC2040420.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2040420/
Core: Hydrodynamics, X-ray Crystallography
4. Kelly BN, Kyere S, Kinde I, Tang C, Howard BR, Robinson H, Sundquist WI, Summers MF, Hill CP. (2007). Structure of the antiviral assembly inhibitor CAP-1 complex with the HIV-1 CA protein. J Mol Biol. 373(2):355-66. PMCID: PMC2066180.
http://www.ncbi.nlm.nih.gov/pubmed/17826792
Cores: X-ray Crystallography, Virology
5. Neil SJ, Sandrin V, Sundquist WI, Bieniasz PD. (2007). An interferon-alpha-induced tethering mechanism inhibits HIV-1 and Ebola virus particle release but is counteracted by the HIV-1 Vpu protein. Cell Host Microb. 2(3):193-203. PMCID: PMC3793644.
http://www.ncbi.nlm.nih.gov/pubmed/18005734
Core: Virology
6. Fisher RD, Chung HY, Zhai Q, Robinson H, Sundquist WI, Hill CP. (2007). Structural and Biochemical Studies of ALIX/AIP1 and Its Role in Retrovirus Budding. Cell. 128(5):841-52. PMID: 17350572.
http://www.ncbi.nlm.nih.gov/pubmed/17350572
Cores: X-ray Crystallography, Virology, Bacterial Protein Expression
7. Higa MM, Alam SL, Sundquist WI, Ullman KS. (2007). Molecular characterization of the Ran-binding zinc finger domain of Nup153. J Biol Chem. 282(23):17090-100. PMID:17426026.
http://www.ncbi.nlm.nih.gov/pubmed/17426026
Core: Protein NMR Spectroscopy
8. Sundquist WI, Hill CP. (2007). How to assemble a capsid. Cell. 131(1):17-9. PMID: 17923081.
https://www.ncbi.nlm.nih.gov/pubmed/?term=17923081
Cores: Virology, X-ray Crystallography
9. Ganser-Pornillos BK, Cheng A, Yeager M. (2007). Structure of full-length HIV-1 CA: a model for the mature capsid lattice. Cell. 131(1):70-9. PMID: 17923088.
http://www.ncbi.nlm.nih.gov/pubmed/17923088
Core: EM Crystallography
10. Stuchell-Brereton MD, Skalicky JJ, Kieffer C, Karren MA, Ghaffarian S, Sundquist WI. (2007). ESCRT-III recognition by VPS4 ATPases. Nature. 449(7163):740-4. PMID: 17928862.
http://www.ncbi.nlm.nih.gov/pubmed/17928862
Cores: Protein NMR Spectroscopy, Virology, Protein Interactions
2008
11. Campbell EM, Perez O, Anderson JL, Hope TJ. (2008). Visualization of a proteasome-independent intermediate during restriction of HIV-1 by rhesus TRIM5alpha. J Cell Biol. 180(3):549-61. PMCID: PMC2234241.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2234241/
Core: Virus Imaging
12. Edgcomb SP, Aschrafi A, Kompfner E, Williamson JR, Gerace L, Hennig M. (2008). Protein structure and oligomerization are important for the formation of export-competent HIV-1 Rev-RRE complexes. Protein Sci. 17(3)420-30. PMCID: PMC2248316.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248316/
Cores: Cell Biology/Imaging, Biochemistry
13. Leblanc JJ, Perez O, Hope TJ. (2008). Probing the structural states of human immunodeficiency virus type 1 pr55gag by using monoclonal antibodies. J. Virol. 82(5):2570-74. PMCID: PMC2258915.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2258915
Cores: Virus Imaging
14. Kim S, Pang HB, Kay MS. (2008). Peptide mimic of the HIV envelope gp120-gp41 interface. J Mol Biol. 376(3):786-9. PMCID: PMC2265733.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265733/
Core: Hydrodynamics
15. Yu Z, Gonciarz MD, Sundquist WI, Hill CP, Jensen GJ. (2008). Cryo-EM structure of dodecameric Vps4p and its 2:1 complex with Vta1p. J Mol Biol. 377(2):364-77. PMCID: PMC2279015.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2279015
Cores: EM Tomography, X-ray Crystallography, Virology, Bacterial Protein Expression
16. McCullough J, Fisher RD, Whitby FG, Sundquist WI, Hill CP. (2008). ALIX-CHMP4 interactions in the human ESCRT pathway. Proc Natl Acad Sci USA. 105(22):7687-91. PMCID: PMC2409388.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2409388
Cores: X-ray Crystallography, Virology
17. Langelier CR, Sandrin V, Eckert DM, Christensen DE, Chandrasekaran V, Alam SL, Aiken C, Olsen JC, Kar AK, Sodroski JG, Sundquist WI. (2008). Biochemical characterization of a recombinant TRIM5alpha protein that restricts human immunodeficiency virus type 1 replication. J Virol. 82(23):11682-94. PMCID: PMC2583683.
http://jvi.asm.org/content/82/23/11682.long
Cores: Eukaryotic Protein Expression, Hydrodynamics, Virology
18. Kieffer C, Skalicky JJ, Morita E, De Dominico I, Ward DM, Kaplan J, Sundquist WI. (2008). Two distinct modes of ESCRT-III recognition are required for VPS4 functions in lysosomal protein targeting and HIV-1 budding. Dev Cell. 15(1):62-73. PMCID: PMC2586299.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2586299
Cores: Protein NMR Spectroscopy, Protein Interactions
19. Eckert DM, Shi Y, Kim S, Welch BD, Kang E, Poff ES, Kay MS. (2008). Characterization of the steric defense of the HIV-1 gp41 N-trimer region. Protein Sci. 17(12):2091-100. PMCID: PMC2590922.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2590922
Core: Hydrodynamics
20. Gonciarz MD, Whitby FG, Eckert DM, Kieffer C, Heroux A, Sundquist WI, Hill CP. (2008). Biochemical and structural studies of yeast Vps4 oligomerization. J Mol Biol. 384(4):878-95. PMCID: PMC2632936.
http://www.ncbi.nlm.nih.gov/pubmed/18929572
Cores: X-ray Crystallography, Virology, Bacterial Protein Expression
21. Ganser-Pornillos BK, Yeager M, Sundquist WI. (2008). The structural biology of HIV assembly. Curr Opin Struct Biol. 18(2):203-17. PMCID: PMC2819415.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2819415
Cores: Virology, EM Crystallography
22. Lee E, Fahimian BP, Iancu CV, Suloway C, Murphy GE, Wright ER, Castano-Diez D, Jensen GJ, Miao J. (2008). Radiation dose reduction and image enhancement in biological imaging through equally sloped tomography. J Struct Biol. 16(2):221-7. PMCID: PMC3099251.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099251/
Core: EM Tomography
23. Natarajan S, Katsamba PS, Miles A, Eckman J, Papalia GA, Rich RL, Gale BK, Myszka DG. (2008). Continuous-flow microfluidic printing of proteins for array-based applications including surface plasmon resonance imaging. Anal Biochem. 373(2):141-6. PMID: 17868635.
http://www.ncbi.nlm.nih.gov/pubmed/17868635
Core: Protein Interactions
24. Zhai Q, Fisher RD, Chung H-Y, Myszka DG, Sundquist WI, Hill CP. (2008). Structural and functional studies of ALIX interactions with YPX(n)L late domains of HIV-1 and EIAV. Nature Struct Mol Biol. 15(1):43-9. PMID: 18066081.
