Water dynamical anomalies evidenced by molecular-dynamics simulations at the solvent-protein interface

被引:169
作者
Rocchi, C
Bizzarri, AR
Cannistraro, S [1 ]
机构
[1] Univ Perugia, Dipartimento Fis, Unita INFM, I-06100 Perugia, Italy
[2] Univ Tuscia, Dipartimento Sci Ambientali, I-01100 Viterbo, Italy
关键词
D O I
10.1103/PhysRevE.57.3315
中图分类号
O35 [流体力学]; O53 [等离子体物理学];
学科分类号
070204 ; 080103 ; 080704 ;
摘要
We present a computer simulation picture of the dynamical behavior, at room temperature, of water in the region close to a protein surface. We analyzed the probability distribution of water molecules diffusing near the surface, and we found that it deviates from a Gaussian, which is predicted for Brownian particles. Consistently, the mean square displacements of water oxygens show a sublinear trend with time. Moreover, the relaxation of hydration layers around the whole protein is found to follow a stretched exponential decay, typical of complex systems, which could as well be ascribed to the non-Gaussian shape of the propagator. In agreement with such findings, the analysis of water translational and reorientational diffusion showed that not only are the solvent molecule motions hindered in the region close to the protein surface, but also the very nature of the particle diffusive processes, both translational and rotational, is affected. The deviations from the bulk water properties, which put into evidence a deep influence exerted by the protein on the solvent molecule motion, are discussed in connection with the presence of spatial (protein surface roughness) and temporal (distribution of water residence times) disorder inherent in the system.
引用
收藏
页码:3315 / 3325
页数:11
相关论文
共 69 条
[1]  
Abseher R, 1996, PROTEINS, V25, P366, DOI 10.1002/(SICI)1097-0134(199607)25:3<366::AID-PROT8>3.0.CO
[2]  
2-D
[3]   MOLECULAR-DYNAMICS SIMULATION OF INTERFACIAL WATER-STRUCTURE AND DYNAMICS IN A PARVALBUMIN SOLUTION [J].
AHLSTROM, P ;
TELEMAN, O ;
JONSSON, B .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1988, 110 (13) :4198-4203
[4]  
ALEXANDER S, 1982, J PHYS LETT-PARIS, V43, pL625, DOI 10.1051/jphyslet:019820043017062500
[5]   FORMATION OF GLASSES FROM LIQUIDS AND BIOPOLYMERS [J].
ANGELL, CA .
SCIENCE, 1995, 267 (5206) :1924-1935
[6]   PROTEIN STATES AND PROTEIN QUAKES [J].
ANSARI, A ;
BERENDZEN, J ;
BOWNE, SF ;
FRAUENFELDER, H ;
IBEN, IET ;
SAUKE, TB ;
SHYAMSUNDER, E ;
YOUNG, RD .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1985, 82 (15) :5000-5004
[7]   Analysis of the velocity autocorrelation function of water [J].
Balucani, U ;
Brodholt, JP ;
Vallauri, R .
JOURNAL OF PHYSICS-CONDENSED MATTER, 1996, 8 (34) :6139-6144
[8]   THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS [J].
BERENDSEN, HJC ;
GRIGERA, JR ;
STRAATSMA, TP .
JOURNAL OF PHYSICAL CHEMISTRY, 1987, 91 (24) :6269-6271
[9]   MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH [J].
BERENDSEN, HJC ;
POSTMA, JPM ;
VANGUNSTEREN, WF ;
DINOLA, A ;
HAAK, JR .
JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) :3684-3690
[10]   INFLUENCE OF THE ENVIRONMENT ON ANOMALOUS DIFFUSION [J].
BETTIN, R ;
MANNELLA, R ;
WEST, BJ ;
GRIGOLINI, P .
PHYSICAL REVIEW E, 1995, 51 (01) :212-219