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Conclusions

The current simulations have not been able to reproduce the 10%expansion expected for the NOCA model on the basis of the experimental data[50]. However, the NOCA model is substantially higher in energy (700 kcal/mol), indicating that it might be driven to expand in more extensive calculations. The NEIMO simulations show substantial contraction of both the PH7 and NOCA models, but the nature of this phenomenon is unknown. The RNA in the interior of the virus may be needed to prevent contraction of the viral coat. Other models of TBSV should be investigated, including those in which all Ca ions are removed, but are not replaced by Na.

References

101
I.T. Weber et al., Science, 243, 928-931 (1989).
102
R.S. Struthers, D.H. Kitson, and A.T. Hagler, Proteins: Structure, Function, Genet., 9, 1-11 (1991).
103
J.F. Leszczynski and G.D. Rose, Science, 234, 849-855 (1986).
104
C. Chothia and A.M. Lesk, J. Mol. Biol., 196, 901-917 (1987).
105
T.A. Jones and S. Thirup, EMBO J., 5, 819-822 (1986).
106
R.E. Bruccoleri and M. Karplus, Biopolymers, 26, 137-168 (1987).
107
P.S. Shenkin et al., Biopolymers, 26, 2053-2085 (1987).
108
A.C.R. Martin, J.C. Cheetham, and A.R. Rees, Proc. Natl. Acad. Sci., USA, 86, 9268-9272 (1989).
109
S.L. Mayo, B.D. Olafson, and W.A. Goddard III, J. Phys. Chem., 94, 8897-8909 (1990).
110
BIOGRAF/POLYGRAF. Copyright by Molecular Simulations, Inc. (1992).
111
N. Go and H.A. Scheraga, Macromolecules, 3, 178-187 (1970).
112
N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, and A.H. Teller, J. Chem. Phys., 21, 1087-1092 (1953).
113
D. Eisenberg and A.D. McLachlan, Nature, 319, 199-203 (1986).
114
Y. Satow et al., J. Mol. Biol., 190, 593-604 (1986).
115
S. Sheriff et al., Proc. Natl. Acad. Sci., USA, 84, 8075-8079 (1987).
116
C. Chothia et al., Nature, 342, 887-883 (1989).
117
R.M. Fine et al., Proteins: Structure, Function, Genet., 1, 342-362 (1986).
118
R.E. Bruccoleri, E. Haber, and J. Novotný, Nature, 335, 564-568 (1988).
119
D.R. Davies, E.A. Padlan, and S. Sheriff, Annu. Rev. Biochem., 59, 439-473, (1990).
120
E.A. Padlan, G.H. Cohen, and D.R. Davies, Ann. Inst. Pasteur/Immunol., 136C, 259-294 (1985).


ktl@sgi1.wag.caltech.edu
Sat Jun 18 14:06:11 PDT 1994