Visual abstractions of solvent pathlines near protein cavities

被引:21
作者
Bidmon, Katrin [1 ]
Grottel, Sebastian [1 ]
Boes, Fabian [2 ]
Pleiss, Juergen [2 ]
Ertl, Thomas [1 ]
机构
[1] Univ Stuttgart, Visualisat Res Ctr, D-7000 Stuttgart, Germany
[2] Univ Stuttgart, Inst Tech Biochem, D-7000 Stuttgart, Germany
关键词
D O I
10.1111/j.1467-8659.2008.01227.x
中图分类号
TP31 [计算机软件];
学科分类号
081202 ; 0835 ;
摘要
Water is known to play a crucial role in protein structure, flexibility and activity. The use of molecular dynamics simulations allows detailed studies of complex protein-solvent interactions. Cluster analysis and density-based approaches have been successfully used for the identification and analysis of conserved water molecules and hydration patterns of proteins. However appropriate tools for analysing long-time molecular dynamics simulations with respect to tracking and visualising the paths of solvent molecules are lacking. Our method focuses on visualising the solvent paths entering and leaving cavities of the protein and allows to study the route and dynamics of the exchange of tightly bound internal water molecules with the bulk solvent. The proposed visualisation also represents dynamic properties such as direction and velocity in the solvent. Especially, by clustering similar pathlines with respect to designated properties the visualisation can be abstracted to represent the principal paths of solvent molecules through the cavities. Its application in the analysis of long-time scale molecular dynamics simulations not only confirmed conjectures based on previous manual observations made by chance, but also led to novel insights into the dynamical and structural role of water molecules and its interplay with protein structure.
引用
收藏
页码:935 / 942
页数:8
相关论文
共 30 条
[1]   TexMol: Interactive visual exploration of large flexible multi-component molecular complexes [J].
Bajaj, C ;
Djeu, P ;
Siddavanahalli, V ;
Thane, A .
IEEE VISUALIZATION 2004, PROCEEEDINGS, 2004, :243-250
[2]   Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding protein [J].
Bakowies, D ;
van Gunsteren, WF .
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 2002, 47 (04) :534-545
[3]   Exploring structurally conserved solvent sites in protein families [J].
Bottoms, Christopher A. ;
White, Tommi A. ;
Tanner, John J. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2006, 64 (02) :404-421
[4]   The Amber biomolecular simulation programs [J].
Case, DA ;
Cheatham, TE ;
Darden, T ;
Gohlke, H ;
Luo, R ;
Merz, KM ;
Onufriev, A ;
Simmerling, C ;
Wang, B ;
Woods, RJ .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2005, 26 (16) :1668-1688
[5]   ANALYTICAL MOLECULAR-SURFACE CALCULATION [J].
CONNOLLY, ML .
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1983, 16 (OCT) :548-558
[6]  
DeLano WL, 2002, CCP4 NEWSLETTER PROT, V40
[7]  
García AE, 2000, PROTEINS, V38, P261, DOI 10.1002/(SICI)1097-0134(20000215)38:3<261::AID-PROT3>3.3.CO
[8]  
2-H
[9]  
Gumhold S, 2003, VISION, MODELING, AND VISUALIZATION 2003, P245
[10]  
HALM A, 2005, P EUR IEEE VGTC S VI