-
2
-
-
0030026807
-
Functional implications of protein-protein interactions in icosahedral viruses
-
Johnson J. Functional implications of protein-protein interactions in icosahedral viruses. Proc Natl Acad Sci USA. 93:1996;27-33.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 27-33
-
-
Johnson, J.1
-
3
-
-
0032616823
-
Picornaviruses: Epitopes, canyons, and pockets
-
Smith T.J., Baker T. Picornaviruses. epitopes, canyons, and pockets Adv Virus Res. 52:1999;1-23.
-
(1999)
Adv Virus Res
, vol.52
, pp. 1-23
-
-
Smith, T.J.1
Baker, T.2
-
4
-
-
0031961961
-
Energetics of quasiequivalence: Computational analysis of protein-protein interactions in icosahedral viruses
-
The dimer association energies of the unique quasi-equivalent interfaces were calculated for human rhinovirus 14 (HRV14), comprising three major coat proteins, and for black beetle virus (BBV) and southern bean mosaic virus (SBMV), with only one type of coat protein. Thus, HRV, along with other picornaviruses, achieves quasi-equivalent packing in an icosahedral particle by having chemically distinct polypeptide chains, whereas BBV and SBMV require conformational differences at interfaces. An assembly pathway based on these energies shows that 15 subunits, assembled either as a closed pentameric unit (five trimer units) or as a hexamer-like unit with one trimer unit missing, have nearly identical energy. This degeneracy allows the occurrence of both hexamers and pentamers in the complete capsid shell, and the switch between a planar and nonplanar assemblage.
-
Reddy V.S., Giesing H.A., Morton R.T., Kumar A., Post C.B., Brooks C.L., Johnson J.E. Energetics of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses. Biophys J. 74:1998;546-558. The dimer association energies of the unique quasi-equivalent interfaces were calculated for human rhinovirus 14 (HRV14), comprising three major coat proteins, and for black beetle virus (BBV) and southern bean mosaic virus (SBMV), with only one type of coat protein. Thus, HRV, along with other picornaviruses, achieves quasi-equivalent packing in an icosahedral particle by having chemically distinct polypeptide chains, whereas BBV and SBMV require conformational differences at interfaces. An assembly pathway based on these energies shows that 15 subunits, assembled either as a closed pentameric unit (five trimer units) or as a hexamer-like unit with one trimer unit missing, have nearly identical energy. This degeneracy allows the occurrence of both hexamers and pentamers in the complete capsid shell, and the switch between a planar and nonplanar assemblage.
-
(1998)
Biophys J
, vol.74
, pp. 546-558
-
-
Reddy, V.S.1
Giesing, H.A.2
Morton, R.T.3
Kumar, A.4
Post, C.B.5
Brooks, C.L.6
Johnson, J.E.7
-
5
-
-
0032696903
-
Molecular dynamics investigation of the effect of an antiviral compound on human rhinovirus
-
Phelps D.K., Post C.B. Molecular dynamics investigation of the effect of an antiviral compound on human rhinovirus. Protein Sci. 8:1999;2281-2289.
-
(1999)
Protein Sci
, vol.8
, pp. 2281-2289
-
-
Phelps, D.K.1
Post, C.B.2
-
6
-
-
0026572864
-
Model for the differential stabilities of rhinovirus and poliovirus to mild acidic pH, based on electrostatics calculations
-
Warwicker J. Model for the differential stabilities of rhinovirus and poliovirus to mild acidic pH, based on electrostatics calculations. J Mol Biol. 223:1992;247-257.
-
(1992)
J Mol Biol
, vol.223
, pp. 247-257
-
-
Warwicker, J.1
-
7
-
-
0032536161
-
Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH
-
The Poisson-Boltzmann method of examining dimer association as a function of pH was applied to foot-and-mouth disease virus of approximately 17,000 atoms in the dimer. Detailed analysis of individual residue contributions was made. Residues important for the observed pH sensitivity (stabilizing and destabilizing) were found to be histidine residues within 5 Å of the interface. H142 and H145 in viral protein 3 were shown to have the greatest effect.
-
Van Vlijmen H.W.T., Curry S., Schaefer M., Karplus M. Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH. J Mol Biol. 275:1998;295-308. The Poisson-Boltzmann method of examining dimer association as a function of pH was applied to foot-and-mouth disease virus of approximately 17,000 atoms in the dimer. Detailed analysis of individual residue contributions was made. Residues important for the observed pH sensitivity (stabilizing and destabilizing) were found to be histidine residues within 5 Å of the interface. H142 and H145 in viral protein 3 were shown to have the greatest effect.
-
(1998)
J Mol Biol
, vol.275
, pp. 295-308
-
-
Van Vlijmen, H.W.T.1
Curry, S.2
Schaefer, M.3
Karplus, M.4
-
8
-
-
0027231258
-
On the pH dependence of protein stability
-
Yang A., Honig B. On the pH dependence of protein stability. J Mol Biol. 231:1993;459-474.
