Computer simulation of polypeptides in a confinement |
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Authors: | Andrzej Sikorski 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 coarse-grained model of polypeptide chains confined in a slit formed by two parallel impenetrable surfaces was studied.
The chains were flexible heteropolymers (polypeptides) built of two kinds of united atoms—hydrophobic and hydrophilic. The
positions of the united atoms were restricted to the vertices of a 310] lattice. The force field consisted of a rigorous
excluded volume, a long-distance potential between a pair of amino-acid residues and a local preference for forming secondary
structure (helices). The properties of the chains were studied at a wide range of temperatures from good to bad solvent conditions.
Monte-Carlo simulations were carried out using the algorithm based on the chain’s local changes of conformation and employing
the Replica Exchange technique. The influence of the chain length, the distances between the confining surfaces, the temperature
and the force field on the dimension and the structure of chains were studied. It was shown that the presence of the confinement
chain complicates the process of the chain collapse to low-temperature structures. For some conditions, one can find a rapid
decrease of chain size and a second transition indicated by the rapid decrease of the total energy of the system.
Figure A scheme of a polypeptide chain built on a 310] lattice and confined to a slit formed by a pair of parallel impenetrable
surfaces
Proceedings of “Modeling Interactions in Biomolecules II,” Prague, September 5th–9th, 2005. |
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Keywords: | Coil-to-globule transition α -helical globular proteins Lattice models Molecular confinement Monte Carlo method Replica Exchange method |
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