Download Advances in Chemical Physics, Computational Methods for by Richard A. Friesner, Ilya Prigogine, Stuart A. Rice PDF

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

Because the first makes an attempt to version proteins on a working laptop or computer begun nearly thirty years in the past, our realizing of protein constitution and dynamics has dramatically elevated. Spectroscopic dimension concepts proceed to enhance in answer and sensitivity, permitting a wealth of data to be bought with reference to the kinetics of protein folding and unfolding, and complementing the particular structural photo of the folded kingdom. simultaneously, algorithms, software program, and computational have advanced to the purpose the place either structural and kinetic difficulties could 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 functional degrees.

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Dinner et al. A. In the case of the 27-residue model described in Section III [6,9], it is likely that the chain length is too short for there to be contacts that are sufficiently long range to slow-folding. In the case of the 125-residue model, which is larger than all but one (2VIK) of the proteins considered in the present study, significant correlations between various measures that characterize the native structure and the folding behavior were observed [10,11] (it should be mentioned that, in contrast to the number of antiparallel sheet contacts discussed in Section III, the contact order is a poor measure for characterizing lattice model structure; 18:7 c 31:0 for the 100 helical proteins in Refs.

Because all the proteins are roughly the same size, the stability of the native state does not depend on contact order (for the overall reaction, ÁS / n). Changes to c that raise or lower the free energy of the transition state (TS) relative to the fixed endpoints (U and F) will change ÁUÀTS and ÁGFÀTS in the same manner. This dependence of the activation free energies is the basis not only for the correlation of log ku with log kf but also that with c. 28 aaron r. dinner et al. 92 VI. HOMOLOGOUS PROTEINS Information about the transition state of a protein can be obtained from protein engineering experiments in which one compares the effects of mutations on the folding rate to their effects on the overall stability (f values).

Karplus, Use of quantitative structure–property relationships to predict the folding ability of model proteins. Proteins 33, 177–203 (1998). 12. K. W. Plaxco, K. T. Simons, and D. Baker, Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277, 985–994 (1998). 13. S. E. Jackson, How do small single-domain proteins fold? Folding & Design 3, R81–R91 (1998). 14. K. W. Plaxco, K. T. Simons, I. Ruczinski, and D. Baker, Topology, stability, sequence, and length: Defining the determinants of two-state protein folding kinetics.

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