http://www.ncbi.nlm.nih.gov/pubmed/18066081
Core: X-ray Crystallography, Virology, Protein Interactions
2009
25. Pond SJ, Ridgeway WK, Robertson R, Wang J, Millar DP. (2009). HIV-1 Rev protein assembles on viral RNA one molecule at a time. Proc Natl Acad Sci. 106(5):1404-8. PMCID: PMC2635779.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2635779
Cores: Fluorescence Spectroscopy, Biochemistry
26. Szymczyna BR, Taurog RE, Young MJ, Snyder JC, Johnson JE, Williamson JR. (2009). Synergy of NMR, computation, and x-ray crystallography for structural biology. Structure. 17(4):499-507. PMCID: PMC2705668.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705668/
Core: Biochemistry
27. Bajorek M, Schubert HL, McCullough J, Langelier C, Eckert DM, Stubblefiel W-M B, Uter NT, Myszka DG, Hill CP, Sundquist WI. (2009). Structural basis for ESCRT-III protein autoinhibition. Nature Struct Mol Biol. 16(7):754-62. PMCID: PMC2712734.
http://www.ncbi.nlm.nih.gov/pubmed/?term=pmc2712734
Cores: Virology, X-ray Crystallography, Bacterial Protein Expression
28. Suloway C, Shi J, Cheng A, Pulokas J, Carragher B, Potter CS, Zheng SQ, Agard DA, Jensen GJ. (2009). Fully automated, sequential tilt-series acquisition with Leginon. J Struct Biol. 167(1):11-8. PMCID: PMC2724967.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2724967/
Core: EM Tomography
29. Pornillos O, Ganser-Pornillos BK, Kelly BN, Hua Y, Whitby FG, Stout CD, Sundquist WI, Hill CP, Yeager M. (2009). X-ray structures of the hexameric building block of the HIV capsid. Cell. 137(7):1282-92. PMCID: PMC2840706.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2840706
Cores: EM Crystallography, X-ray Crystallography, Virology
30. Tivol WF, Briegel A, Jensen GJ. (2009). An improved cryogen for plunge freezing. Microscopy and Microanalysis. 14(5):375-9. PMCID: PMC3058946.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058946/
Core: EM Tomography
31. Eddings MA, Eckman JW, Arana CA, Connolly JE, Papalia GA, Gale BK, Myszka DG. (2009). Spot and Hop – Internal referencing for surface plasmon resonance imaging using a three-dimensional microfluidic flow cell array. Anal Biochem. 385(2):309-13. PMID: 19059374.
http://www.ncbi.nlm.nih.gov/pubmed/?term=19059374
Core: Protein Interactions
2010
32. Krishna V, Ayton GS, Voth GA. (2010). Role of protein interactions in defining HIV-1 capsid shape and stability: A coarse-grained analysis. J Biophys. 98(1):18-26. PMCID: PMC2800964.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800964/
Core: Computation
33. Chow JYH, Jeffries CM, Kwan AH, Guss JM, Trewhella J. (2010). Calmodulin disrupts the structure of the HIV-1 MA protein. J Mol Biol. 400(4):702-14. PMCID: PMC2902600.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2902600
Core: Small Angle Scattering
34. Rich RL, Quinn JG, Morton T, Stepp JD, Myszka DG. (2010). Biosensor-based fragment screening using FastStep injections. Analytical Biochemistry. 407(2):270-7. PMCID: PMC2949542.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2949542
Core: Protein Interactions
35. Welch BD, Francis JN, Redman JS, Paul S, Weinstock MT, Whitby FG, Eckert DM, Hill CP, Root MJ, Kay MS. (2010). Design of a potent D-peptide HIV-1 entry inhibitor with a strong barrier to resistance. J Virol. 84(21):11235-44. PMCID: PMC2953169.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2953169
Core: Hydrodynamics, X-ray Crystallography
36. Schubert HL, Zhai Q, Sandrin V, Eckert DM, Garcia-Maya M, Saul L, Sundquist WI, Steiner RA, Hill CP. (2010). Structural and functional studies on the extracellular domain of BST2/Tetherin in its reduced and oxidized conformations. Proc Natl Acad Sci. 107(42):17951-6. PMCID: PMC2964199.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2964199
Cores: X-ray Crystallography, Virology, Bacterial Protein Expression
37. Ayton GS, Voth GA. (2010). Multiscale computer simulation of the immature HIV-1 virion. Biophys J. 99(9):2757-65. PMCID: PMC2966041.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2966041
Core: Computation
38. Koirala S, Bui HT, Schubert HL, Eckert DM, Hill CP, Kay MS, Shaw JM. (2010). Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes. J Cell Biol. 191(6):1127-39. PMCID: PMC3002026.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3002026
Cores: Hydrodynamics, X-ray Crystallography
39. Fu CY, Wang K, Gan L, Lanman J, Khayat R, Young MJ, Jensen GJ, Doerschuk PC, Johnson JE. (2010). In vivo assembly of an archaeal virus studied with whole-cell electron cryotomography. Structure. 18(12):1579-85. PMCID: PMC3042139.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3042139
Core: EM Tomography
40. Pornillos OW, Ganser-Pornillos BK, Banumathi S, Hua Y, Yeager M. (2010). Disulfide bond stabilization of the hexameric capsomer of human immunodeficiency virus. J Mol Biol. 401(5):985-95. PMCID: PMC3050670.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3050670
Core: EM Crystallography
41. Briegel A, Chen S, Koster AJ, Plitzko JM, Schwartz CL, Jensen GJ. (2010). Correlated light and electron microscopy. Meth Enzymol. 481:317-41. PMID: 20887863.
http://www.ncbi.nlm.nih.gov/pubmed/?term=20887863
Core: EM Tomography
2011
42. Zhai Q, Landesman MB, Robinson H, Sundquist WI, Hill CP. (2011). Identification and structural characterization of the ALIX-binding late domains of simian immunodeficiency virus SIVmac239 and SIVagmTan-1. J Virol. 85(1):632-7. PMCID: PMC3014167.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3014167
Cores: X-ray Crystallography, Virology, Protein Interactions
43. Ganser-Pornillos BK, Chandrasekaran V, Pornillos OW, Sodroski JG, Sundquist WI, Yeager M. (2011). Hexagonal assembly of a restricting TRIM5a protein. Proc Natl Acad Sci. 108(2):534-9. PMCID: PMC3021009.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3021009
Cores: EM Crystallography, Eukaryotic Expression, Hydrodynamics, Virology
44. Pornillos O, Ganser-Pornillos BK, Yeager M. (2011). Atomic-level modeling of the HIV capsid. Nature. 469(7330):424-7. PMCID: PMC3075868.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3075868
Core: EM Crystallography
45. Swulius MT, Chen S, Ding JH, Li Z, Briegel A, Pilhofer M, Tocheva EI, Lybarger SR, Johnson TL, Sandkvist M, Jensen GJ. (2011). Long helical filaments are not seen encircling cells in electron cryotomograms of rod-shaped bacteria. Biochem Biophys Res Commun. 407(4):650-5. PMCID: PMC3093302.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3093302
Core: EM Tomography
46. Guerrero-Ferreira R, Viollier P, Ely B, Poindexter J, Goergieva M, Jensen GJ, Wright E. (2011). Alternative mechanism for bacteriophage adsorption to the motile bacterium Caulobacter crescentus. Proc Natl Acad Sci. 108(24):9963-8. PMCID: PMC3116389.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3116389
Core: EM Tomography
47. Hulme A, Perez O, Hope TJ. (2011). Complementary assays reveal a relationship between HIV-1 uncoating and reverse transcription. Proc Natl Acad Sci. 108(24):9975-80. PMCID: PMC3116424.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3116424
Core: Virus Imaging
48. Diaz-Griffero F, Gallo DE, Hope TJ, Sodroski J. (2011). Trafficking of some old world primate TRIM5a proteins through the nucleus. Retrovirology. 8:38. PMCID: PMC3120760.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120760/
Core: Virus Imaging
49. Schultheisz HL, Szymczyna BR, Scott LG, Williamson JR. (2011). Enzymatic de Novo Pyrimidine Nucleotide Synthesis. J Am Chem Soc. 133(2):297-304. PMCID: PMC3134529.
