A METHOD TO EXPLORE TRANSITION PATHS IN MACROMOLECULES - APPLICATIONS TO HEMOGLOBIN AND PHOSPHOGLYCERATE KINASE

被引：37

作者：

GUILBERT, C ^{[1
]}

PERAHIA, D ^{[1
]}

MOUAWAD, L ^{[1
]}

机构：

[1] UNIV PARIS 11,ENZYMOL PHYSICOCHIM & MOLEC LAB,CNRS,UNITE RECH,F-91405 ORSAY,FRANCE

来源：

COMPUTER PHYSICS COMMUNICATIONS | 1995年 / 91卷 / 1-3期

关键词：

MACROMOLECULES; CONFORMATIONAL PATHWAYS;

D O I：

10.1016/0010-4655(95)00052-H

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

A method to find low energy paths in macromolecules is described, It can be applied either to determine paths between two given energy minimum conformations, or to explore low energy paths departing from one energy minimized conformation. The principle of the method consists in carrying out energy minimizations or molecular dynamics simulations with root mean square distance constraints with respect to a reference structure. The method is illustrated by applications to N-methyl-alanyl-acetamide, hemoglobin and phosphoglycerate kinase.

引用

页码：263 / 273

页数：11

共 18 条

[1] SEQUENCE, STRUCTURE AND ACTIVITY OF PHOSPHOGLYCERATE KINASE - POSSIBLE HINGE-BENDING ENZYME
BANKS, RD
BLAKE, CCF
EVANS, PR
HASER, R
RICE, DW
HARDY, GW
MERRETT, M
PHILLIPS, AW
[J]. NATURE, 1979, 279 (5716) : 773 - 778
[2] GLUCOSE-INDUCED CONFORMATIONAL CHANGE IN YEAST HEXOKINASE
BENNETT, WS
STEITZ, TA
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1978, 75 (10) : 4848 - 4852
[3] STRUCTURE OF A COMPLEX BETWEEN YEAST HEXOKINASE-A AND GLUCOSE .2. DETAILED COMPARISONS OF CONFORMATION AND ACTIVE-SITE CONFIGURATION WITH THE NATIVE HEXOKINASE-B MONOMER AND DIMER
BENNETT, WS
STEITZ, TA
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1980, 140 (02) : 211 - 230
[4] CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS
BROOKS, BR
BRUCCOLERI, RE
OLAFSON, BD
STATES, DJ
SWAMINATHAN, S
KARPLUS, M
[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) : 187 - 217
[5] ON FINDING TRANSITION-STATES
CERJAN, CJ
MILLER, WH
[J]. JOURNAL OF CHEMICAL PHYSICS, 1981, 75 (06) : 2800 - 2806
[6] A METHOD FOR DETERMINING REACTION PATHS IN LARGE MOLECULES - APPLICATION TO MYOGLOBIN
ELBER, R
KARPLUS, M
[J]. CHEMICAL PHYSICS LETTERS, 1987, 139 (05) : 375 - 380
[7] THEORETICAL DETERMINATION OF CONFORMATIONAL PATHS IN CITRATE SYNTHASE
ELKETTANI, MAEC
DURUP, J
[J]. BIOPOLYMERS, 1992, 32 (05) : 561 - 574
[8] THE CRYSTAL-STRUCTURE OF HUMAN DEOXYHEMOGLOBIN AT 1.74A RESOLUTION
FERMI, G
PERUTZ, MF
SHAANAN, B
FOURME, R
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1984, 175 (02) : 159 - 174
[9] CONJUGATE PEAK REFINEMENT - AN ALGORITHM FOR FINDING REACTION PATHS AND ACCURATE TRANSITION-STATES IN SYSTEMS WITH MANY DEGREES OF FREEDOM
FISCHER, S
KARPLUS, M
[J]. CHEMICAL PHYSICS LETTERS, 1992, 194 (03) : 252 - 261
[10] CRYSTAL-STRUCTURE OF THE BINARY COMPLEX OF PIG MUSCLE PHOSPHOGLYCERATE KINASE AND ITS SUBSTRATE 3-PHOSPHO-D-GLYCERATE
HARLOS, K
VAS, M
BLAKE, CF
[J]. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1992, 12 (02): : 133 - 144

← 1 2 →