Folding Behavior of Polypeptides. A Monte Carlo Study of Simplified Models |
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Authors: | Andrzej Sikorski and Piotr Romiszowski |
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Institution: | (1) Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland |
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Abstract: | A simple model of polypeptide chains was designed and studied. The chains were constructed on a flexible 310] lattice and
consisted of united atoms located at the position of alpha carbons. Each united atom represented amino acid residues of two
kinds: hydrophilic and hydrophobic. The sequence of the residues was assumed to be characteristic for α- and β-type of proteins.
The force field used consisted of the long-range contact potential between polymer segments, the short range repulsion, and
the local potential preferring conformational states characteristic for α-helices and β-strands. The Monte Carlo simulations
of this model were carried out using the replica exchange technique coupled with the histogram method. The influence of temperature
and the local potential on the size and internal structure of collapsed low temperature chains were studied. Thermodynamics
of these systems consisting mainly of α and β secondary structures were determined. The properties of the coil-to-globule
transition were presented and compared with other theoretical predictions and simulation results. |
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