http://www.ncbi.nlm.nih.gov/pubmed/21166398
Core: Biochemistry
50. Robertson-Anderson R, Wang J, Edgcomb S, Carmel A, Williamson JR, Millar DP. (2011). Single-molecule studies reveal that DEAD-Box protein DDX1 promotes oligomerization of HIV-1 Rev on the Rev Response Element. J Mol Biol. 410(5):959. PMCID: PMC3140434.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3140434
Cores: Fluorescence Spectroscopy, Biochemistry
51. Zhai Q, Landesman MB, Chung H-Y, Dierkers A, Jeffries CM, Trewhella J, Hill CP, Sundquist WI. (2011). Activation of the retroviral budding factor ALIX. J Virol. 85(17):9222-6. PMCID: PMC3165844.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3165844
Cores: X-ray Crystallography, Virology, Protein Interactions
52. Yeager M. (2011). Design of in vitro Symmetric Complexes and Analysis by Hybrid Methods Reveal Mechanisms of HIV Capsid Assembly. J Mol Biol. 410(4):534-52. PMCID: PMC3166646.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166646/
Core: EM Crystallography
53. Zhai Q, Landesman M, Robinson H, Sundquist WI, Hill CP. (2011). Structure of the Bro1 domain containing protein BROX and functional analyses of the ALIX Bro1 domain in HIV-1 budding. PLoS One. 6(12):e27466. PMCID: PMC3230590.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3230590
Cores: X-ray Crystallography, Virology, Protein Interactions
54. Gan L, Ladinsky MS, Jensen GJ. (2011). Organization of the smallest eukaryotic spindle. Curr Bio. 21(18):1578-83. PMCID: PMC3234289.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3234289
Core: EM Tomography
55. Puglisi, EV & Puglisi, JD (2011). Secondary structure of the HIV reverse transcription initiation complex by NMR. J. Mol Biol. 410(5):863-74. PMCID: PMC3710119
https://www.ncbi.nlm.nih.gov/pubmed/21763492
Core: RNA Structure and Dynamics
2012 (cont. after Cycle II grant award)
56. Edgcomb SP, Carmel AB, Naji S, Ambrus-Aikelin G, Reyes JR, Thompson J, Saphire AC, Gerace L, Williamson JR. (2012). DDX1 is an RNA-Dependent ATPase Involved in HIV-1 Rev Function and Virus Replication. J Mol Biol. 415(1):61-74. PMCID: PMC3249508.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249508/
Cores: Biochemistry, Cell Biology/Imaging
57. Jägger S, Cimermancic P, Gulbahce N, Johnson J, McGovern K, Clarke SC, Shales M, Mercenne G, Li K, Barry H, Jang GM, Akiva E, Pache L, Marlett J, Shoshannah LR, Stephens M, D’Orso I, Fernandes J, Fahey M, Mahon C, O’Donoghue AJ, Todorovic A, Morris JH, Maltby D, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez R, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. (2012). Global landscape of HIV-human protein complexes. Nature. 481(7381):365-70. PMCID: PMC3310911.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3310911
Core: Virology
58. Naji S, Ambrus G, Cimermančič P, Reyes JR, Johnson J, Filbrandt R, Huber MD, Vesely P, Yates 3rd JR, Krogan NJ, Saphire AC, Gerace L. (2012). Host cell interactome of HIV-1 Rev revealed by comparative proteomics includes RNA helicases that function in multiple steps of virus replication. Mol Cell Proteom. 11(4):M111.015313. PMCID: PMC3322577.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322577/
Core: Cell Biology/Imaging
59. Kräusslich H-G, Sundquist WI. (2012). HIV Assembly, Budding and Maturation. HIV in Cold Spring Harbor Perspectives. 2(7):95-118. PMCID: PMC3385941.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3385941
Core: Virology
60. Lemke CT, Titolo S, von Schwedler U, Goudreau N, Mercier JF, Wardrop E, Faucher AM, Coulombe R, Banik SS, Fader L, Gagnon A, Kawai SH, Rancourt J, Tremblay M, Yoakim C, Simoneau B, Archambault J, Sundquist WI, Mason SW. (2012). Distinct effects of two HIV-1 capsid assembly inhibitor families that bind the same site within the N-terminal domain of the viral CA protein. J Virol. 86(12):6643-55. PMCID: PMC3393593.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3393593/
Core: Virology
61. Grime JMA, Voth GA. (2012). Early Stages of the HIV-1 capsid protein lattice formation. Biophys J. 103(8):1774-83. PMCID: PMC3475334.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3475334
Core: Computation
62. Skalicky JJ, Arii J, Wenzel D, Stubblefield W-MB, Kztsuyama A, Uter NT, Bajorek M, Myszka DG, Sundquist WI. (2012). ESCRT-III interactions of the human LIP5 protein. J Biol Chem. 287(52):43910-26. PMCID: PMC3527974.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527974/
Core: Protein NMR Spectroscopy, Protein Interactions
63. Neves MA, Yeager M, Abagyan R. (2012). Unusual arginine formations in protein function and assembly: rings, stirngs, and stacks. J Phys Chem B. 116(23):7006-13. PMCID: PMC3613333.
http://www.ncbi.nlm.nih.gov/pubmed/?term=22497303
Core: Administration (Administrative supplement)
64. Gallo D., Hope TJ. (2012). Knockdown of MAP4 and DNAL1 produces a post-fusion and pre-nuclear translocation impairment in HIV-1 replication. Virology. 422(1):13-21. PMCID: PMC3732191
http://www.ncbi.nlm.nih.gov/pubmed/?term=22018492
Core: Virus Imaging
65. Pljevaljcic P, Robertson-Anderson R, Millar DP. (2012). Analysis of RNA folding and ribonucleoprotein assembly by single-molecule fluorescence spectroscopy. Meth Mol Bio. 875:271-95. PMCID: PMC3744346.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744346/
Core: Fluorescence Spectroscopy
66. Danielson CM, Cianci GC, Hope TJ. (2012). Recruitment and dynamics of proteasome association with rhTRIM5α cytoplasmic complexes during HIV-1 infection. Traffic. 13(9):1206-17. PMCID: PMC3760259.
http://www.ncbi.nlm.nih.gov/pubmed/22624877
Core: Virus Imaging
67. Effanin G, Dordor A, Sandrin V, Martinelli N, Sundquist WI, Schoehn G, Weissenhorn W. (2012). ESCRT-III CHMP2A and CHMP3 form variable helical polymers in vitro and act synergistically during HIV-1 budding. Cell Microbiol. 15(2): 213-26. PMCID: PMC3783020.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783020/
Core: Virology
68. Gan L, Jensen GJ. (2012). Electron tomography of cells. Quart Rev Biophys. 45(1):27-56. PMID: 22082691.
http://www.ncbi.nlm.nih.gov/pubmed/?term=22082691
Core: EM Tomography
69. Ganser-Pornillos BK, Yeager M, Pornillos O. (2012). Assembly and Architecture of HIV. Adv Exp Med Biol. 726:441-65. PMID: 22297526.
http://www.ncbi.nlm.nih.gov/pubmed/?term=22297526
Core: EM Crystallography
70. Sundquist WI, Krug RM. (2012). Structural Biology: Assemble, replicate, remodel and evade. Curr Opin Virol. 2(2):111-4. PMID: 22482706.
