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A heteropolymer model study for the mechanism of protein folding
Author(s) -
Fukugita Masataka,
Lancaster David,
Mitchard Mark G.
Publication year - 1997
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(199703)41:3<239::aid-bip1>3.0.co;2-t
Subject(s) - folding funnel , maxima and minima , folding (dsp implementation) , downhill folding , cluster (spacecraft) , chemistry , contact order , statistical physics , sequence (biology) , protein folding , chemical physics , mechanism (biology) , similarity (geometry) , ground state , chain (unit) , excited state , physics , phi value analysis , computer science , quantum mechanics , mathematics , mathematical analysis , biochemistry , image (mathematics) , artificial intelligence , electrical engineering , programming language , engineering
A heteropolymer model of randomly self‐interacting chains in two dimensions is studied with numerical simulations in order to elucidate the folding mechanism of protein. We find that the model occasionally shows folding propensity depending on the sequence of random numbers given to the chain. We study the thermodynamic and kinematic roles in the folding mechanism by grouping the local energy minima found in the simulations into clusters according to the similarity of their conformations. It is suggested that the local minima to which some heteropolymers show a folding tendency are always the lowest energy states of the energy spectrum within a cluster, though which cluster is selected depends on the sequence. For the eight random sequences we study, we find that the energy gap between the ground state and excited states is little correlated with folding or nonfolding. We rather find that folding propensities are correlated with the global structure of the average energy surface, implying a dominant kinetic role in the folding mechanism, although thermal factors cannot be ignored as the mechanism of choosing the ground state within a cluster of states connected by small deformations. We suggest that a hierarchical cluster structure plays an important role in selecting a unique folded state out of the huge number of local minima of heteropolymers. © 1997 John Wiley & Sons, Inc.