-
(1993)
J Mol Biol
, vol.231
, pp. 459-474
-
-
Yang, A.1
Honig, B.2
-
9
-
-
0029619776
-
A novel basis for capsid stabilization by antiviral compounds
-
Phelps D.K., Post C.B. A novel basis for capsid stabilization by antiviral compounds. J Mol Biol. 254:1995;544-551.
-
(1995)
J Mol Biol
, vol.254
, pp. 544-551
-
-
Phelps, D.K.1
Post, C.B.2
-
10
-
-
0032548990
-
Influence of an antiviral compound on the temperature dependence of viral protein flexibility and packing: A molecular dynamics study
-
Thermodynamic compressibilities estimated from molecular dynamics simulations had found that unligated human rhinovirus 14 (HRV14) has a lower compressibility than HRV14 bound to an antiviral compound. The higher compressibility of drug-bound HRV14 is contrary to expectation, as filling the drug-binding pocket is thought to limit conformational flexibility. The compressibility results predict a certain behavior for the temperature dependence of the protein thermal fluctuations. This prediction was tested by estimating Tg from stochastic-boundary molecular dynamics simulations. Tg, generally referred to as the glass-transition temperature, is the temperature of a transition point in the conformational mobility of proteins. The drug was found to lower Tg relative to the unligated state, consistent with the prediction made on the basis of relative compressibilities.
-
Phelps D.K., Rossky P.J., 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. 276:1998;331-337. Thermodynamic compressibilities estimated from molecular dynamics simulations had found that unligated human rhinovirus 14 (HRV14) has a lower compressibility than HRV14 bound to an antiviral compound. The higher compressibility of drug-bound HRV14 is contrary to expectation, as filling the drug-binding pocket is thought to limit conformational flexibility. The compressibility results predict a certain behavior for the temperature dependence of the protein thermal fluctuations. This prediction was tested by estimating Tg from stochastic-boundary molecular dynamics simulations. Tg, generally referred to as the glass-transition temperature, is the temperature of a transition point in the conformational mobility of proteins. The drug was found to lower Tg relative to the unligated state, consistent with the prediction made on the basis of relative compressibilities.
-
(1998)
J Mol Biol
, vol.276
, pp. 331-337
-
-
Phelps, D.K.1
Rossky, P.J.2
Post, C.B.3
-
11
-
-
0034681288
-
Stabilization of poliovirus by capsid binding antiviral drugs is due to entropic effects
-
Tsang S., Danthi P., Chow M., Hogle J. Stabilization of poliovirus by capsid binding antiviral drugs is due to entropic effects. J Mol Biol. 296:1999;335-340.
-
(1999)
J Mol Biol
, vol.296
, pp. 335-340
-
-
Tsang, S.1
Danthi, P.2
Chow, M.3
Hogle, J.4
-
12
-
-
0025273268
-
Cell-induced conformational change in poliovirus: Externalization of the amino terminus of VP1 is responsible for liposome binding
-
Fricks C., Hogle J. Cell-induced conformational change in poliovirus. externalization of the amino terminus of VP1 is responsible for liposome binding J Virol. 64:1990;1934-1945.
-
(1990)
J Virol
, vol.64
, pp. 1934-1945
-
-
Fricks, C.1
Hogle, J.2
-
13
-
-
0030910591
-
The pentamer channel stiffening model for drug action on human rhinovirus HRV-1A
-
Vaidehi N., Goddard W.A. III The pentamer channel stiffening model for drug action on human rhinovirus HRV-1A. Proc Natl Acad Sci USA. 94:1997;2466-2471.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 2466-2471
-
-
Vaidehi, N.1
Goddard W.A. III2
-
14
-
-
0030963674
-
Use of the multiple copy simultaneous search (MCSS) methods to design a new class of picornavirus capsid binding drugs
-
Joseph-McCarthy D., Hogle J.M., Karplus M. Use of the multiple copy simultaneous search (MCSS) methods to design a new class of picornavirus capsid binding drugs. Proteins. 29:1997;32-58.
-
(1997)
Proteins
, vol.29
, pp. 32-58
-
-
Joseph-Mccarthy, D.1
Hogle, J.M.2
Karplus, M.3
-
15
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U., Perrera L., Berkovitz M.L., Darden T., Lee H., Pedersen L.G. A smooth particle mesh Ewald method. J Chem Phys. 103:1995;8577-8593.
-
(1995)
J Chem Phys
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perrera, L.2
Berkovitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
16
-
-
33846823909
-
Particle mesh Ewald (PME): An Nlog(N) method for Ewald sums in large systems
-
Darden T., York D., Pedersen L. Particle mesh Ewald (PME). an Nlog(N) method for Ewald sums in large systems J Chem Phys. 98:1993;10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
17
-
-
0028063256
-
III 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
-
Mathiowetz A.M., Jain A., Karasawa N., Goddard W.A. III 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. 20:1994;227-247.