http://www.sciencedirect.com/science/article/pii/S1879625712000351
Core: Virology
2013
71. Hill CP, Sundquist WI. (2013). Building a super elongation complex for HIV. eLIFE. 2:e00577. PMCID: PMC3592195.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3592195
Cores: X-ray Crystallography and Virology
72. Yu Z, Dobro MJ, Woodward CL, Levandoski A, Danielson C, Sandrin V, Shi J, Aiken C, Zandi R, Hope TJ, Jensen GJ. (2013). Unclosed HIV-1 capsids suggest a curled sheet model of assembly. J Mol Biol. 425(1):112-23. PMCID: PMC3597093.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597093/
Cores: EM Tomography, Virus Imaging, Virology
73. Koirala S, Guo Q, Kalia R, Bui HT, Eckert DM, Frost A, Shaw JM. (2013). Interchangeable adaptors regulate mitochondrial dynamin assembly for membrane scission. Proc Natl Acad Sci USA. 110(15):E1342-51. PMCID: PMC3625255.
http://www.ncbi.nlm.nih.gov/pubmed/?term=23530241
Core: Protein Interactions
74. Dobro MJ, Samson RY, Yu Z, McCullough J, Ding HJ, Chong PL, Bell SD, Jensen GJ. (2013). Electron cryotomography of ESCRT assemblies and dividing Sulfolobus cells suggest spiraling filaments are involved in membrane scission. Mol Biol Cell. 24(15), 2319–27. PMCID: PMC3727925.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3727925/
Core: Electron Tomography
75. Kono K, Takeda E, Tsutsui H, Kuroishi A, Hulme AE, Hope TJ, Nakayama EE, Shioda T. (2013). Slower uncoating is associated with impaired replicative capability of simian-tropic HIV-1. PloS One. 8(8):e72531. PMCID: PMC3742594.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3742594/
Core: Virus Imaging
76. Briegel A, Pilhofer M, Mastronarde D, Jensen GJ. (2013). The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards. J Struct Biol. 183(1):95-8. PMCID: PMC3765063.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765063/
Core: Electron Tomography
77. Danielson CM, Hope TJ. (2013). Using anti-ubiquitin antibodies to probe the ubiquitination state within rhTRIM5α cytoplasmic bodies. AIDS Res Hum Retroviruses. 29(10):1373-85. PMCID: PMC3785812.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785812/
Core: Virus Imaging
78. Lamorte L, Titolo S, Lemke CT, Goudreau N, Mercier JF, Wardrop E, Shah VB, von Schwedler UK, Langelier C, Banik SS, Aiken C, Sundquist WI, Mason SW. (2013). Discovery of Novel Small-Molecule HIV-1 Replication Inhibitors That Stabilize Capsid Complexes. Antimicrob Agents Chemother. 57(10):4622-31. PMCID: PMC3811413.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811413/
Core: Virology
79. Votteler J, Sundquist WI. (2013). Virus Budding and the ESCRT Pathway. Cell Host Microbe. 14(3):232-41. PMCID: PMC3819203.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819203/
Core: Virology
80. Brandariz-Nuñez A, Valle-Casuso JC, White TE, Nguyen L, Bhattacharya A, Wang Z, Demeler B, Amie S, Knowlton C, Kim B, Ivanov DN, Diaz-Griffero F. (2013). Contribution of oligomerization to the anti-HIV-1 properties of SAMHD1. Retrovirology. 10(1):131. PMCID: PMC3882887.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3882887/
Core: Administration (Collaborative Development Award)
81. Monroe N, Han H, Gonciarz MD, Eckert DM, Karren MA, Whitby FG, Sundquist WI, Hill CP. (2013). The oligomeric state of the active Vps4 AAA ATPase. J Mol Biol. 426(3):510-25. PMCID: PMC3919030.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919030/
Cores: X-ray Crystallography, Bacterial Protein Expression, Virology, Protein Interactions
82. McCullough J, Colf LA, Sundquist WI. (2013). Membrane fission reactions of the mammalian ESCRT pathway. Annu Rev Biochem. 82:663-92. PMCID: PMC4047973.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4047973/
Core: Virology
83. Yeager M, Dryden KA, Ganser-Pornillos BK. (2013). Lipid monolayer and sparse matrix screening for growing two-dimensional crystals for electron crystallography: methods and examples. Methods Mol. Bio. 955:527-37. PMCID: PMC4127334.
http://www.ncbi.nlm.nih.gov/pubmed/?term=23132079
Cores: Eukaryotic Protein Expression, EM Tomography, Electron Crystallography, Administration (Collaborative Development Award), Virology
84. Biris N, Tomashevski A, Bhattacharya A, Diaz-Griffero F, Ivanov DN. (2013). Rhesus monkey TRIM5α SPRY domain recognizes multiple epitopes that span several capsid monomers on the surface of the HIV-1 mature viral core. J Mol Biol. 425(24):5032-44. PMCID: PMC416666.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116666/
Core: Administration (Collaborative Development Award)
85. Rey FA, Sundquist WI. (2013). Macromolecular assemblies. Curr Opin Struct Biol. 23(2):224-8. PMID:23663961.
https://www.ncbi.nlm.nih.gov/pubmed/?term=23663961
Core: Virology
86. Petrov A, Wu T, Puglisi EV, Puglisi JD. (2013). RNA purification by preparative polyacrylamide gel electrophoresis. Methods Enzymol. 2013;530:315-30. PMID: 24034329.
https://www.ncbi.nlm.nih.gov/pubmed/?term=24034329
Core: RNA Structure and Dynamics
2014
87. Yang Y, Brandariz-Nuñez A, Fricke T, Ivanov DN, Sarnak Z, Diaz-Griffero F. (2014). The binding ability of the rhesus TRIM5α PRYSPRY domain to the capsid is necessary but not sufficient for HIV-1 restriction. Virology. 448:217-28. PMCID: PMC3900861.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3900861
Core: Administration (Collaborative Development Award)
88. Ladinsky MS, Kieffer C, Olson G, Deruaz M, Vrbanac V, Tager AM, Kwon DS, Bjorkman PJ. (2014). Electron tomography of HIV-1 infection in gut-associated lymphoid tissue. PLoS Pathogens. 10(1):e003899. PMCID: PMC3907528.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3907528
Core: Tissue EM
89. Sanchez JG, Okreglicka K, Chandrasekaran V, Welker JM, Sundquist WI, Pornillos O. (2014). The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer. Proc Natl Acad Sci. 111(7):2494-9. PMCID: PMC3932864.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932864/
Cores: Eukaryotic Protein Expression, Protein Interactions
90. Ren J, Pei-Chen LC, Pathak MC, Temple BR, Nile AH, Mousley CJ, Duncan MC, Eckert DM, Leiker TJ, Ivanova PT, Myers DS, Murphy RC, Brown HA, Verdaasdonk J, Bloom KS, Ortlund EA, Neiman AM, Bankaitis VA. (2014). A phosphatidylinositol transfer protein integrates phosphoinositide signaling with lipid droplet metabolism to regulate a developmental program of nutrient stress-induced membrane biogenesis. Mol Biol Cell. 25(5):712-27. PMCID: PMC3937096.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937096/
Core: Protein Interactions
91. Narayan K, Danielson CM, Lagarec K, Lowekamp BC, Coffman P, Laquerre A, Phaneuf MW, Hope TJ, Subramaniam S. (2014). Multi-resolution correlative focused ion beam scanning electron microscopy: applications to cell biology. J Struct Biol. 85(3):278-84. PMCID: PMC3943650.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943650/
Core: Virus Imaging
92. Hulme AE, Hope TJ. (2014). The cyclosporin A washout assay to detect HIV-1 uncoating in infected cells. Methods Mol Biol. 1087:37-46. PMCID: PMC4084958.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084958/
Core: Virus Imaging
93. Kovalskyy DB, Ivanov DN. (2014). Recognition of the HIV capsid by the TRIM5α restriction factor is mediated by a subset of pre-existing conformations of the TRIM5α SPRY domain. Biochemistry. 53(9):1466-76. PMCID: PMC4119003.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119003/
Core: Administration (Collaborative Development Award)
94. Sastri J, Johnsen L, Smolin N, Imam S, Mukherjee S, Lukic Z, Brandariz-Nunez A, Robia SL, Diaz-Griffero F, Wiethoff C, Campbell EM. (2014) Restriction of HIV-1 by rhesus TRIM5alpha is governed by alpha helices in the Linker2 region. J Virol 88, 8911-23. PMCID: PMC4136267.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136267/
Core: Administration (Collaborative Development Award)
95. Fricke T, White TE, Schulte B, de Souza Aranha Vieira DA, Dharan A, Campbell EM, Brandariz-Nunez A, Diaz-Griffero F. (2014) MxB binds to the HIV-1 core and prevents the uncoating process of HIV-1. Retrovirology 11(68). PMCID: PMC4145229.
