By Richard A. Friesner, Ilya Prigogine, Stuart A. Rice

Because the first makes an attempt to version proteins on a working laptop or computer all started nearly thirty years in the past, our realizing of protein constitution and dynamics has dramatically elevated. Spectroscopic dimension ideas proceed to enhance in answer and sensitivity, permitting a wealth of data to be received with reference to the kinetics of protein folding and unfolding, and complementing the exact structural photograph of the folded nation. simultaneously, algorithms, software program, and computational have advanced to the purpose the place either structural and kinetic difficulties should be studied with a good measure of realism. regardless of those advances, many significant demanding situations stay in figuring out protein folding at either the conceptual and useful degrees.

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19, 31–37 (1994). A. Sˇ ali, E. Shakhnovich, and M. Karplus, Kinetics of protein folding: A lattice model study of the requirements for folding to the native state. J. Mol. Biol. 235, 1614–1636 (1994). H. S. Chan and K. A. Dill, Transition states and folding dynamics of proteins and heteropolymers. J. Chem. Phys. 100, 9238–9257 (1994). N. D. Socci and J. N. Onuchic, Folding kinetics of proteinlike heteropolymers. J. Chem. Phys. 101, 1519–1528 (1994). A. R. Dinner, V. Abkevich, E. Shakhnovich, and M.

1). Free energy surfaces for folding have now been determined for highresolution (all-atom) models of several peptides and proteins [72–77]. 34 26 aaron r. dinner et al. energies) and configurational entropies indicated that the free energy barriers derive primarily from the fact that the entropy decreases more rapidly than the energy [75–77], as in Ref. 36 discussed above. However, consistent with the statistical analyses of proteins, differences in secondary structure content correspond to differences in the general shapes of the free energy surfaces.

USA 95, 1562–1567 (1998). 74. B. D. Bursulaya and C. L. Brooks III, Folding free energy surface of a three-stranded b-sheet protein. J. Am. Chem. Soc. 121, 9947–9951 (1999). 75. A. R. Dinner, T. Lazaridis, and M. Karplus, Understanding b-hairpin formation. Proc. Natl. Acad. Sci. USA 96, 9068–9073 (1999). 76. P. Ferrara and A. Caflisch, Folding simulations of a three-stranded antiparallel b-sheet. Proc. Natl. Acad. Sci. USA 97, 10780–10785 (2000). 77. A. Hiltpold, P. Ferrara, J. Gsponer, and A. Caflisch, Free energy surface of the helical peptide Y(MEARA)6, J.

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