Molecular dynamics analysis of HIV-1 matrix protein: Clarifying differences between crystallographic and solution structures

Journal of Molecular Graphics and Modelling

Volumn 26, Issue 1, 2007, Pages 62-68

  Verli, Hugo ^a   Calazans, Alexandre ^b   Brindeiro, Rodrigo ^b   Tanuri, Amilcar ^b   Guimarães, Jorge A ^a  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^b FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

Author keywords

Crystallographic contacts; HIV 1 matrix protein; Molecular dynamics; p17; p24

Indexed keywords

COMPUTER SIMULATION; CRYSTALLOGRAPHY; DISEASES; MOLECULAR DYNAMICS; MONOMERS; NUCLEAR MAGNETIC RESONANCE;

GLOBULAR PROTEIN; MATRIX PROTEIN (P17); SOLUTION STRUCTURES; VIRION ASSEMBLY;

PROTEIN FOLDING;

GAG PROTEIN; MATRIX PROTEIN; PROTEIN P17;

ARTICLE; COMPUTER SIMULATION; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN STABILITY; VIRION; X RAY CRYSTALLOGRAPHY;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; GENE PRODUCTS, GAG; HIV ANTIGENS; HIV CORE PROTEIN P24; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; SOFTWARE; SOLUTIONS; THERMODYNAMICS; VIRAL PROTEINS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 34347227780     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2006.09.009     Document Type: Article

References (35)