https://www.ncbi.nlm.nih.gov/pmc/?term=PMC4145229
Core: Administration (Collaborative Development Award)
96. Stieh DJ, Maric D, Kelley ZL, Anderson MR, Hattaway HZ, Beilfuss BA, Rothwangl KB, Veazey RS, Hope TJ. (2014). Vaginal challenge with an SIV-based dual reporter system reveals that infection can occur throughout the upper and lower female reproductive tract. PLoS Pathog. 10(10):e1004440 PMCID: PMC4192600.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4192600
Core: Virus Imaging
97. Lukic Z, Dharan A, Fricke T, Diaz-Griffero F, Campbell EM. (2014) HIV-1 uncoating is facilitated by dynein and kinesin 1. J Virol 88, 13613-25. PMCID: PMC4248982.
https://www.ncbi.nlm.nih.gov/pmc/?term=PMC4248982
Core: Administration (Collaborative Development Award)
98. Chen J, Grünwald D, Sardo L, Galli A, Plisov S, Nikolaitchik OA, Chen D, Lockett S, Larson DR, Pathak VK, Hu WS. (2014). Cytoplasmic HIV-1 RNA is mainly transported by diffusion in the presence or absence of Gag protein. Proc Natl Acad Sci USA. 111(48):E5205-13. PMCID: PMC4260538.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4260538
Core: Administration (Collaborative Development Award)
99. Bhattacharya A, Alam, SL Fricke T, Zadrozny K, Sedzicki J, Taylor AB, Demeler B, Pornillos O, Ganser-Pornillos BK, Diaz-Griffero F, Ivanov DN, Yeager, M. (2014). Structural basis of HIV-1 capsid recognition by PF74 and CPSF6. Proc Natl Acad Sci. 111(52):18625-30. PMCID: PMC4284599.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284599/
Cores: EM Crystallography, Administration (Collaborative Development Award), Eukaryotic Protein Expression
100. Purdy MD, Bennett BC, McIntire WE, Khan AK, Kasson PM, Yeager M. (2014). Function and dynamics of macromolecular complexes explored by integrative structural and computational biology. Curr Opin Struct Biol. 27:138-48. PMID: 25238653.
http://www.ncbi.nlm.nih.gov/pubmed/?term=25238653
Cores: Administration (Administrative supplement) and EM Crystallography
2015
101. Woodward CL, Cheng SN, Jensen GJ. (2015). Electron cryotomography studies of maturing HIV-1 particles reveal the assembly pathway of the viral core. J Virol. 89(2):1267-77. PMCID: PMC4300640.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4300640
Core: Electron Tomography
102. Hulme AE, Kelley Z, Okocha EA, Hope TJ. (2015). Identification of capsid mutations that alter the rate of HIV-1 uncoating in infected cells. J Virol. 89(1):643-51. PMCID: PMC4301138.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4301138
Core: Virus Imaging
103. Mercenne G, Alam SL, Arii J, Lalonde MS, Sundquist WI. (2015). Angiomotin functions in HIV-1 assembly and budding. eLife. 4:e03778. PMCID: PMC4337731.
http://www.ncbi.nlm.nih.gov/pubmed/25633977
Core: Virology
104. VanderLinden RT, Hemmis CW, Schmitt B, Ndoja A, Whitby FG, Robinson H, Cohen RE, Yao T, Hill CP. (2015). Structural basis for the activation and inhibition of the UCH37 deubiquitylase. Mol Cell. 57(5):901-11. PMCID: PMC4355076.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355076/
Cores: X-ray Crystallography, Bacterial Expression
105. Takeda E, Kono K, Hulme AE, Hope TJ, Nakayama EE, Shioda T. (2015). Fluorescent image analysis of HIV-1 and HIV-2 uncoating kinetics in the presence of old world monkey TRIM5α. PLoS One. 10(3):e0121199. PMCID: PMC4372348.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4372348/
Core: Virus Imaging
106. Clinton TR, Weinstock MT, Jacobsen MT, Szabo-Fresnais N, Pandya MJ, Whitby FG, Herbert AS, Prugar LI, McKinnon R, Hill CP, Welch BD, Dye JM, Eckert DM, Kay MS. (2015). Design and characterization of ebolavirus GP prehairpin intermediate mimics as drug targets. Protein Sci. 24(4):446-63. PMCID: PMC4380977.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380977/
Cores: Protein Interactions, X-ray Crystallography
107. Hancks DC, Hartley MK, Hagan C, Clark NL, Elde NC. (2015). Overlapping patterns of rapid evolution in the nucleic acid sensors cGAS and OAS suggest a common mechanism of pathogen antagonism and escape. PLOS Genetics. 11(5): e1005203. PMCID: PMC4420275.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4420275
Core: Administration (Collaborative Development Award)
108. Zhao H, Eckert DM. (2015). A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation. Plos One. 10(5):e0126420. PMCID: PMC4440767.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4440767
Core: Protein Interactions
109. Smith CSS, Preibisch S, Joseph A, Abrahamsson S, Rieger B, Myers E, Singer RHS, Grünwald D. (2015). Nuclear accessibility of beta-actin mRNA is measured by 3D single-molecule real-time tracking. J Cell Biol. 209(4):609-19. PMCID: PMC4442804.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4442804
Core: Administration (Collaborative Development Award)
110. DePaula-Silva AB, Cassiday PA, Chumley J, Bosque A, Monteiro-Filho CM, Mohan CS, Cone KR, Krogan N, Elde NC, Planelles V. (2015). Determinants for degradation of SAMHD1, Mus81 and induction of G2 arrest in HIV-1 Vpr and SIVagm Vpr. Virology 477:10-17. PMCID: PMC4455942.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4455942
Core: Administration (Collaborative Development Award) and Administrative Supplement
111. Han H, Monroe N, Votteler J, Shakya B, Sundquist WI, Hill CP. (2015). Binding of substrates to the central pore of the Vps4 ATPase is autoinhibited by the microtubule interacting and trafficking (MIT) domain and activated by MIT interacting motifs (MIMs). J Biol Chem. 290(21):13490-9. PMCID: PMC4505595.
http://www.ncbi.nlm.nih.gov/pubmed/25833946
Cores: X-ray Crystallography, Protein NMR Spectroscopy.
