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Domains in folding of model proteins
Author(s) -
Abkevich V.I.,
Gutin A.M.,
Shakhnovich E.I.
Publication year - 1995
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560040615
Subject(s) - native state , protein folding , folding (dsp implementation) , lattice protein , contact order , crystallography , monte carlo method , chemistry , amino acid residue , physics , protein structure , quantitative biology , chemical physics , statistical physics , peptide sequence , biological system , biology , mathematics , biochemistry , statistics , electrical engineering , gene , engineering
By means of Monte Carlo simulation, we investigated the equilibrium between folded and unfolded states of lattice model proteins. The amino acid sequences were designed to have pronounced energy minimum target conformations of different length and shape. For short fully compact (36‐mer) proteins, the all‐or‐none transition from the unfolded state to the native state was observed. This was not always the case for longer proteins. Among 12 designed sequences with the native structure of a fully compact 48‐mer, a simple all‐or‐none transition was observed in only three cases. For the other nine sequences, three states of behavior — the native, denatured, and intermediate states — were found. The contiguous part of the native structure (domain) was conserved in the intermediate state, whereas the remaining part was completely unfolded and structureless. These parts melted separately from each other.