Computational Analysis of Protein Tunnels and Channels
Language English Country United States Media print
Document type Journal Article, Research Support, Non-U.S. Gov't
- Keywords
- Binding, CAVER, Channel, Gate, Protein, Rational design, Software, Transport, Tunnel,
- MeSH
- Algorithms MeSH
- Protein Conformation MeSH
- Ligands MeSH
- Models, Molecular MeSH
- Protein Engineering methods MeSH
- Proteins chemistry MeSH
- Solvents chemistry MeSH
- Software MeSH
- Computational Biology methods MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Ligands MeSH
- Proteins MeSH
- Solvents MeSH
Protein tunnels connecting the functional buried cavities with bulk solvent and protein channels, enabling the transport through biological membranes, represent the structural features that govern the exchange rates of ligands, ions, and water solvent. Tunnels and channels are present in a vast number of known proteins and provide control over their function. Modification of these structural features by protein engineering frequently provides proteins with improved properties. Here we present a detailed computational protocol employing the CAVER software that is applicable for: (1) the analysis of tunnels and channels in protein structures, and (2) the selection of hot-spot residues in tunnels or channels that can be mutagenized for improved activity, specificity, enantioselectivity, or stability.
References provided by Crossref.org
Structural Analysis of the Ancestral Haloalkane Dehalogenase AncLinB-DmbA