112. Yudina Z, Roa A, Johnson R, Biris N, de Souza Aranha Vieira DA, Tsiperson V, Reszka N, Taylor AB, Hart PJ, Demeler B, Diaz-Griffero F, Ivanov DN. (2015). RING Dimerization Links Higher-Order Assembly of TRIM5α to Synthesis of K63-Linked Polyubiquitin. Cell Rep. 12(5):788-97. PMCID: PMC4526822.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4526822
Core: Administration (Collaborative Development Award)
113. Fletcher AJ, Christensen DE, Nelson C, Tan CP, Schaller T, Lehner PJ, Sundquist WI, Towers GJ. (2015). TRIM5α requires Ube2W to anchor Lys63-linked ubiquitin chains and restrict reverse transcription. EMBO J. 34(15):2078-95. PMCID: PMC4551353.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4551353
Cores: Virology, Eukaryotic Protein Expression
114. Pickett CL, Corb BW, Matthews CR, Sundquist WI, Berg JM. (2015). Toward a sustainable biomedical research enterprise: Finding consensus and implementing recommendations. Proc Natl Acad Sci. 112(35):10832-6. PMCID: PMC4568264.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4568264 http://www.pnas.org/content/112/35/10832.full
Core: Administration
115. Wong RW, Mamede JI, Hope TJ. (2015). Impact of nucleoporin-mediated chromatin localization and nuclear architecture on HIV integration site selection. J Virol. 89(19):9702-5. PMCID: PMC4577903.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4577903
Core: Virus Imaging
116. Scharf L, Wang H, Gao H, Chen S, McDowall AW, Bjorkman PJ. (2015). Broadly neutralizing antibody 8ANC195 recognizes closed and open States of HIV-1 Env. Cell. 162(6):1379-90. PMCID: PMC4587768.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4587768
Core: Tissue EM
117. Kemble DJ, McCullough LL, Whitby FG, Formosa T, Hill CP. (2015). FACT Disrupts Nucleosome Structure by Binding H2A-H2B with Conserved Peptide Motifs. Molecular Cell. 60(2):294-306. PMCID: PMC4620744.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4620744
Cores: X-ray Crystallography, Bacterial Protein Expression
118. Ding HJ, Oikonomou C, Jensen GJ. (2015). The Caltech Tomography Database and Automatic Processing Pipeline. J Struct Biol. 192(2):279-86. PMCID: PMC4633326.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4633326
Core: Electron Tomography
119. Sewald X, Ladinsky MS, Uchil PD, Beloor J, Pi R, Herrmann C, Motamedi N, Murooka TT, Brehm MA, Greiner DL, Shultz LD, Mempel TR, Bjorkman PJ, Kumar P, Mothes W. (2015). Retroviruses use CD169-mediated trans-infection of permissive lymphocytes to establish infection. Science. 350(6260):563-7. PMCID: PMC4651917.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4651917
Core: Administration (Collaborative Development Award), Tissue EM
120. McCullough J, Clippinger AK, Talledge N, Skowyra ML, Saunders MG, Naismith TV, Colf LA, Afonine P, Arthur C, Sundquist WI, Hanson PI, Frost A. (2015). Structure and membrane remodeling activity of ESCRT-III helical polymers. Science. 350(6267):1548-51. PMCID: PMC4684769.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4684769
Core: Administration (Collaborative Development Award), Virology
121. Smith CS, Lari A, Derrer CP, Ouwehand A, Rossouw A, Huisman M, Dange T, Hopman M, Joseph A, Zenklusen D, Weis K, Grünwald D, Montpetit B. (2015). In vivo single particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p. J Cell Biol. 211(6):1121-30. PMCID: PMC4687877.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4687877
Core: Administration (Collaborative Development Award)
122. Smith CS, Stallinga S, Lidke KA, Rieger B, Grünwald D. (2015). Probability-based particle detection that enables threshold-free and robust in vivo single-molecule tracking. Mol Biol Cell. 26(22):4057-62. PMCID: PMC4710236.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4710236
Core: Administration (Collaborative Development Award)
123. Campbell EM, Weingart J, Sette P, Opp S, Sastri J, O'Connor SK, Talley S, Diaz-Griffero F, Hirsch V, Bouamr F. (2015) TRIM5alpha-Mediated Ubiquitin Chain Conjugation Is Required for Inhibition of HIV-1 Reverse Transcription and Capsid Destabilization. J Virol 90, 1849-57. PMCID: PMC4733990.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733990/
Core: Administration (Collaborative Development Award)
124. Smith CS, Tu LC, Grünwald D. (2015). A 4D view on mRNA. Oncotarget. 6(30):28515-6. PMCID: PMC4745664.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4745664
Core: Administration (Collaborative Development Award)
125. Sundquist WI, Ullman KS. (2015). An ESCRT to seal the envelope. Science. 348(6241):1314-5. PMID: 26089496
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+26089496
Core: Virology
126. Campbell EM, Hope TJ. (2015). HIV-1 capsid: the multifaceted key player in HIV-1 infection. Nat Rev Microbiol. 13(8):471-83. PMCID: PMC4876022.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26179359
Cores: Virus Imaging, Administration (Collaborative Development Award)
127. Forest, KT, Hill CP. (2015) Macromolecular machines and assemblies: rise and fall at the molecular level. Curr Opin Struct Biol. 31:7-8. PMCID: PMC4878820.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878820/
Core: X-ray Crystallography
128. Woodward CL, Mendonca LM, Jensen GJ. (2015). Direct visualization of vaults within intact cells by electron cryo-tomography. Cell Mol Life Sci. 72(17):3401-9. PMCID: PMC4898762.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4898762
Core: Electron Tomography
129. Treweek, JB, Chan KY, Flytzanis NC, Yang B, Deverman BE, Greenbaum A, Lignell A, Xiao C, Cai L, Ladinsky MS, Bjorkman PJ, Fowlkes CC, Gradinaru V. (2015). Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. Nat Protoc. 10(11):1860-96. PMCID: PMC4917295.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26492141
Core: Tissue EM
130. Millar DP, Trewhella, J. (2015). New frontiers of biophysical methods: Tools for structural biology and beyond. Curr Opin Struc Biol. 28:vii-x. PMID: 25292464.
https://www.ncbi.nlm.nih.gov/pubmed/?term=New+frontiers+of+biophysical+methods%3A+Tools+for+structural+biology+and+beyond
Core: Fluorescence Spectroscopy
131. Hope T. (2015). Visualizing trans-infection. Science. 350(6260):511-2. PMID: 26516268.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+26516268
Core: Virus Imaging
2016
132. Imam S, Talley S, Nelson RS, Dharan A, O'Connor C, Hope TJ, Campbell EM. (2016). TRIM5α degradation via autophagy is not required for retroviral restriction. J Virol. 90(7):3400-10. PMCID: PMC4794682.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4794682
Cores: Administration (Collaborative Development Award), Virus Imaging
133. Stieh DJ, Matias E, Xu H, Fought AJ, Blanchard JL, Marx PA, Veazey RS, Hope TJ. (2016). Th17 cells are preferentially infected very early after vaginal transmission of SIV in macaques. Cell Host Microbe. 19(4):529-40. PMCID: PMC4841252.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4841252
Core: Virus Imaging
134. Monroe N, Hill CP. (2016). Meiotic Clade AAA ATPases: Protein Polymer Disassembly Machines. J Mol Biol. 428(9B):1897-1911. PMCID: PMC4860049.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4860049
Core: X-ray Crystallography, Bacterial Protein Expression
135. Ma H, Tu LC, Naseri A, Huiman M, Zhang S, Grünwald D, Pederson T. (2016). Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow Nat Biotechnol. 34(5):528-30. PMCID: PMC4864854.
http://www.ncbi.nlm.nih.gov/pubmed/?term=27088723
Core: Administration (Collaborative Development Award)
136. Grime JMA, Dama JF, Ganser-Pornillos BK, Woodward CL, Jensen GJ, Yeager M, Voth GA. (2016). Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly. Nature Comm. 7:11568. PMCID: PMC4869257.
