Detailed Information on Publication Record
2011
CAVER 3.0
CHOVANCOVÁ, Eva, Antonín PAVELKA, Petr BENEŠ, Ondřej STRNAD, Jan BREZOVSKÝ et. al.Basic information
Original name
CAVER 3.0
Name in Czech
CAVER 3.0
Authors
CHOVANCOVÁ, Eva (203 Czech Republic, belonging to the institution), Antonín PAVELKA (203 Czech Republic, belonging to the institution), Petr BENEŠ (203 Czech Republic), Ondřej STRNAD (203 Czech Republic), Jan BREZOVSKÝ (203 Czech Republic, belonging to the institution), Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution), Artur Wiktor GORA (616 Poland, belonging to the institution), Vilém ŠUSTR (203 Czech Republic, belonging to the institution), Martin KLVAŇA (203 Czech Republic), Petr MEDEK (203 Czech Republic), Lada BIEDERMANNOVÁ (203 Czech Republic, belonging to the institution), Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution) and Jiří SOCHOR (203 Czech Republic)
Edition
2011
Other information
Language
English
Type of outcome
Software
Field of Study
10201 Computer sciences, information science, bioinformatics
Country of publisher
Czech Republic
Confidentiality degree
není předmětem státního či obchodního tajemství
RIV identification code
RIV/00216224:14310/11:00050643
Organization unit
Faculty of Science
Keywords in English
software; Tunnels; channels
Technical parameters
licence GNU - General public licence verison 3
Změněno: 10/4/2012 08:30, prof. Mgr. Jiří Damborský, Dr.
Abstract
V originále
Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations from molecular dynamics simulations. CAVER 3.0 implements new algorithms for calculation and clustering of pathways. Trajectories from molecular dynamic simulations serve as the inputs, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied to the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3 safely identified and reliably estimated the importance of all previously published DhaA pathways, including the pathways closed in DhaA crystal structures. Moreover, five examples of DhaA variants carrying substitutions in the bottleneck residues identified by CAVER 3.0 with substantially modified catalytic activity, binding affinity and kinetic stability are provided. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available command-line application at http://www.caver.cz.
Links
| GAP202/10/1435, research and development project |
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