Side-chain conformations cooperatively restricted in protein secondary structure .2. Side-chain configurational entropies of alpha-helices in the folding nuclei

被引：5
|
作者：
Nakamura, H
Tanimura, R
Kidera, A
机构：
[1] TORAY INDUSTRIES LTD, BASIC RES LABS, KAMAKURA, KANAGAWA 248, JAPAN
[2] KYOTO UNIV, GRAD SCH SCI, SAKYO KU, KYOTO 60601, JAPAN
来源：
PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES | 1996年 / 72卷 / 07期
关键词：
protein structure; side-chain conformation; secondary structure; configurational entropy; folding nucleus; Levinthal paradox;
D O I：
10.2183/pjab.72.149
中图分类号：
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
Protein side-chain configurational entropies and their correlations were analyzed for alpha-helices in several proteins. The conformations of several bulky side-chains in helices were found to be cooperatively fixed by the restricted side-chain conformations of the neighboring beta-branched amino acids. Such helices correspond well to the experimentally observed nuclei in the folding procedures, so that the folding rates should be significantly accerelated. This phenomenon may be a reasonable answer to the Levinthal paradox.
引用
收藏
页码：149 / 152
页数：4
相关论文
共 50 条
  • [1] Side-chain conformations cooperatively restricted in protein secondary structure .1. A novel method for exhaustive structure searching
    Nakamura, H
    Tanimura, R
    Kidera, A
    PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES, 1996, 72 (07): : 143 - 148
  • [2] EFFECT OF SIDE-CHAIN BACKBONE ELECTROSTATIC INTERACTIONS ON THE STABILITY OF ALPHA-HELICES
    SCHERAGA, HA
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1985, 82 (17) : 5585 - 5587
  • [3] Side-chain dynamics and protein folding
    Kussell, E
    Shimada, J
    Shakhnovich, EI
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2003, 52 (02) : 303 - 321
  • [4] A HIERARCHICAL NESTING APPROACH TO DESCRIBE THE STABILITY OF ALPHA-HELICES WITH SIDE-CHAIN INTERACTIONS
    ROBERT, CH
    BIOPOLYMERS, 1990, 30 (3-4) : 335 - 347
  • [5] Side-chain control of folding of the homologous α-, β-, and γ-peptides into "mixed" helices (β-helices)
    Baldauf, C
    Günther, R
    Hofmann, HJ
    BIOPOLYMERS, 2005, 80 (05) : 675 - 687
  • [6] Prediction of side-chain conformations on protein surfaces
    Xiang, Zhexin
    Steinbach, Peter J.
    Jacobson, Matthew P.
    Friesner, Richard A.
    Honig, Barry
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007, 66 (04) : 814 - 823
  • [7] Effects of side-chain packing on the formation of secondary structures in protein folding
    Yasuda, Satoshi
    Yoshidome, Takashi
    Oshima, Hiraku
    Kodama, Ryota
    Harano, Yuichi
    Kinoshita, Masahiro
    JOURNAL OF CHEMICAL PHYSICS, 2010, 132 (06):
  • [8] Fast and accurate prediction of protein side-chain conformations
    Liang, Shide
    Zheng, Dandan
    Zhang, Chi
    Standley, Daron M.
    BIOINFORMATICS, 2011, 27 (20) : 2913 - 2914
  • [9] EFFECT OF PROTEIN PACKING STRUCTURE ON SIDE-CHAIN METHYL ROTOR CONFORMATIONS
    KOSSIAKOFF, AA
    SHTEYN, S
    NATURE, 1984, 311 (5986) : 582 - 583
  • [10] Side-chain entropy effects on protein secondary structure formation
    Chellgren, BW
    Creamer, TP
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2006, 62 (02) : 411 - 420
12345