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The effect of sequence patterns and local conformational preferences on the structure of collapsed polypeptide
Author(s) -
Romiszowski Piotr,
Sikorski Andrzej
Publication year - 2000
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/1097-0282(20001005)54:4<262::aid-bip30>3.0.co;2-n
Subject(s) - chemistry , chemical physics , molecule , monte carlo method , polar , crystallography , polypeptide chain , lattice protein , sequence (biology) , molecular dynamics , lattice (music) , protein structure , computational chemistry , physics , organic chemistry , biochemistry , statistics , mathematics , astronomy , acoustics , enzyme
We studied the structure of a polypeptide model by means of the Monte Carlo method. The model chain consisting of two kinds of residues (hydrophobic and hydrophilic) was confined on the (310) hybrid lattice. The residues interacted with the long‐range contact potential. The short‐range potential was also used by introducing the preferences of conformations corresponding to the helical structure. Simulations of the coil‐to‐globule collapse were done by an annealing process starting from high‐temperature structures and then gradual cooling of the system. The parameters describing the behavior of the system were monitored. It has been found that in a case of a helical pattern –HHPPHPP‐ the collapsed chains consisted of helical fragments. The resulting structures were formed in such way that the polar residues were located in the outer shell of the molecule since the hydrophobic residues filled the inner part of molecule. The results showed that the proper balance between the magnitude of the potentials used in a model is important and its influence on final structures of molecules was discussed. © 2000 John Wiley & Sons, Inc. Biopoly 54: 262–272, 2000