PICOSECOND TIMESCALE RIGID-HELIX AND SIDE-CHAIN MOTIONS IN DEOXYMYOGLOBIN

被引:43
作者
FUROISCORBIN, S
SMITH, JC
KNELLER, GR
机构
[1] CTR ETUD SACLAY,DEPT BIOL CELLULAIRE & MOLEC,BIOPHYS PROTEINES & MEMBRANES SECT,F-91191 GIF SUR YVETTE,FRANCE
[2] INST BIOL PHYSICOCHIM,BIOCHIM THEOR LAB,CNRS,UA77,F-75005 PARIS,FRANCE
[3] IBM FRANCE,F-75012 PARIS,FRANCE
来源
PROTEINS-STRUCTURE FUNCTION AND GENETICS | 1993年 / 16卷 / 02期
关键词
PROTEIN DYNAMICS; MYOGLOBIN; MOLECULAR DYNAMICS; RIGID-BODY MOTIONS;
D O I
10.1002/prot.340160203
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The contribution of rigid-body motions to the atomic trajectories in a 100 ps molecular dynamics simulation of deoxymyoglobin is examined. Two types of rigid-body motions are considered: one in which the helices are rigid units and one in which the side-chains are rigid units. Using a quaternion-based algorithm, fits of the rigid reference structures are made to each time frame of the simulation to derive trajectories of the rigid-body motions. The fitted trajectories are analysed in terms of atomic position fluctuations, mean-square displacements as a function of time, velocity autocorrelation functions and densities of states. The results are compared with the corresponding quantities calculated from the full trajectory. The relative contribution of the rigid helix motions to the helix atom dynamics depends on which quantity is examined and on which subset of atoms is chosen; rigid-helix motions contribute 86% of the rms helix backbone atomic position fluctuations, but 30% of the helix atom (backbone and side-chain) mean square displacements and only 1.1% of total kinetic energy. Only very low-frequency motions contribute to the rigid-helix dynamics; the rigid-body analysis allows characteristic rigid-helix vibrations to be identified and described. Treating the side-chains as rigid bodies is found to be an excellent approximation to both their diffusive and vibrational mean-square displacements: 96% of side-chain atom mean-square displacements originate from rigid side-chain motions. However, the errors in the side-chain atomic positional fits are not always small. An analysis is made of factors contributing to the positional error for different types of side-chain.
引用
收藏
页码:141 / 154
页数:14
相关论文
共 41 条
[1]  
Abramowitz A., 1972, HDB MATH FUNCTIONS
[2]   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
[3]  
Brigham E. O., 1974, FAST FOURIER TRANSFO
[4]   CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].
BROOKS, BR ;
BRUCCOLERI, RE ;
OLAFSON, BD ;
STATES, DJ ;
SWAMINATHAN, S ;
KARPLUS, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217
[5]   POLAR HYDROGEN POSITIONS IN PROTEINS - EMPIRICAL ENERGY PLACEMENT AND NEUTRON-DIFFRACTION COMPARISON [J].
BRUNGER, AT ;
KARPLUS, M .
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1988, 4 (02) :148-156
[6]  
CLEMENTI E, 1990, MOTECC MODERN TECHNI, P805
[7]   TEMPERATURE-DEPENDENCE OF THE LOW-FREQUENCY DYNAMICS OF MYOGLOBIN - MEASUREMENT OF THE VIBRATIONAL FREQUENCY-DISTRIBUTION BY INELASTIC NEUTRON-SCATTERING [J].
CUSACK, S ;
DOSTER, W .
BIOPHYSICAL JOURNAL, 1990, 58 (01) :243-251
[8]   DYNAMICAL TRANSITION OF MYOGLOBIN REVEALED BY INELASTIC NEUTRON-SCATTERING [J].
DOSTER, W ;
CUSACK, S ;
PETRY, W .
NATURE, 1989, 337 (6209) :754-756
[9]   MULTIPLE CONFORMATIONAL STATES OF PROTEINS - A MOLECULAR-DYNAMICS ANALYSIS OF MYOGLOBIN [J].
ELBER, R ;
KARPLUS, M .
SCIENCE, 1987, 235 (4786) :318-321
[10]   SINGULARITY FREE ALGORITHM FOR MOLECULAR-DYNAMICS SIMULATION OF RIGID POLYATOMICS [J].
EVANS, DJ ;
MURAD, S .
MOLECULAR PHYSICS, 1977, 34 (02) :327-331