-
(1994)
Proteins
, vol.20
, pp. 227-247
-
-
Mathiowetz, A.M.1
Jain, A.2
Karasawa, N.3
Goddard, W.A.4
-
18
-
-
0001546375
-
III Molecular dynamics for very large systems on massively parallel computers: The MPSim program
-
Lim K-T., Brunett S., Iotov M., McClurg R.B., Vaidehi N., Dasgupta S., Taylor S., Goddard W.A. III Molecular dynamics for very large systems on massively parallel computers. the MPSim program J Comput Chem. 18:1997;501-521.
-
(1997)
J Comput Chem
, vol.18
, pp. 501-521
-
-
Lim, K.-T.1
Brunett, S.2
Iotov, M.3
McClurg, R.B.4
Vaidehi, N.5
Dasgupta, S.6
Taylor, S.7
Goddard, W.A.8
-
19
-
-
84986505721
-
A method for modeling icosahedral virions: Rotational symmetry boundary conditions
-
Cagin T., Holder M., Pettitt B.M. A method for modeling icosahedral virions. rotational symmetry boundary conditions J Comput Chem. 12:1991;627-634.
-
(1991)
J Comput Chem
, vol.12
, pp. 627-634
-
-
Cagin, T.1
Holder, M.2
Pettitt, B.M.3
-
20
-
-
0000438267
-
Molecular dynamics simulation of a rhinovirus capsid under rotational symmetry boundary conditions
-
Yoneda S., Kitazawa M., Umeyama H. Molecular dynamics simulation of a rhinovirus capsid under rotational symmetry boundary conditions. J Comput Chem. 17:1996;191-203.
-
(1996)
J Comput Chem
, vol.17
, pp. 191-203
-
-
Yoneda, S.1
Kitazawa, M.2
Umeyama, H.3
-
21
-
-
0027087369
-
Calculation of the free energy of association for protein complexes
-
Horton N., Lewis M. Calculation of the free energy of association for protein complexes. Protein Sci. 1:1992;169-181.
-
(1992)
Protein Sci
, vol.1
, pp. 169-181
-
-
Horton, N.1
Lewis, M.2
-
22
-
-
0033517792
-
A theoretical model successfully identifies features of hepatitis B virus capsid assembly
-
A general kinetic model is described for the self-assembly of spherical viruses that includes a nucleation event. Experimentally, the hepatitis B virus capsid is suggested to fit the kinetically limiting model, as assembly rates and equilibria are consistent with a nucleated process that is resistant to disassembly and is not susceptible to kinetic traps.
-
Zlotnick A., Johnson J.M., Wingfield P.W., Stahl S.J., Endres D. A theoretical model successfully identifies features of hepatitis B virus capsid assembly. Biochemistry. 38:1999;14644-14652. A general kinetic model is described for the self-assembly of spherical viruses that includes a nucleation event. Experimentally, the hepatitis B virus capsid is suggested to fit the kinetically limiting model, as assembly rates and equilibria are consistent with a nucleated process that is resistant to disassembly and is not susceptible to kinetic traps.
-
(1999)
Biochemistry
, vol.38
, pp. 14644-14652
-
-
Zlotnick, A.1
Johnson, J.M.2
Wingfield, P.W.3
Stahl, S.J.4
Endres, D.5
-
23
-
-
0028059187
-
To build a virus capsid - An equilibrium-model of the self-assembly of polyhedral protein complexes
-
Zlotnick A. To build a virus capsid - an equilibrium-model of the self-assembly of polyhedral protein complexes. J Mol Biol. 241:1994;59-67.
-
(1994)
J Mol Biol
, vol.241
, pp. 59-67
-
-
Zlotnick, A.1
-
24
-
-
0031737889
-
Local rules simulation of the kinetics of virus capsid self-assembly
-
The simplified simulation model integrates the equation of motion from binding energies and tolerance of errors in binding orientations, without an all-atom system. The assembly units, corresponding to one or more coat protein, interact according to local rules, reflecting icosahedral symmetry, for spatially directing the addition of new subunits.
-
Schwartz R., Shor P.W., Prevelige P.E. Jr., Berger B. Local rules simulation of the kinetics of virus capsid self-assembly. Biophys J. 75:1998;2626-2636. The simplified simulation model integrates the equation of motion from binding energies and tolerance of errors in binding orientations, without an all-atom system. The assembly units, corresponding to one or more coat protein, interact according to local rules, reflecting icosahedral symmetry, for spatially directing the addition of new subunits.
-
(1998)
Biophys J
, vol.75
, pp. 2626-2636
-
-
Schwartz, R.1
Shor, P.W.2
Prevelige P.E., Jr.3
Berger, B.4
|