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Titolo:
Development of physics-based energy functions that predict medium-resolution structures for proteins of the alpha,beta and alpha/beta structural classes
Autore:
Pillardy, J; Czaplewski, C; Liwo, A; Wedemeyer, WJ; Lee, J; Ripoll, DR; Arlukowicz, P; Oldziej, S; Arnautova, YA; 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 Cornell Theory Ctr, Ithaca, NY 14853 USA Cornell Theory Ctr Ithaca NY USA14853 l Theory Ctr, Ithaca, NY 14853 USA
Titolo Testata:
JOURNAL OF PHYSICAL CHEMISTRY B
fascicolo: 30, volume: 105, anno: 2001,
pagine: 7299 - 7311
SICI:
1520-6106(20010802)105:30<7299:DOPEFT>2.0.ZU;2-C
Fonte:
ISI
Lingua:
ENG
Soggetto:
RESIDUE FORCE-FIELD; MEMBRANE-BOUND PORTION; STRUCTURE SIMULATIONS; INTERACTION POTENTIALS; NONBONDED INTERACTIONS; CRYSTAL-STRUCTURES; GLOBULAR-PROTEINS; AMINO-ACIDS; OPTIMIZATION; POLYPEPTIDES;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
42
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:
J. Pillardy et al., "Development of physics-based energy functions that predict medium-resolution structures for proteins of the alpha,beta and alpha/beta structural classes", J PHYS CH B, 105(30), 2001, pp. 7299-7311

Abstract

The development of three physics-based energy functions (force fields), designed to simulate the restricted free energy of proteins of the alpha, beta, and alpha/beta structural classes. is described. Each force field corresponds to a particular weighting of the united-residue (UNRES) interactions defined in earlier work.(1-6) To find the optimal weights for the alpha, beta, and alpha/beta force fields. both the Z-score and energy gap of the native versus normative structures are minimized simultaneously for four benchmark proteins: 1pou for the (alpha force field), 1tpm (for the beta force field), and 1bdd and betanova (for the alpha/beta force field). The simultaneous minimization was carried out by using a novel Monte Carlo method, Vector Monte Carlo (VMC). For alpha -helical proteins, another weighting of theUNRES interactions (denoted as the ao force field) was developed; this fourth force field is described in a companion publication (Lee, J. et al. J. Phys. Chem. B 2001, 105, 7291). The structural implications of the final weights of the four force fields, i.e., the relative contributions of the various UNRES interactions to stabilizing common structural motifs of proteins, are analyzed. The alpha (0), alpha, beta, and alpha/beta force fields were used in the CASP4 exercise for ab initio protein -structure prediction with reasonable success. Finally, using a simple model system it was shown that the VMC protocol does not require exhaustive sampling of medium- and high-energy structures in order to optimize the parameters of the potential energy adequately.

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Documento generato il 14/08/20 alle ore 04:59:36