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United‐residue force field for off‐lattice protein‐structure simulations: III. Origin of backbone hydrogen‐bonding cooperativity in united‐residue potentials
Author(s) -
Liwo A.,
Kaźmierkiewicz R.,
Czaplewski C.,
Groth M.,
Ołdziej S.,
Wawak R. J.,
Rackovsky S.,
Pincus M. R.,
Scheraga H. A.
Publication year - 1998
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(199802)19:3<259::aid-jcc1>3.0.co;2-s
Subject(s) - cooperativity , chemistry , dipole , force field (fiction) , residue (chemistry) , interaction energy , hydrogen bond , thermodynamics , statistical physics , crystallography , computational chemistry , physics , quantum mechanics , molecule , biochemistry , organic chemistry
Based on the dipole model of peptide groups developed in our earlier work [Liwo et al., Prot. Sci., 2, 1697 (1993)], a cumulant expansion of the average free energy of the system of freely rotating peptide‐group dipoles tethered to a fixed α‐carbon trace is derived. A graphical approach is presented to find all nonvanishing terms in the cumulants. In particular, analytical expressions for three‐ and four‐body (correlation) terms in the averaged interaction potential of united peptide groups are derived. These expressions are similar to the cooperative forces in hydrogen bonding introduced by Koliński and Skolnick [ J. Chem. Phys., 97, 9412 (1992)]. The cooperativity arises here naturally from the higher order terms in the power‐series expansion (in the inverse of the temperature) for the average energy. Test calculations have shown that addition of the derived four‐body term to the statistical united‐residue potential of our earlier work [Liwo et al., J. Comput. Chem., 18, 849, 874 (1997)] greatly improves its performance in folding poly‐ l ‐alanine into an α‐helix. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 259–276, 1998