Theoretical probes of conformational fluctuations in S-peptide and RNase A/3'-UMP enzyme product complex

Proteins
J E Straub, D Thirumalai

Abstract

The dynamic properties of the RNase A/3'-UMP enzyme/product complex and the S-peptide of RNase A have been investigated by molecular dynamics simulations using suitable generalization of ideas introduced to probe the energy landscape in structural glasses. We introduce two measures, namely, the kinetic energy fluctuation metric and the force metric, both of which are used to calculate the time needed for sampling the conformation space of the molecules. The calculation of the fluctuation metric requires a single trajectory whereas the force metric is computed using two independent trajectories. The vacuum MD simulations show that for both systems the time required for kinetic energy equipartitioning is surprisingly long even at high temperatures. We show that the force metric is a powerful means of probing the nature and relative importance of conformational substates which determine the dynamics at low temperatures. In particular the time dependence of the non-bonded force metric is used to demonstrate that at low temperatures the system is predominantly localized in a single cluster of conformational substates. The force metric is used to show that relaxation of long range (in sequence space) interactions must be mediated by ...Continue Reading

References

Dec 13, 1991·Science·H FrauenfelderP G Wolynes
Apr 23, 1991·Biochemistry·P J SteinbachD C Lamb
Jan 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·J Berendzen, D Braunstein
May 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·J D Honeycutt, D Thirumalai
Jan 1, 1988·Annual Review of Biophysics and Biophysical Chemistry·H FrauenfelderR D Young
May 9, 1987·Biophysical Chemistry·A AnsariT B Sauke
Nov 5, 1983·Journal of Molecular Biology·M Levitt
Aug 1, 1980·Medical Hypotheses·S Cantor
Apr 1, 1989·Physical Review A: General Physics·D ThirumalaiT R Kirkpatrick
Oct 15, 1990·Physical Review. a·D Thirumalai, R D Mountain
Jun 1, 1980·Biophysical Chemistry·N Ise, T Okubo
Jul 19, 1991·Science·D P Hamilton

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Citations

Apr 16, 1998·Protein Science : a Publication of the Protein Society·L S CavesM Karplus
Jul 23, 1999·Annals of the New York Academy of Sciences·C ManettiJ P Zbilut
Apr 1, 1996·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·I Andricioaei, J E Straub
Jul 13, 2010·Journal of Chemical Theory and Computation·Michael P EastwoodDavid E Shaw

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