Role of the hydrophobic and hydrophilic sites in the dynamic crossover of the protein-hydration water

被引:25
作者
Kohler, Mateus Henrique [1 ]
Barbosa, Rafael C. [1 ]
da Silva, Leandro B. [2 ]
Barbosa, Marcia C. [1 ]
机构
[1] Univ Fed Rio Grande do Sul, Inst Fis, Caixa Postal 15051, BR-91501970 Porto Alegre, RS, Brazil
[2] Univ Fed Santa Maria, Dept Fis, Ave Roraima 1000, Santa Maria, RS, Brazil
关键词
Hydration water; Diffusion coefficient; Hydrophobicity; Hydrophilicity; MOLECULAR-DYNAMICS; NEUTRON-SCATTERING; MOTIONS; TRANSITIONS; ANOMALIES; DIFFUSION; SOLVENT; EQUATIONS; PEPTIDES; CRYSTALS;
D O I
10.1016/j.physa.2016.11.127
中图分类号
O4 [物理学];
学科分类号
0702 ;
摘要
Molecular dynamics simulations were performed to study the water structure and dynamics in the hydration shell of the globular TS-Kappa protein. The results show that for a wide range of temperatures the diffusion coefficient of water near the protein surface is lower than in bulk. A crossover in the diffusion behavior of hydration water is observed at different temperatures for hydrophilic and hydrophobic vicinities. We have found a correlation between the crossover in the hydrophilic case and the protein dynamical transition. An explanation in terms of the competition between water-water water-protein H-bond formation is provided based on H-bond network analysis. (C) 2016 Elsevier B.V. All rights reserved.
引用
收藏
页码:733 / 739
页数:7
相关论文
共 55 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] Allen M. P., 2017, Computer simulation of liquids
  • [4] Water dynamics in the hydration layer around proteins and micelles
    Bagchi, B
    [J]. CHEMICAL REVIEWS, 2005, 105 (09) : 3197 - 3219
  • [5] Water as an active constituent in cell biology
    Ball, Philip
    [J]. CHEMICAL REVIEWS, 2008, 108 (01) : 74 - 108
  • [6] Hydration shell of the TS-Kappa protein: Higher density than bulk water
    Barbosa, Rafael de C.
    Barbosa, Marcia C.
    [J]. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 2015, 439 : 48 - 58
  • [7] Water Determines the Structure and Dynamics of Proteins
    Bellissent-Funel, Marie-Claire
    Hassanali, Ali
    Havenith, Martina
    Henchman, Richard
    Pohl, Peter
    Sterpone, Fabio
    van der Spoel, David
    Xu, Yao
    Garcia, Angel E.
    [J]. CHEMICAL REVIEWS, 2016, 116 (13) : 7673 - 7697
  • [8] MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH
    BERENDSEN, HJC
    POSTMA, JPM
    VANGUNSTEREN, WF
    DINOLA, A
    HAAK, JR
    [J]. JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) : 3684 - 3690
  • [9] The Protein Data Bank
    Berman, HM
    Westbrook, J
    Feng, Z
    Gilliland, G
    Bhat, TN
    Weissig, H
    Shindyalov, IN
    Bourne, PE
    [J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 235 - 242
  • [10] Molecular dynamics of water at the protein-solvent interface
    Bizzarri, AR
    Cannistraro, S
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2002, 106 (26) : 6617 - 6633