Influence of an antiviral compound on the temperature dependence of viral protein flexibility and packing: A molecular dynamics study

Journal of Molecular Biology

Volumn 276, Issue 2, 1998, Pages 331-337

  Phelps, Donald K ^a   Rossky, Peter J ^b   Post, Carol B ^a  

^a PURDUE UNIVERSITY   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Antiviral; Mobility transition; Molecular dynamics; Protein stability; Rhinovirus

Indexed keywords

3 METHYL 5 [7 [4 (4 METHYL 2 OXAZOLIN 2 YL)PHENOXY]HEPTYL]ISOXAZOLE; ANTIVIRUS AGENT; VIRUS PROTEIN;

ANTIVIRAL ACTIVITY; ARTICLE; COMPUTER SIMULATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DRUG MECHANISM; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; RHINOVIRUS; TEMPERATURE DEPENDENCE;

MIRIDAE; RHINOVIRUS;

EID: 0032548990     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1542     Document Type: Article

References (35)

1. Angell C.A. Formation of glasses from liquids and biopolymers. Science. 267:1995;1924-1935
2. Ansari A., DiIorio E.E., Dlott D.D., Frauenfelder H., Iben I.E.T., Langer P., Roder H., Sauke R.B., Shyamsunder E. Ligand binding to heme proteins relevance of low-temperature data. Biochemistry. 25:1986;3139-3146
3. Bibler-Muckelbauer J.K., Kremer M.J., Rossman M.G., Diana G.D., Dutko F.J., Pevear D.C., McKinlay M.A. Human rhinovirus 14 complexed with fragments of active antiviral compounds. Virology. 202:1994;360-369
4. 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 calculations. J. Comp. Chem. 4:1983;187-217
5. Brooks C.L. III, Karplus M. Deformable stochastic boundaries in molecular dynamics. J. Chem. Phys. 79:1983;6312-6325
6. Cohen M.H., Grest G.S. Liquid-glass transition, a free-volume approach. Phys. Rev. B. 20:1979;1077-1098
7. Da Poian A.T., Oliveira A.C., Silva J.L. Cold denaturation of an icosahedral virus. The role of entropy in virus assembly. Biochemistry. 34:1995;2672-2677
8. Donth E.-J. Relaxation and Thermodynamics in Polymers: Glass Transition. 1992;Akademie, Berlin
9. Doster W., Cusack S., Petry W. Dynamical transition of myoglobin revealed by inelastic neutron scattering. Nature. 337:1989;754-756
10. Filman D., Syed R., Chow M., Macadam A., Minor P., Hogle J. Structural factors that control conformational transition and serotype specificity in type 3 poliovirus. EMBO J. 8:1989;1567-1579
11. Fox M.P., Otto M.J., McKinlay M. The prevention of rhinovirus and poliovirus uncoating by win 51711 a new antiviral drug. Antimicrob. Agents Chemotherapy. 30:1986;110-116
12. Fox T.G., Flory P.J. Second-order transition temperatures and related properties of polystyrene. I. Influence of molecular weight. J. Appl. Phys. 21:1950;581-591
13. Frauenfelder H., Hartmann H., Karplus M., Kuntz I.D. Jr, Kuriyan J., Parak F., Petsko G.A., Ringe D., Tilton F.R. Jr, Connolly M.L., Max N. Thermal expansion of a protein. Biochemistry. 26:1987;254-261
14. Frick B., Ritcher D. The microscopic basis of the glass transition in polymers from neutron scattering studies. Science. 267:1995;1939-1945
15. Grant R.A., Hiremath C.N., Filman D.J., Syed R., Andries K., Hogle J.M. Structures of poliovirus complexes with antiviral drugs Implications for viral stability and drug design. Curr. Biol. 4:1994;784-797
16. Green J.L., Fan J., Angell C.A. The protein-glass analogy some insights from homopeptide comparisons. J. Phys. Chem. 98:1994;13780-13790
17. Hagen S.J., Hofrichter J., Eaton W.A. Protein reaction kinetics in a room-temperature glass. Science. 269:1995;959-962
18. Ichiye T., Karplus M. Anisotropy and anharmonicity of atomic fluctuation in proteins analysis of a molecular dynamics simulation. Proteins: Struct. Funct. Genet. 2:1987;236-259
19. Kim K., Willingmann P., Gong Z., Kremer M., Chapman M., Minor I., Oliveira M., Rossmann M.G., Andries K., Diana G., Dutko F., McKinlay M., Pevear D. A comparison of the antirhinoviral drug binding pocket in hrv14 and hrvla. J. Mol. Biol. 230:1993;206-226
20. Kohler W., Friedrich J., Scheer H. Conformational barriers in low-temperature proteins and glasses. Phys. Rev. A. 37:1988;660-662
21. Kraulis P. Molscript a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950
22. Kuczera K., Kuriyan J., Karplus M. Temperature dependence of the structure and dynamics of myoglobin a simulation approach. J. Mol. Biol. 213:1990;351-373
23. Lauffer M.A., Ansevin A.T., Cartwright T.E., Brinton C.C. Polymerization-depolymerization of tobacco mosaic virus protein. Nature. 181:1958;1338-1339
24. Loncharich R.J., Brooks B.R. Temperature dependence of dynamics of hydrated myoglobin. J. Mol. Biol. 215:1990;439-455
25. Mao B., Pear M.R., McCammon J.A. Molecular dynamics of ferrocytochrome c anharmoniticity of atomic displacements. Biopolymers. 21:1982;1979-1989
26. Phelps D.K., Post C.B. A novel basis for capsid stabilization by antiviral compounds. J. Mol. Biol. 254:1995;544-551
27. Prevelige P.E. Jr, King J., Silva J.L. Pressure denaturation of bactoriophage p22 coat protein and its entropic stabilization in icosahedral shells. Biophys. J. 66:1994;1631-1641
28. Rombaut B., Andries K., Boeye A. A comparison of win 51711 and r78206 as stabilizers of poliovirus virions and procapsids. J. Gen. Virol. 72:1991;2153-2157
29. Rossmann M.G. Viral cell recognition and entry. Protein Sci. 3:1994;1712-1725
30. Rossmann M.G., Arnold E., Erikson 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., Vriend G. Structure of a human cold virus and functional relationship of other picornaviruses. Nature. 317:1985;145-153
31. Ryckaert J.-P., Ciccotti G., Berendsen H.J.C. Numerical integration of the Cartesian equations of motion of a system with constraints molecular dynamics of n-alkalines. J. Comp. Phys. 23:1977;327-341
32. Smith J., Kuczera K., Karplus M. Dynamics of myoglobin comparison of simulations results with neutron scattering spectra. Proc. Natl Acad. Sci. USA. 87:1990;1601-1605
33. Smith T.J., Kremer M.J., Luo M., Vriend G., Arnold E., Kamer G., Rossmann M.G., McKinlay M.A., Diana G.D., Otto M.J. The site of attachment of human rhinovirus 14 for antiviral agents that inhibit uncoating. Science. 233:1986;1286-1293
34. Tidor B., Karplus M. The contribution of vibrational entropy to molecular association. J. Mol. Biol. 238:1994;405-414
35. Young R.D., Scholl R. Proteins as complex systems. J. Non-Cryst. Sol. 131:(133):1991;302-309