Characterization of fold diversity among proteins with the same number of amino acid residues

被引:28
作者
Arteca, GA
Tapia, O
机构
[1] Uppsala Univ, Dept Phys Chem, S-75121 Uppsala, Sweden
[2] Laurentian Univ, Dept Chim & Biochim, Sudbury, ON P3E 2C6, Canada
来源
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES | 1999年 / 39卷 / 04期
关键词
D O I
10.1021/ci990323i
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Chain entanglements provide a simple and global measure of folding in a macromolecule. The complexity of these entanglements can be expressed by the pattern of projected bond-bond crossings, or "overcrossings", associated with the molecular backbone. In this work, we use this approach to characterize quantitatively the range of tertiary folds observed in proteins with a given chain length. To discriminate among folding features, we use two shape descriptors derived from the probability distribution of overcrossings: the mean overcrossing number, (N) over bar, and the most probable overcrossing number, N*. The values of (N) over bar and N* relate to the content of secondary structure in a protein as well as its global three-dimensional organization. We propose a measure of folding diversity based on the properties of these descriptors. In addition, we discuss the application of our method to study how tertiary folds evolve during protein dynamics.
引用
收藏
页码:642 / 649
页数:8
相关论文
共 59 条
[51]   Conformations, unfolding, and refolding of apomyoglobin in vacuum: An activation barrier for gas-phase protein folding [J].
Shelimov, KB ;
Jarrold, MF .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1997, 119 (13) :2987-2994
[52]   ''Denaturation'' and refolding of cytochrome c in vacuo [J].
Shelimov, KB ;
Jarrold, MF .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, 118 (42) :10313-10314
[53]  
Thornton JM, 1992, CURR OPIN STRUC BIOL, V2, P888
[54]  
Tooze J., 1999, INTRO PROTEIN STRUCT
[55]   Disulfide-intact and -reduced lysozyme in the gas phase: Conformations and pathways of folding and unfolding [J].
Valentine, SJ ;
Anderson, JG ;
Ellington, AD ;
Clemmer, DE .
JOURNAL OF PHYSICAL CHEMISTRY B, 1997, 101 (19) :3891-3900
[56]  
Van Gunsteren W. F., 1987, GRONINGEN MOL SIMULA
[57]   GLOBAL STATISTICS OF PROTEIN SEQUENCES - IMPLICATIONS FOR THE ORIGIN, EVOLUTION, AND PREDICTION OF STRUCTURE [J].
WHITE, SH .
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE, 1994, 23 :407-439
[58]   BIOMOLECULAR FOLDING IN VACUO() [J].
WOLYNES, PG .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1995, 92 (07) :2426-2427
[59]   Favorable domain size in proteins [J].
Xu, D ;
Nussinov, R .
FOLDING & DESIGN, 1998, 3 (01) :11-17