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
[41]   CLASSIFICATION OF PROTEIN FOLDS [J].
ORENGO, C .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 1994, 4 (03) :429-440
[42]   IDENTIFICATION AND CLASSIFICATION OF PROTEIN FOLD FAMILIES [J].
ORENGO, CA ;
FLORES, TP ;
TAYLOR, WR ;
THORNTON, JM .
PROTEIN ENGINEERING, 1993, 6 (05) :485-500
[43]   Proteins in vacuo.: Denaturing of disulfide-intact and disulfide-broken lysozyme probed by molecular dynamics simulations [J].
Reimann, CT ;
Velázquez, I ;
Tapia, O .
JOURNAL OF PHYSICAL CHEMISTRY B, 1998, 102 (12) :2277-2283
[44]   Proteins in vacuo.: Denaturation of highly-charged lysozyme studied by molecular dynamics simulations [J].
Reimann, CT ;
Velázquez, I ;
Tapia, O .
JOURNAL OF PHYSICAL CHEMISTRY B, 1998, 102 (46) :9344-9352
[45]   Conformation of highly-charged gas-phase lysozyme revealed by energetic surface imprinting [J].
Reimann, CT ;
Sullivan, PA ;
Axelsson, J ;
Quist, AP ;
Altmann, S ;
Roepstorff, P ;
Velázquez, I ;
Tapia, O .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, 120 (30) :7608-7616
[46]  
Richardson J S, 1981, Adv Protein Chem, V34, P167, DOI 10.1016/S0065-3233(08)60520-3
[47]  
RICHARDSON JS, 1985, METHOD ENZYMOL, V115, P341
[48]   THE ASPHERICITY OF RANDOM-WALKS [J].
RUDNICK, J ;
GASPARI, G .
JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL, 1986, 19 (04) :L191-L193
[49]   THE SHAPES OF RANDOM-WALKS [J].
RUDNICK, J ;
GASPARI, G .
SCIENCE, 1987, 237 (4813) :384-389
[50]   PROTEINS WITH SELECTED SEQUENCES FOLD INTO UNIQUE NATIVE CONFORMATION [J].
SHAKHNOVICH, EI .
PHYSICAL REVIEW LETTERS, 1994, 72 (24) :3907-3910