Structural Plasticity and Conformational Transitions of HIV Envelope Glycoprotein gp120

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Korkut, Anil ^a,b   Hendrickson, Wayne A ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CD4 ANTIGEN; CHEMOKINE RECEPTOR; GLYCOPROTEIN GP 120;

ANTIGEN BINDING; ARTICLE; CALORIMETRY; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MUTATIONAL ANALYSIS; PROTEIN STRUCTURE; RECEPTOR BINDING; STRUCTURE ANALYSIS;

ANTIBODIES, NEUTRALIZING; ANTIGENS, CD4; COMPUTER SIMULATION; EPITOPES; HIV ANTIBODIES; HIV ENVELOPE PROTEIN GP120; HIV-1; HUMANS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 84871641830     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0052170     Document Type: Article

References (54)

1. Pantophlet R, Burton DR, (2006) GP120: target for neutralizing HIV-1 antibodies. Annu Rev Immunol 24: 739-769.
2. Poignard P, Saphire EO, Parren PWHI, Burton DR, (2001) GP120: Biologic aspects of structural features. Annu Rev Immunol 19: 253-274.
3. Choe H, Farzan M, Sun Y, Sullivan N, Rollins B, et al. (1996) The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell 85: 1135-1148.
4. Dalgleish AG, Beverley PCL, Clapham PR, Crawford DH, Greaves MF, et al. (1984) The Cd4 (T4) Antigen Is an Essential Component of the Receptor for the Aids Retrovirus. Nature 312: 763-767.
5. Maddon PJ, Dalgleish AG, Mcdougal JS, Clapham PR, Weiss RA, et al. (1986) The T4 Gene Encodes the Aids Virus Receptor and Is Expressed in the Immune-System and the Brain. Cell 47: 333-348.
6. Wu LJ, Gerard NP, Wyatt R, Choe H, Parolin C, et al. (1996) CD4-induced interaction of primary HIV-1 gp120 glycoproteins with the chemokine receptor CCR-5. Nature 384: 179-183.
7. Chen B, Vogan EM, Gong HY, Skehel JJ, Wiley DC, et al. (2005) Structure of an unliganded simian immunodeficiency virus gp120 core. Nature 433: 834-841.
8. Kwong PD, Doyle ML, Casper DJ, Cicala C, Leavitt SA, et al. (2002) HIV-1 evades antibody-mediated neutralization through conformational masking of receptor-binding sites. Nature 420: 678-682.
9. Zhang WT, Canziani G, Plugariu C, Wyatt R, Sodroski J, et al. (1999) Conformational changes of gp120 in epitopes near the CCR5 binding site are induced by CD4 and a CD4 miniprotein mimetic. Biochemistry 38: 9405-9416.
10. Kwong PD, Wyatt R, Majeed S, Robinson J, Sweet RW, et al. (2000) Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure 8: 1329-1339.
11. Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, et al. (1998) Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 393: 648-659.
12. Myszka DG, Sweet RW, Hensley P, Brigham-Burke M, Kwong PD, et al. (2000) Energetics of the HIV gp120-CD4 binding reaction. Proc Natl Acad Sci USA 97: 9026-9031.
13. Olshevsky U, Helseth E, Furman C, Li J, Haseltine W, et al. (1990) Identification of individual human immunodeficiency virus type 1 gp120 amino acids important for CD4 receptor binding. J Virol 64: 5701-5707.
14. Dey B, Pancera M, Svehla K, Shu Y, Xiang SH, et al. (2007) Characterization of human immunodeficiency virus type 1 monomeric and trimeric gp120 glycoproteins stabilized in the CD4-bound state: Antigenicity, biophysics, and immunogenicity. J Virol 81: 5579-5593.
15. Xiang SH, Kwong PD, Gupta R, Rizzuto CD, Casper DJ, et al. (2002) Mutagenic stabilization and/or disruption of a CD4-bound state reveals distinct conformations of the human immunodeficiency virus type 1 gp120 envelope glycoprotein. J Virol 76: 9888-9899.
16. Huang CC, Stricher F, Martin L, Decker JM, Majeed S, et al. (2005) Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120: Crystal structures, molecular mimicry, and neutralization breadth. Structure 13: 755-768.
17. Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, et al. (2007) Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature 445: 732-737.
18. Zhou T, Georgiev I, Wu X, Yang ZY, Dai K, et al. (2010) Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Science 329: 811-817.
19. Diskin R, Scheid JF, Marcovecchio PM, West AP Jr, Klein F, et al. (2011) Increasing the potency and breadth of an HIV antibody by using structure-based rational design. Science 334: 1289-1293.
20. Chen L, Kwon YD, Zhou T, Wu X, O'Dell S, et al. (2009) Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120. Science 326: 1123-1127.
21. Pancera M, Majeed S, Ban YE, Chen L, Huang CC, et al. (2010) Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility. Proc Natl Acad Sci USA 107: 1166-1171.
22. Rizzuto CD, Wyatt R, Hernandez-Ramos N, Sun Y, Kwong PD, et al. (1998) A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding. Science 280: 1949-1953.
23. Wei XP, Decker JM, Wang SY, Hui HX, Kappes JC, et al. (2003) Antibody neutralization and escape by HIV-1 (vol 422, pg 307, 2003). Nature 423: 197-197.
24. Yuan W, Bazick J, Sodroski J, (2006) Characterization of the multiple conformational states of free monomeric and trimeric human immunodeficiency virus envelope glycoproteins after fixation by cross-linker. J Virol 80: 6725-6737.