http://www.ncbi.nlm.nih.gov/pubmed/?term=27174390
Cores: Computation, Electron Crystallography, Electron Tomography, Administration (Collaborative Development Award)
137. Mamede JI, Hope TJ. (2016). Detection and tracking of dual-labeled HIV particles using wide-field live cell imaging to follow viral core integrity. Methods Mol Biol. 1354:49-59. PMCID: PMC4876021.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26714704
Core: Virus Imaging
138. Chuong EB, Elde NC, Feschotte C. (2016). Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science. 351(6277):1083-7. PMCID: PMC4887275.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26941318
Core: Administration (Collaborative Development Award)
139. Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster AS, Young ID, Michels-Clark T, Aquila A, Liang M, Hunter MS, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H. (2016). Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nature Methods. 13(1):59-62. PMCID: PMC4890631.
http://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+26619013
Core: RNA Structure and Dynamics
140. Iwasa JH. (2016). The Scientist as Illustrator. Trends Immunol. 37(4):247-50. PMCID: PMC4900463.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26968491
Core: Administration (Administrative supplement)
141. Musser SM, Grünwald D. (2016). Deciphering the structure and function of nuclear pores using single-molecule fluorescence approaches. J Mol Biol. Epublication ahead of print. 428(10):2091-119. PMCID: PMC4909493.
http://www.ncbi.nlm.nih.gov/pubmed/?term=26944195
Core: Administration (Collaborative Development Award)
142. Dharan A, Talley S, Tripathi A, Mamede JI, Majetschak M, Hope TJ, Campbell EM. (2016). KIF5B and Nup358 Cooperatively Mediate the Nuclear Import of HIV-1 during Infection. PLoS Pathog 12, e1005700. PMCID: PMC4915687.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915687/
Cores: Virus Imaging, Administration (Collaborative Development Award)
143. Wagner JM, Roganowicz MD, Skorupka K, Alam SL, Christensen DE, Doss G, Wan Y, Frank GA, Ganser-Pornillos BK, Sundquist WI, Pornillos O. (2016). Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5α. eLife.5:e16309. PMCID: PMC4936894.
https://www.ncbi.nlm.nih.gov/pubmed/?term=27253059
Cores: Eukaryotic Protein Expression, Administration (Collaborative Development Award), Protein Interactions, Virology
144. Li Y-L, Chandrasekaran V, Carter SD, Woodward CL, Christensen DE, Dryden KA, Pornillos O, Yeager M, Ganser-Pornillos BK, Jensen GJ, Sundquist WI. (2016). Primate TRIM5 proteins form hexagonal nets on HIV-1 capsids. eLife.5:e16269. PMCID: PMC4936896.
http://www.ncbi.nlm.nih.gov/pubmed/?term=27253068
Cores: Eukaryotic Protein Expression, EM Tomography, Electron Crystallography, Administration (Collaborative Development Award), Virology
145. Wagner JM, Zadrozny K, Chrustowicz J, Purdy MD, Yeager M, Ganser-Pornillos BK, Pornillos O. (2016). Crystal structure of an HIV assembly and maturation switch. eLife. 5:e17063. PMCID: PMC4946879.
http://www.ncbi.nlm.nih.gov/pubmed/?term=27416583
Core: Administration (Collaborative Development Award), Electron Crystallography, Collaboration with Owen Pornillos (CRNA).
146. Bhattacharya A, Wang Z, White T, Buffone C, Nguyen LA, Shepard CN, Kim B, Demeler B, Diaz-Griffero F, Ivanov DN. (2016). Effects of T594 phosphomimetic mutations on tetramer stability and dNTPase activity of SAMHD1 cannot explain the retroviral restriction defect. Sci Rep. 6:31353. PMCID: PMC4980677.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980677/#
Core: Administration (Collaborative Development Award)
147. Sewald X, Motamedi N, Mothes W. (2016) Viruses exploit the tissue physiology of the host to spread in vivo. Curr Opin Cell Biol. 41:81-90. PMCID: PMC4983526.
https://www.ncbi.nlm.nih.gov/pubmed/?term=Viruses+exploit+the+tissue+physiology+of+the+host+to+spread+in+vivo
Core: Administration (Collaborative Development Award)
148. Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grünwald D, Pederson T. (2016). CRISPR-Cas9 nuclear dynamics and target recognition in living cells. J Cell Biol. 214(5):529-37. PMCID: PMC5004447.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC5004447
Core: Administration (Collaborative Development Award)
149. Coey A, Larsen K, Puglisi JD, Viani Puglisi E. (2016). Heterogeneous Structures Formed by Conserved Sequences Found in the HIV Reverse Transcription Initiation Site. RNA. 22(10):1-10. PMCID: PMC5066621.
http://www.ncbi.nlm.nih.gov/pubmed/?term=27613581
Core: RNA structure and Dynamics
150. Wang H, Cohen AA, Galimidi RP, Gristick HB, Jensen GJ, Bjorkman PJ. (2016). Cryo-EM structure of a CD4-bound open HIV-1 Envelope trimer reveals structural rearrangements of the gp120 V1V2 loop. Proc Natl Acad Sci USA. 113: E7151-E7158 PMCID: PMC5135367.
https://www.ncbi.nlm.nih.gov/pubmed/?term=Cryo-EM+structure+of+a+CD4-bound+open+HIV-1
Cores: Tissue EM, EM Tomography
151. Smith CS, Huisman M, Siemons M, Grünwald D, Stallinga S. (2016). Simultaneous measurement of emission color and 3D position of single molecules. Optics Express. 24(5):4996-5013. PMCID: 5499633.
https://www.osapublishing.org/oe/abstract.cfm?uri=oe-24-5-4996
Core: Administration (Collaborative Development Award)
152. Bayro MJ, Ganser-Pornillos BK, Zadrozny KK, Yeager M, Tycko R. (2016). Helical Conformation in the CA-SP1 Junction of the Immature HIV-1 Lattice Determined from Solid-State NMR of Virus-like Particles. J Am Chem Soc. 138(37):12029-32. PMID: 27593947.
https://www.ncbi.nlm.nih.gov/pubmed/27593947
Core: Electron Crystallography, Administration (Collaborative Development Award)
153. Votteler J, Ogohara C, Yi S, Hsia Y, Natterman U, Belnap DM, King NP, Sundquist WI. (2016). Designed proteins induce the formation of nanocage-containing extracellular vesicles. Nature. 540(7632):292-5. PMID: 27919066.
https://www.ncbi.nlm.nih.gov/pubmed/27919066
Core: Virology
154. Schommers P, Martrus G, Matschl U, Sirignano M, Lütgehetmann M, Richert L, Hope TJ, Fätkenheuer G, Altfeld M. (2016) Changes in HIV-1 Capsid Stability Induced by Common Cytotoxic-T-Lymphocyte-Driven Viral Sequence Mutations. J Virol. 2016 90(16):7579-86. PMCID: PMC4984629.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC4984629
Core: Virus Imaging
2017
155. Schoeneberg J, Lee I, Iwasa JH, Hurley, JH. (2017). Reverse-topology membrane scission by the ESCRT proteins. Nat Rev Mol Cell Biol. 18(1):5-17. PMCID: PMC5198518.
https://www.ncbi.nlm.nih.gov/pubmed/27703243
Core: Administration (Administrative supplement)
156. Hammond JA, Lamichhane R, Millar DP, Williamson JR. (2017) A DEAD-Box helicase mediates an RNA structural transition in the HIV-1 Rev Response Element. J Mol Biol. 429(5):697-714. PMCID: PMC5510989.
