# Protein Folding Kinetics: Time Scales, Pathways, and Energy Landscapes in Terms of Sequence Dependent Properties

Source: [Protein Folding Kinetics: Time Scales, Pathways, and Energy Landscapes in Terms of Sequence Dependent Properties](<https://www.sota2.com/research/paper/68fa21677a2b558e29336ff0>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-24T01:01:14.272Z

Authors: T. Veitshans, D. K. Klimov, D. Thirumalai

Published: 1996-11-08T15:50:55.000Z

## Abstract

The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times, $\\tau \_{F}$, and $\\sigma = (T\_{\\theta } - T\_{F})/T\_{\\theta } $, where $T\_{\\theta }$ and $T\_{F}$ are the equilibrium collapse and folding transition temperatures, respectively. The microscopic dynamics reveals several scenarios for the refolding kinetics depending on the values of $\\sigma $. Proteins with small $\\sigma $ reach the native conformation via a nucleation collapse mechanism and their energy landscape is characterized by single dominant native basin of attraction. Proteins with large $\\sigma $ get trapped in competing basins of attraction, in which they adopt misfolded structures. In this case only a small fraction of molecules $\\Phi $ access the native state rapidly, the majority of them approach the native state by a three stage multipathway mechanism. The partition factor $\\Phi $ is determined by $\\sigma $: smaller the value of $\\sigma $ larger is $\\Phi $. The qualitative aspects of our results are found to be independent of the friction coefficient. Estimates for time scales for folding of small proteins via a nucleation collapse mechanism are presented.

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/cond-mat/9611065>)

[PDF](<https://arxiv.org/pdf/cond-mat/9611065.pdf>)