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. 2002 Aug;83(2):819–835. doi: 10.1016/S0006-3495(02)75211-9

Protein folding pathways and kinetics: molecular dynamics simulations of beta-strand motifs.

Hyunbum Jang 1, Carol K Hall 1, Yaoqi Zhou 1
PMCID: PMC1302189  PMID: 12124267

Abstract

The folding pathways and the kinetic properties for three different types of off-lattice four-strand antiparallel beta-strand protein models interacting via a hybrid Go-type potential have been investigated using discontinuous molecular dynamics simulations. The kinetic study of protein folding was conducted by temperature quenching from a denatured or random coil state to a native state. The progress parameters used in the kinetic study include the squared radius of gyration R(2)(g), the fraction of native contacts within the protein as a whole Q, and between specific strands Q(ab). In the time series of folding, the denatured proteins undergo a conformational change toward the native state. The model proteins exhibit a variety of kinetic folding pathways that include a fast-track folding pathway without passing through an intermediate and multiple pathways with trapping into more than one intermediate. The kinetic folding behavior of the beta-strand proteins strongly depends on the native-state geometry of the model proteins and the size of the bias gap g, an artificial measure of a model protein's preference for its native state.

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Selected References

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