1. Turner B.G., and Summers M.F. Structural biology of HIV. J. Mol. Biol. 285 (1999) 1-32
2. Massiah M.A., Starich M.R., Paschall C., Summers M.F., Christensen A.M., and Sundquist W.I. Three-dimensional structure of the Human Immunodeficiency Virus type 1 matrix protein. J. Mol. Biol. 244 (1994) 198-223
3. Nermut M.V., Hockley D.J., Jowett J.B., Jones I.M., Garreau M., and Thomas D. Fullerene-like organization of HIV gag-protein shell in virus-like particles produced by recombinant baculovirus. Virology 198 (1994) 288-296
4. Matthews S., Barlow P., Clark N., Kingsman S., Kingsman A., and Campbell I. Refined solution structure of p17, the HIV matrix protein. Biochem. Soc. Trans. 23 (1995) 725-729
5. Hill C.P., Worthylake D., Bancroft D.P., Christensen A.M., and Sundquist W.I. Crystal structures of the trimeric human immunodeficiency virus type 1 matrix protein: implications for membrane association assembly. Proc. Natl. Acad. Sci. 93 (1996) 3099-3104
6. Massiah M.A., Worthylake D., Christensen A.M., Sundquist W.I., Hill C.P., and Summers M.F. Comparison of the NMR and X-ray structures of the HIV-1 matrix protein: evidence for conformational changes during viral assembly. Prot. Sci. 5 (1996) 2391-2398
7. Nermut M.V., Hockley D.J., Bron P., Thomas D., Zhang W.H., and Jones I.M. Further evidence for hexagonal organization of HIV gag protein in prebudding assemblies and immature virus-like particles. J. Struct. Biol. 123 (1998) 143-149
8. Bouamr F., Scarlata S., and Carter C. Role of myristylation in HIV-1 Gag assembly. Biochemistry 42 (2003) 6408-6417
9. Tang C., Loeliger E., Luncsford P., Kinde I., Beckett D., and Summers M.F. Entropic switch regulates myristate exposure in the HIV-1 matrix protein. Proc. Natl. Acad. Sci. 101 (2004) 517-522
10. Huseby D., Barklis R.L., Alfadhli A., and Barklis E. Assembly of human immunodeficiency virus precursor Gag proteins. J. Biol. Chem. 280 (2005) 17664-17670
11. Forster M.J., Mulloy B., and Nermut M.V. Molecular modeling study of p17gag (MA) protein shell utilizing data from electron microscopy and X-ray crystallography. J. Mol. Biol. 298 (2000) 841-857
12. Momany C., Kovari L.C., Prongay A.J., Keller W., Gitti R.K., Lee B.M., Gorbalenya A.E., Tong L., McClure J., Ehrlich L.S., Summers M.F., Carter C., and Rossmann M.G. Crystal structure of dimeric HIV-1 capsid protein. Nat. Struct. Biol. 3 (1996) 763-769
13. Berendsen H.J.C., van der Spoel D., and van Drunen R. GROMACS-a message-passing parallel molecular-dynamics implementation. Comput. Phys. Commun. 91 (1995) 43-56
14. D. van der Spoel, E. Lindahl, B. Hess, A.R. van Buuren, E. Apol, P.J. Meulenhoff, D.P. Tieleman, A.L.T.M. Sijbers, K.A. Feenstra, R. van Drunen, H.J.C. Berendsen, GROMACS User Manual Version 3.2, Nijenborgh 4, 9747 AG Groningen, The Netherlands, 2004.
15. Guex N., and Peitsch M.C. Swiss-model and the Swiss-Pdb Viewer: and environment for comparative protein modeling. Electrophoresis 18 (1997) 2714-2723. http://www.expasy.org/spdbv
16. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
17. Frishman D., and Argos P. Knowledge-based protein secondary structure assignment. Proteins 23 (1995) 566-579
18. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
19. DeLano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific, Sao Carlos, CA, USA. http://www.pymol.org
20. Berendsen H.J.C., Postma J.P.M., van Gunsteren W., and Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B. (Ed). Intermolecular Forces (1981), Reidel, Dordrecht, The Netherlands 331-342
21. de Groot B.L., and Grubmüller H. Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF. Science 294 (2001) 2353-2357
22. Hess B., Bekker H., Berendsen H.J.C., and Fraaije J.G.E.M. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18 (1997) 1463-1472
23. Miyamoto S., and Kollman P.A. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13 (1992) 952-962
24. Darden T., York D., and Pedersen L. Particle mesh Ewald-an N log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
25. Tironi I.G., Sperb R., Smith P.E., and van Gunsteren W.F. A generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 102 (1995) 5451-5459
26. Berendsen H.J.C., Postma J.P.M., DiNola A., and Haak J.R. Molecular-dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
27. Verli H., and Guimarães J.A. Insights into the induced fit mechanism in antithrombin-heparin interaction using molecular dynamics simulations. J. Mol. Graph. Mod. 24 (2005) 203-212
28. Hirst J.D., and Brooks III C.L. Helicity, circular dichroism and molecular dynamics of proteins. J. Mol. Biol. 243 (1994) 173-178
29. Baumketner A., and Shea J.-E. The influence of different treatments of electrostatic interactions on the thermodynamics of folding peptides. J. Phys. Chem. B 109 (2005) 21322-21328
30. Eaton W.A., Munoz V., Thompson P.A., Henry E.R., and Hofrichter J. Kinetics and dynamics of loops, α-helices, β-hairpins, and fast-folding proteins. Acc. Chem. Res. 31 (1998) 745-753
31. Snow C.D., Nguyen H., Pande V.S., and Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420 (2002) 102-106
32. Bukrinsky M.I., Haggerty S., Dempsey M.P., Sharova N., Adzhubel A., Spitz L., Lewis P., Goldfarb D., Emerman M., and Stevenson M. A nuclear localization signal within HIV-1 matrix protein that governs infection of non-dividing cells. Nature 365 (1993) 666-669
33. Trono D. HIV accessory proteins: leading roles for the supporting cast. Cell 82 (1995) 189-192
34. Spearman P., Wang J.J., Van der Heyden N., and Ratner L. Identification of human immunodeficiency virus type 1 Gag protein domains essential to membrane binding and particle assembly. J. Virol. 68 (1994) 3232-3242
35. Eisenhaber F., Lijnzaad P., Argos P., Sander C., and Scharf M. The double cube lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J. Comp. Chem. 16 (1995) 273-284