https://www.ncbi.nlm.nih.gov/pubmed/28153748
157. Freund NT, Wang H, Scharf L, Noguiera L, Horwitz JA, Sievers SA, Sok D, Cai H, Golijanin J, Lorenzi JC, Halper-Stromber A, Toth I, Piechocka-Torcha A, Gristick HB, Sanders RW, Moore JP, Wang L-X, Seaman MS, Burton D, Gazumyan A, Walker BD, West AP, Bjorkman PJ, Nussenzweig MC. (2016). Co-existence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller. Science Translational Medicine. 9(373). PMCID: PMC5467220.
https://www.ncbi.nlm.nih.gov/pubmed/?term=28100831
Core: Tissue EM
158. Lamichhane, R, Hammond, J.A., Pauszek, R.A. 3rd, Anderson, R.M., Pedron, I., van der Schans, E., Williamson, J.R., Millar, D.P. (2017) A DEAD-Box Protein Acts Through RNA to Promote HIV-1 Rev-RRE Assembly. Nucleic Acids Res, 45(8):4632-4641. PMCID: PMC5416872.
https://www.ncbi.nlm.nih.gov/pubmed/28379444
159. Yang S, Kreutzberger AJB, Kiessling V, Ganser-Pornillos BK, White JV, Tamm LK. (2017). HIV virions sense plasma membrane heterogeneity for cell entry. Sci Adv. 3(6):e1700338. PMCID: PMC5489272.
https://www.ncbi.nlm.nih.gov/pubmed/28782001
160. Mamede JI, Cianci GC , Anderson MR, Hope TJ. (2017). Early cytoplasmic uncoating is associated with infectivity of HIV-1. PNAS. 114(34):e7169-7178. PMCID: PMC5576815.
https://www.ncbi.nlm.nih.gov/pubmed/28784755
161. Pak AJ, Grime JMA, Sengupta P, Chen AK, Durumeric AEP, Srivastava A, Yeager M, Briggs JAG, Lippincott-Schwartz J, Voth GA. (2017). Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane. PNAS. 114(47):e10056-65. PMCID: PMC5703280.
https://www.ncbi.nlm.nih.gov/pubmed/29114055
162. Hammond JA, Zhou L, Lamichhane R, Chu H-Y, Millar DP, Gerace L, Williamson JR. (2017). A survey of DDX21 activity during Rev/RRE complex formation. J Mol Biol. 430(4):537-53. PMCID: 5762417.
https://www.ncbi.nlm.nih.gov/pubmed/28705764
163. Carter SD, Mageswaran SK, Farino ZJ, Mamede JI, Oikonomou CM, Hope TJ, Freyberg Z, and Jensen GJ. (2017). Distinguishing signal from autofluorescence in cryogenic correlated light and electron microscopy of mammalian cells. J Struct Biol. 201(1):15-25. PMCID: PMC5771259.https://www.ncbi.nlm.nih.gov/pubmed/29078993
164. Swulius MT, Nguyen LT, Ladinsky MS, Mishra M, Jensen GJ. (2017). Structure of the actomyosin ring and implications for constriction. PNAS. 115(17):e1455-64. PMCID: PMC5816141.https://www.ncbi.nlm.nih.gov/pubmed/28705764
165. Redman JS, Francis JN, Marquardt R, Papac D, Mueller AL, Eckert DM, Welch BD, Kay MS. (2018). Pharmacokinetic and chemical synthesis optimization of a potent D-peptide HIV entry inhibitor suitable for extended-release delivery. Mol Pharm. 15(3):1169-79. PMCID: PMC5893306.https://www.ncbi.nlm.nih.gov/pubmed/29436835
166. Kieffer C, Ladinsky MS, Ninh A, Galimidi RP, Bjorkman PJ, (2016). Longitudinal imaging of HIV-1 spread in humanized mice with parallel 3D immunofluorescence and electron tomography. Elife.5:e23282. PMCID: PMC5338924.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC5338924
Core: Tissue EM
167. Gu M, Chen OS, LaJoie D, Ladinsky MS, Redd, MJ, Nikolova L, Bjorkman PJ, Ullman KS, Sundquist WI, Frost A. (2016). LEM2 and CHMP7 function in ESCRT-dependent nuclear envelope closure in fission yeast and human cells. BioRxiv. 114(11):E2166-E2175. PMCID: PMC5358359.
https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC5358359
Cores: Administration (Collaborative Development Award), Virology, Tissue EM
168. Monroe N, Han H, Shen PS, Sundquist WI, Hill C. (2017). Structural Basis of Protein Translocation by the Vps4-Vta1 AAA ATPase. Elife.6:e24487. PMCID: PMC5413351.
https://www.ncbi.nlm.nih.gov/pubmed/28379137
Core: Bacterial Protein Expression, X-ray Crystallography, Virology
169. Wang, H, Gristick, HB, Scharf, L, West, AP, Jr, Galimidi, RP, Seaman, MS, Freund, NT, Nussenzweig, MC, Bjorkman, PJ. (2017). Asymmetric recognition of HIV-1 Env trimer by V1V2 loop-targeting antibodies. eLife 6: e27389. PMCID: PMC5472438.
https://www.ncbi.nlm.nih.gov/pubmed/28994411
170. Sdano, MA, Fulcher, JM, Palani, S, Chandrasekharan, MB, Parnell, TJ, Whitby, FG, Formosa, T, Hill, CP. (2017). A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription. Elife. pii: e28723. PMCID: PMC5599234.
https://www.ncbi.nlm.nih.gov/pubmed/28826505
171. Schneider JR, Carias AM, Bastian AR, Cianci GC, Kiser PF, Veazey RS, Hope TJ. (2017). Long-term direct visualization of passively transferred fluorophore-conjugated antibodies. J Immunol Methods, 450:66-72, PMCID: PMC5603196.
https://www.ncbi.nlm.nih.gov/pubmed/28780040
172. Trettin KD, Sinha NK, Eckert DM, Apple SE, Bass BL (2017). Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA. PNAS 114: E7939-48. PMCID: PMC5617286.
https://www.ncbi.nlm.nih.gov/pubmed/28874570
173. Gristick, HB, Wang, H, Bjorkman, PJ. (2017). X-ray and EM structures of a natively glycosylated HIV-1 envelope trimer. Acta Cryst. D 73: 822-8. PMCID: PMC5633907.
https://www.ncbi.nlm.nih.gov/pubmed/28994411
174. Dawidziak DM, Sanchez JG, Wagner JM, Ganser-Pornillos BK, Pornillos O. (2017). Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase. Proteins. 85(10):1957-1961. PMCID: PMC5638660.
https://www.ncbi.nlm.nih.gov/pubmed/29187540
175. Schaller MD, McDowell G, Porter A, Shippen D, Friedman KL, Gentry MS, Serio TR, Sundquist WI. (2017). What’s in a name? Elife pii: e32437. PMCID: PMC5655148.
https://www.ncbi.nlm.nih.gov/pubmed/29063834
176. Roganowicz MD, Komurlu S, Mukherjee S, Plewka J, Alam SL, Skorupka KA, Wan Y, Dawidowski D, Cafiso DS, Ganser-Pornillos BK, Campbell EM, Pornillos O. (2018). TRIM5α SPRY/coiled-coil interactions optimize avid retroviral capsid recognition. PLoS Pathog. 13(10): e1006686. PMCID: PMC5667893.
https://www.ncbi.nlm.nih.gov/pubmed/29187540
177. Kieffer, C, Ladinsky MS, Bjorkman, PJ. (2017). Multiscale imaging of HIV-1 transmission in humanized mice. AIDS Res Hum Retroviruses. 33(S1):S6-7. PMCID: PMC5685215.
https://www.ncbi.nlm.nih.gov/pubmed/28882056
178. Han H, Monroe N, Sundquist WI, Shen PS, Hill CP. (2017). The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets. Elife pii:e31324. PMCID: PMC5716660.
https://www.ncbi.nlm.nih.gov/pubmed/29165244
2018
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