A REDUCED MODEL OF SHORT-RANGE INTERACTIONS IN POLYPEPTIDE-CHAINS

被引：27

作者：

KOLINSKI, A ^{[1
]}

MILIK, M ^{[1
]}

RYCOMBEL, J ^{[1
]}

SKOLNICK, J ^{[1
]}

机构：

[1] SCRIPPS RES INST, DEPT MOLEC BIOL, LA JOLLA, CA 92037 USA

来源：

JOURNAL OF CHEMICAL PHYSICS | 1995年 / 103卷 / 10期

关键词：

D O I：

10.1063/1.470670

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

A simple model of short range interactions is proposed for a reduced lattice representation of polypeptide conformation. The potential is derived on the basis of statistical regularities seen in the known crystal structures of globular proteins. This potential accounts for the generic stiffness of polypeptides, the correlation between peptide bond plates, and the sequence dependent correlations between consecutive segments of the C alpha-trace. This model is used for simulation of the equilibrium and dynamic properties of polypeptides in the denatured state. It is shown that the proposed factorization of the local conformational propensities reproduces secondary structure tendencies encoded in the protein sequence. Possible applications for modeling of protein folding are briefly discussed. (C) 1995 American Institute of Physics.

引用

页码：4312 / 4323

页数：12

共 60 条

[1] PRINCIPLES THAT GOVERN FOLDING OF PROTEIN CHAINS [J].

ANFINSEN, CB .

SCIENCE, 1973, 181 (4096) :223-230

[2]

[Anonymous], 1986, MONTE CARLO METHODS

[3]

[Anonymous], 1979, SCALING CONCEPTS POL

[4]

BAUMGARTNER A, 1984, ANNU REV PHYS CHEM, V35, P419

[5] PROTEIN DATA BANK - COMPUTER-BASED ARCHIVAL FILE FOR MACROMOLECULAR STRUCTURES [J].

BERNSTEIN, FC ;

KOETZLE, TF ;

WILLIAMS, GJB ;

MEYER, EF ;

BRICE, MD ;

RODGERS, JR ;

KENNARD, O ;

SHIMANOUCHI, T ;

TASUMI, M .

JOURNAL OF MOLECULAR BIOLOGY, 1977, 112 (03) :535-542

[6] ENERGY LANDSCAPES AND THE COLLAPSE DYNAMICS OF HOMOPOLYMERS [J].

CHAN, HS ;

DILL, KA .

JOURNAL OF CHEMICAL PHYSICS, 1993, 99 (03) :2116-2127

[7]

Chou P Y, 1978, Adv Enzymol Relat Areas Mol Biol, V47, P45

[8]

CLASSENS M, 1989, PROTEIN ENG, V2, P335

[9] THE BUILDING OF PROTEIN STRUCTURES FROM ALPHA-CARBON COORDINATES [J].

CORREA, PE .

PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1990, 7 (04) :366-377

[10] FOLDING PROTEIN ALPHA-CARBON CHAINS INTO COMPACT FORMS BY MONTE-CARLO METHODS [J].

COVELL, DG .

PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1992, 14 (03) :409-420

← 1 2 3 4 5 6 →