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Titolo:
Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
Autore:
Liwo, A; Czaplewski, C; Pillardy, J; Scheraga, HA;
Indirizzi:
Cornell Univ, Baker Lab Chem & Chem Biol, Ithaca, NY 14853 USA Cornell Univ Ithaca NY USA 14853 b Chem & Chem Biol, Ithaca, NY 14853 USA Univ Gdansk, Fac Chem, PL-80952 Gdansk, Poland Univ Gdansk Gdansk PolandPL-80952 sk, Fac Chem, PL-80952 Gdansk, Poland
Titolo Testata:
JOURNAL OF CHEMICAL PHYSICS
fascicolo: 5, volume: 115, anno: 2001,
pagine: 2323 - 2347
SICI:
0021-9606(20010801)115:5<2323:CEFTMT>2.0.ZU;2-1
Fonte:
ISI
Lingua:
ENG
Soggetto:
PROTEIN-STRUCTURE SIMULATIONS; MONTE-CARLO SIMULATIONS; MEMBRANE-BOUND PORTION; GLOBULAR-PROTEINS; CONFORMATIONAL-ANALYSIS; GLOBAL OPTIMIZATION; HOMOLOGOUS PROTEINS; DATA-BANK; DE-NOVO; ENERGY;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
68
Recensione:
Indirizzi per estratti:
Indirizzo: Scheraga, HA Cornell Univ, Baker Lab Chem & Chem Biol, Ithaca, NY 14853 USA Cornell Univ Ithaca NY USA 14853 Biol, Ithaca, NY 14853 USA
Citazione:
A. Liwo et al., "Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field", J CHEM PHYS, 115(5), 2001, pp. 2323-2347

Abstract

A general method to derive site-site or united-residue potentials is presented. The basic principle of the method is the separation of the degrees offreedom of a system into the primary and secondary ones. The primary degrees of freedom describe the basic features of the system, while the secondary ones are averaged over when calculating the potential of mean force, which is hereafter referred to as the restricted free energy (RFE) function. The RFE can be factored into one-, two-, and multibody terms, using the cluster-cumulant expansion of Kubo. These factors can be assigned the functionalforms of the corresponding lowest-order nonzero generalized cumulants, which can, in most cases, be evaluated analytically, after making some simplifying assumptions. This procedure to derive coarse-grain force fields is very valuable when applied to multibody terms, whose functional forms are hardto deduce in another way (e.g., from structural databases). After the functional forms have been derived, they can be parametrized based on the RFE surfaces of model systems obtained from all-atom models or on the statisticsderived from structural databases. The approach has been applied to our united-residue force field for proteins. Analytical expressions were derived for the multibody terms pertaining to the correlation between local and electrostatic interactions within the polypeptide backbone; these expressions correspond to up to sixth-order terms in the cumulant expansion of the RFE. These expressions were subsequently parametrized by fitting to the RFEs ofselected peptide fragments, calculated with the empirical conformational energy program for peptides force field. The new multibody terms enable not only the heretofore predictable alpha -helical segments, but also regular beta -sheets, to form as the lowest-energy structures, as assessed by test calculations on a model helical protein A, as well as a model 20-residue polypeptide (betanova); the latter was not possible without introducing these new terms. (C) 2001 American Institute of Physics.

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Documento generato il 24/09/20 alle ore 05:04:40