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Phys. A, 2014, Volume 393, Pages 86–95
(Mi pha1)
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Quinary lattice model of secondary structures of polymers
S. V. Kozyrev, I. V. Volovich Steklov Mathematical Institute, Russian Academy of Sciences, Moscow, Russia
Abstract:
In the standard approach to lattice proteins models based on nearest neighbor interaction
are used. In this kind of model it is difficult to explain the existence of secondary
structures—special preferred conformations of protein chains.
In the present paper a new lattice model of proteins is proposed which is based on nonlocal
cooperative interactions. In this model the energy of a conformation of a polymer is
equal to the sum of energies of conformations of fragments of the polymer chain of length
five.
It is shown that this quinary lattice model is able to describe at a qualitative level
secondary structures of proteins: for this model all conformations with minimal energy
are combinations of lattice models of alpha-helix and beta-strand. Moreover for lattice
polymers of length not longer that 38 monomers we can describe all conformations with
minimal energy.
DOI:
https://doi.org/10.1016/j.physa.2013.09.020
Bibliographic databases:
Received: 05.05.2013 Revised: 04.09.2013
Language:
Linking options:
http://mi.mathnet.ru/eng/pha1
Citing articles on Google Scholar:
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English citations
Related articles on Google Scholar:
Russian articles,
English articles
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