25. Pan Y, Ma B, Keskin O, Nussinov R, (2004) Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain. J Biol Chem 279: 30523-30530.
26. Tan H, Rader AJ, (2009) Identification of putative, stable binding regions through flexibility analysis of HIV-1 gp120. Proteins: Struct Funct Bioinf 74: 881-894.
27. Pan Y, Ma B, Nussinov R, (2005) CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible. J Mol Biol 350: 514-527.
28. Shrivastava I, LaLonde JM, (2010) Fluctuation dynamics analysis of gp120 envelope protein reveals a topologically based communication network. Proteins: Struct Funct Bioinf 78: 2935-2949.
29. Shrivastava I, LaLonde JM, (2011) Enhanced dynamics of HIV gp120 glycoprotein by small molecule binding. Biochemistry 50: 4173-4183.
30. Korkut A, Hendrickson WA, (2009) A force field for virtual atom molecular mechanics of proteins. Proc Natl Acad Sci USA 106: 15667-15672.
31. Korkut A, Hendrickson WA, (2009) Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase. Proc Natl Acad Sci USA 106: 15673-15678.
32. Bahar I, Atilgan AR, Erman B, (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 2: 173-181.
33. Haliloglu T, Bahar B, Erman B, (1997) Gaussian dynamics of folded proteins. Physical Review Letters 79: 3090-3093.
34. Brooks B, Karplus M, (1985) Normal-Modes for Specific Motions of Macromolecules- Application to the Hinge-Bending Mode of Lysozyme. Proc Natl Acad Sci USA 82: 4995-4999.
35. Ma JP, Karplus M, (1997) Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis. J Mol Biol 274: 114-131.
36. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) Charmm- a Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J Comput Chem 4: 187-217.
37. Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, et al. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80: 505-515.
38. Rost B, Sander C, Schneider R, (1994) PHD-an automatic mail server for protein secondary structure prediction. Comput Appl Biosci 10: 53-60.
39. Madani N, Perdigoto AL, Srinivasan K, Cox JM, Chruma JJ, et al. (2004) Localized changes in the gp120 envelope glycoprotein confer resistance to human immunodeficiency virus entry inhibitors BMS-806 and #155. J Virol 78: 3742-3752.
40. Haliloglu T, Bahar I, (1999) Structure-based analysis of protein dynamics: Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data. Proteins: Struct Funct Bioinf 37: 654-667.
41. Mechulam A, Cerutti M, Pugniere M, Misse D, Gajardo J, et al. (2005) Highly conserved beta16/beta17 beta-hairpin structure in human immunodeficiency virus type 1 YU2 gp120 is critical for CCR5 binding. Journal of Molecular Medicine 83: 542-552.
42. Yang X, Mahony E, Holm GH, Kassa A, Sodroski J, (2003) Role of the gp120 inner domain beta-sandwich in the interaction between the human immunodeficiency virus envelope glycoprotein subunits. Virology 313: 117-125.
43. Kwon YD, Finzi A, Wu X, Dogo-Isonagie C, Lee LK, et al. (2012) Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops. Proc Natl Acad Sci USA 109: 5663-5668.
44. Wyatt R, Kwong PD, Desjardins E, Sweet RW, Robinson J, et al. (1998) The antigenic structure of the HIV gp120 envelope glycoprotein. Nature 393: 705-711.
45. Yang X, Tomov V, Kurteva S, Wang L, Ren X, et al. (2004) Characterization of the outer domain of the gp120 glycoprotein from human immunodeficiency virus type 1. J Virol 78: 12975-12986.
46. Miller DW, Agard DA, (1999) Enzyme specificity under dynamic control: a normal mode analysis of alpha-lytic protease. J Mol Biol 286: 267-278.
47. Henzler-Wildman KA, Lei M, Thai V, Kerns SJ, Karplus M, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450: 913-916.
48. Ichiye T, Karplus M, (1991) Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins: Struct Funct Bioinf 11: 205-217.
49. Berkower I, Patel C, Ni Y, Virnik K, Xiang Z, et al. (2008) Targeted deletion in the beta20-beta21 loop of HIV envelope glycoprotein gp120 exposes the CD4 binding site for antibody binding. Virology 377: 330-338.
50. de Bakker PI, DePristo MA, Burke DF, Blundell TL, (2003) Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model. Proteins: Struct Funct Bioinf 51: 21-40.
51. Sanchez R, Sali A, (2000) Comparative protein structure modeling. Introduction and practical examples with modeller. Methods in Molecular Biology 143: 97-129.
52. Krol M, Borowski T, Roterman I, Piekarska B, Stopa B, et al. (2004) Force-field parametrization and molecular dynamics simulations of Congo red. J Comput Aided Mol Des 18: 41-53.
53. Mouawad L, Perahia D, (1993) Diagonalization in a Mixed Basis- a Method to Compute Low-Frequency Normal-Modes for Large Macromolecules. Biopolymers 33: 599-611.
54. Kabsch W, Sander C, (1983) Dictionary of Protein Secondary Structure- Pattern-Recognition of Hydrogen-Bonded and Geometrical Features. Biopolymers 22: 2577-2637.