A homology modeling method of an icosahedral viral capsid: Inclusion of surrounding protein structures

Journal of Molecular Graphics and Modelling

Volumn 17, Issue 2, 1999, Pages 114-119

  Yoneda, Teruyo ^a   Yoneda, Shigetaka ^a   Takayama, Naoko ^b   Kitazawa, Masako ^a   Umeyama, Hideaki ^a  

^a KITASATO UNIVERSITY   (Japan)

^b PharmaDesign Inc   (Japan)

Author keywords

Homology modeling; Icosahedral capsid; Poliovirus; Protein assembly; Rhinovirus

Indexed keywords

VIRUS PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER GRAPHICS; MOLECULAR GENETICS; POLIOMYELITIS VIRUS; PROTEIN CONFORMATION; RHINOVIRUS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; VIRUS CAPSID;

AMINO ACID SEQUENCE; CAPSID; COMPUTER GRAPHICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; POLIOVIRUS; PROTEIN CONFORMATION; RHINOVIRUS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; VIRAL PROTEINS;

EID: 0033106945     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(99)00024-8     Document Type: Article

References (50)

1. Bloomer, A.C., Champness, J.N., Bricogne, G., Staden, R., and Klug, A. Protein disk of tobacco mosaic virus at 2.8 Å resolution showing the interactions within and between subunits. Nature (London) 1978, 276, 362-368
2. Harrison, S.C., Olson, A., Schutt, C.E., Winkler, F.K., and Bricogne, G. Tomato bushy stunt virus at 2.9 Å resolution. Nature (London) 1978, 276, 368-373
3. Rossmann, M.G., Arnold, E., Erickson, J.W., Frankenberger, E.A., Griffith, J.P., Hecht, H.-J., Johnson, J.E., Kamer, G., Luo, M., Mosser, A.G., Rueckert, R.R., Sherry, B., and Vriend, G. Structure of a human common cold virus and functional relationship to other picornaviruses. Nature (London) 1985, 317, 145-153
4. Hogle, J.M., Chow, M., and Filman, D.J. Three-dimensional structure of poliovirus at 2.9 Å resolution. Science 1985, 229, 1358-1365
5. Wien, M.W., Chow, M., and Hogle, J.M. Poliovirus: New insights from an old paradigm. Structure 1996, 4, 763-767
6. Diana, G.D., McKinlay, M.A., and Treasurywala, A. The use of structural information in the design of picornavirus capsid binding agents. In: Structural Biology of Viruses (Chiu, W., Burnett, R.M., and Garcea, R.L., eds.). Oxford University Press, New York, 1997, pp. 432-450
7. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 1977, 112, 535-542
8. Johnson, M.S., Srinivasan, N., Sowdhamini, R., and Blundell, T.L. Knowledge-based protein modeling. Crit. Rev. Biochem. Mol. Biol. 1994, 29, 1-68
9. Venclovas, C., Zemla, A., Fidelis, K., and Moult, J. Criteria for evaluating protein structures derived from comparative modeling. Proteins 1997, SI, 7-13
10. Liljas, L., Lindberg, A.M., and Pettersson, U. Modelling of the tertiary structure of coxsackievirus B3 from the structure of poliovirus and rhinovirus. Scand. J. Infect. Dis. 1993, S88, 15-24
11. Akahane, K., Umeyama, H., Nakagawa, S., Moriguchi, I., Hirose, S., lizuka, K., and Murakami, K. Three-dimensional structure of human renin. Hypertension 1985, 7, 3-12
12. Shiratori, Y., Nakagawa, S., Hori, H., Murakami, K., and Umeyama, H. Protein modeling of human prorenin using the molecular dynamics method. J. Mol. Graphics 1990, 8, 163-167
13. Kajihara, A., Komooka, H., Kamiya, K., and Umeyama, H. Protein modelling using a chimera reference protein derived from exons. Protein Eng. 1993, 6, 615-620
14. Matsui, I., Yoneda, S., Ishikawa, K., Miyairi, S., Fukui, S., Umeyama, H., and Honda, K. Roles of the aromatic residues conserved in the active center of Saccharomycopsis a-amylase for transglycosylation and hydrolysis activity. Biochemistry 1994, 3, 451-458
15. Yoneda, T., Komooka, H., and Umeyama, H. A computer modeling study of the interaction between tissue factor pathway inhibitor and blood coagulation factor Xa. J. Protein Chem. 1997, 16, 597-605
16. Takeda-Shitaka, M., and Umeyama, H. Elucidation of the cause of for reduced activity of abnormal human plasmin containing an Ala55-Thr mutation: Importance of highly conserved Ala55 in serine proteases. FEBS Lett. 1998, 425, 448-452
17. Cagin, T., Holder, M., and Pettitt, B.M. A method for modeling icosahedral virions: Rotational symmetry boundary conditions. J. Comput. Chem. 1991, 12,627-634
18. Lau, W.F., Pettitt, B.M., and Lybrand, T.P. Molecular dynamics of coat proteins of the human rhinovirus. Mol. Simulation 1988, 1, 385-398
19. Lau, W.F., and Pettitt, B.M. Dynamics of an oxazole compound bound to a common cold virus. J. Am. Chem. Soc. 1989, 111,4111-4113
20. Lau, W.F., and Pettitt, B.M. Selective elimination of interactions: A method for assessing thermodynamic contributions to ligand binding with application to rhinovirus antivirais. J. Med. Chem. 1989, 32, 2542-2547
21. Lybrand, T.P., Lau, W.F., McCammon, J.A., and Pettitt, B.M. Molecular dynamics studies on antiviral agents: Thermodynamics of solvation and binding. In: Protein Structure, Folding, and Design (Oxender, D.L., ed.), Vol. 2. Alan R. Liss, New York, 1987, pp. 227-233
