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Kinetics of cytochrome C folding: atomically detailed simulations by Alfredo E. Cárdenas; Ron Elber is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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The vast range of time scales (from nanoseconds to seconds) during protein folding is a challenge for experiments and computations. To make concrete predictions on folding mechanisms, atomically detailed simulations of protein folding, using potentials derived from chemical physics principles, are desired. However, due to their computational complexity, straightforward molecular dynamics simulations of protein folding are impossible today. An alternative algorithm is used that makes it possible to compute approximate atomically detailed long time trajectories (the Stochastic Difference Equation in Length). This algorithm is used to compute 26 atomically detailed folding trajectories of cytochrome c (a millisecond process). The early collapse of the protein chain (with marginal formation of secondary structure), and the earlier formation of the N and C helices (compare to the 60's helix) are consistent with the experiment. The existence of an energy barrier upon entry to the molten globule is examined as well. In addition to (favorable) comparison to experiments, we show that non-native contacts drive the formation of the molten globule. In contrast to popular folding models, the no

Who reads Kinetics of cytochrome C folding: atomically detailed simulations?

Author

Alfredo E. Cárdenas; Ron Elber

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)

Published

2003

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)