Improved theoretical description of protein folding kinetics from rotations in the phase space of relevant order parameters

2004 ◽  
Vol 121 (2) ◽  
pp. 1114-1120 ◽  
Author(s):  
A. Baumketner ◽  
J.-E. Shea ◽  
Y. Hiwatari
Keyword(s):  
Protein Folding ◽  
Phase Space ◽  
Theoretical Description ◽  
Order Parameters ◽  
Folding Kinetics

scholarly journals Cooperativity in protein-folding kinetics.

1993 ◽  
Vol 90 (5) ◽  
pp. 1942-1946 ◽  
Author(s):  
K. A. Dill ◽  
K. M. Fiebig ◽  
H. S. Chan
Keyword(s):  
Protein Folding ◽  
Folding Kinetics

scholarly journals Protein folding kinetics and thermodynamics from atomistic simulation

2012 ◽  
Vol 109 (44) ◽  
pp. 17845-17850 ◽  
Author(s):  
S. Piana ◽  
K. Lindorff-Larsen ◽  
D. E. Shaw
Keyword(s):  
Protein Folding ◽  
Atomistic Simulation ◽  
Folding Kinetics ◽  
Kinetics And Thermodynamics

scholarly journals Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation

2006 ◽  
pp. 410-424 ◽  
Author(s):  
Tsung-Han Chiang ◽  
Mehmet Serkan Apaydin ◽  
Douglas L. Brutlag ◽  
David Hsu ◽  
Jean-Claude Latombe
Keyword(s):  
Protein Folding ◽  
Folding Kinetics

Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory†

2004 ◽  
Vol 108 (21) ◽  
pp. 6571-6581 ◽  
Author(s):  
William C. Swope ◽  
Jed W. Pitera ◽  
Frank Suits
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Molecular Dynamics Simulations ◽  
Folding Kinetics ◽  
Dynamics Simulations

Transition-States in Protein Folding Kinetics: The Structural Interpretation of Φ values

2007 ◽  
Vol 365 (5) ◽  
pp. 1578-1586 ◽  
Author(s):  
Thomas R. Weikl ◽  
Ken A. Dill
Keyword(s):  
Protein Folding ◽  
Transition States ◽  
Folding Kinetics ◽  
Structural Interpretation

Self-Similarity of Protein Folding Flows

2012 ◽  
Vol 7 (4) ◽  
pp. 136-141
Author(s):  
I. Kalgin ◽  
Sergey Chekmarev
Keyword(s):  
Protein Folding ◽  
Sh3 Domain ◽  
Atomic Level ◽  
The Self ◽  
Coarse Grained ◽  
Folding Kinetics ◽  
Native State ◽  
Self Similarity ◽  
Folding Dynamics ◽  
Fractal Character

The problem of how a protein folds into its functional (native) state is one of the central problems of molecular biology, which attracts the attention of researchers from biology, physics and chemistry for many years. Of particular interest are general properties of the folding process, because the mechanisms of folding of different proteins can be essentially different. Previously, in the study of folding of fyn SH3 domain, we found that despite all the diversity and complexity of individual folding trajectories, the folding flows possess a well pronounced property of self-similarity, with a fractal character of the flow distributions. In the present paper, we study this phenomenon for another protein – beta3s, which is essentially different from the SH3 domain in its structure and folding kinetics. Also, in contrast to the fyn SH3 domain, for which a coarse-grained representation was used, we perform simulations on the atomic level of resolution. We show that the self-similarity and fractality of folding flows are observed is this case too, which suggests that these properties are characteristic of the protein folding dynamics

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