22. Lybrand, T.P., and McCammon, J.A. Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus. J. Comput.Aided Mol. Design 1988, 2, 259-266
23. Wade, R.C., and McCammon, J.A. Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. I. Mapping the rotamers of residue 188 of viral protein 1. J. Mol. Biol. 1992, 225, 679-696
24. Wade, R.C., and McCammon, J.A. Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. II. Calculation of free-energy differences by thermodynamic integration. J. Mol. Biol. 1992, 255, 697-712
25. Guha-Biswas, M., Holder, M., and Pettitt, B.M. On the mechanism of HRV-14 antiviral compounds: "Slow growth" as a conformational search procedure. J. Med. Chem. 1993, 36, 3489-3495
26. Phelps, D.K., and Post, C.B. A novel basis for capsid stabilization by antiviral compounds. J. Mol. Dial. 1995, 254, 544-551
27. Joseph-McCarthy, D., Hogle, J.M., and Karplus, M. Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs. Proteins 1997, 29, 32-58
28. Phelps, D.K., Rossky, P.J., and Post, C.B. Influence of an antiviral compound on the temperature dependence of viral protein flexibility and packing: A molecular dynamics study. J. Mol. Biol. 1998, 276, 331-337
29. Mathiowetz, A.M., Jain, A., Karasawa, N., and Goddard, W.A., Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. Proteins 1994, 20, 227-247
30. Vaidehi, N., and Goddard, W.A., The pentamer channel stiffening model for drug action on human rhinovirus HRV-1A. Proc. Natl. Acacl. Sci. U.S.A. 1997, 94, 2466-2471
31. van Vlijmen, H.W.T., Curry, S., Schaefer, M., and Karplus, M. Titration calculation of foot-and-mouth disease virus capsids and their stabilities as a function of pH. J. Mol. Biol. 1998, 275, 295-308
32. Reddy, V.S., Giesing, H.A., Morton, R.T., Kumar, A., Post, C.B., Brooks, C.L., III, and Johnson, J.E. Energetics of quasiequivalence: Computational analysis of protein-protein interactions in icosahedral viruses. Biophys. J. 1998, 74, 546-558
33. Bruenger, A.T., Karplus, M., and Petsko, G.A. Crystallographic refinement by simulated annealing: Application to crambin. Acta Crystallogr. 1989, A45, 50-61
34. Weis, W.I., Bruenger, A.T., Skehel, J.J., and Wiley, D.C. Refinement of the influenza virus hemagglutinin by simulated annealing. J. Mol. Biol. 1990, 212,737-761
35. Yoneda, S., Kitazawa, M., and Umeyama, H. Molecular dynamics simulation of a rhinovirus capsid under rotational symmetry boundary conditions. J. Comput. Chem. 1996, 17, 191-203
36. 12 symmetry crystals. J. Mol. Graphics Modelling 1997, 15, 233-237
37. Kanaoka, M., Kishimoto, F., Ueki, Y., and Umeyama, H. Alignment of protein sequences using the hydrophobic core scores. Protein Eng. 1989, 2, 347-351
38. Needleman, S.B., and Wunsch, C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol Biol. 1970, 48, 443-453
39. Yoneda, S., and Umeyama, H. Free energy perturbation calculations on multiple mutation bases. J. Chem. Phys. 1992, 97, 6730-6736
40. Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., III, Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P.K., and Kollman, P.A. AMBER 4.1. University of California, San Francisco, 1995.
41. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. CHARMM: A program for macromolecular energy, minimization and dynamics calcultions. J. Compitt. Chem. 1983, 4, 187-217
42. van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Huenenberger, P.H., Krueger, P., Mark, A.E., Scott, W.R.P., and Tironi, I.G. Biomolecular simulation: The GROMOS96 manual and user guide. BIOMOS, Zurich, Switzerland, 1996
43. Kajihara, A., Komooka, H., Kamiya, K., Yoneda, T., Yoneda, S., Nakamura, M., Shimizu, T., and Umeyama, H. Three-dimensional model of human PAF receptor. J. Lipid Mediators Cell Signalling, 1994, 9, 185-196
44. Higo, J., and Umeyama, H. Protein dynamics determined by backbone conformation and atom packing. Protein Eng., 1997, 10, 373-380
45. Takeda-Shitaka, M., and Umeyama, H. Effect of exceptional valine replacement for highly conserved alanine55 on the catalytic site structure of chymotrypsin-like serine protease. Chem. Pharm. Bull. 1998, 46, 1343-1348
46. Takeda-Shitaka, M., Kamiya, K., Miyata, T., Ohkura, N., Madoiwa, S., Sakata, Y., and Umeyama, H. Structural studies of the interactions of normal and abnormal human plasmins with bovine basic pancreatic trypsin inhibitor. Chem. Pharm. Bull. 1999, 47, 322-328
47. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S, Jr., and Weiner, P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 1984, 106, 765-784
48. Page, G.S., Mosser, A.G., Hogle, J.M., Filman, D.J., Rueckert, R.R., and Chow, M. Three-dimensional structure of poliovirus serotype l neutralizing determinants. J. Virol. 1988, 62, 1781-1794
49. Sali, A., and Blundell, T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234, 779-815
50. Ogata, K., and Umeyama, H. The role played by environmental residues on sidechain torsional angles within homologous families of proteins: A new method of sidechain modeling. Proteins 1998, 31, 355-369