Title |
Anatomy of enzyme channels
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Published in |
BMC Bioinformatics, November 2014
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DOI | 10.1186/s12859-014-0379-x |
Pubmed ID | |
Authors |
Lukáš Pravda, Karel Berka, Radka Svobodová Vařeková, David Sehnal, Pavel Banáš, Roman A Laskowski, Jaroslav Koča, Michal Otyepka |
Abstract |
BackgroundEnzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in common.ResultsHere, we analyze the long channels (i.e. >15 Å) leading to the active sites of 4,306 enzyme structures. We find that over 64% of enzymes contain two or more long channels, their typical length being 28 Å. We show that amino acid compositions of the channel significantly differ both to the composition of the active site, surface and interior of the protein.ConclusionsThe majority of enzymes have buried active sites accessible via a network of access channels. This indicates that enzymes tend to have buried active sites, with channels controlling access to, and egress from, them, and that suggests channels may play a key role in helping determine enzyme substrate. |
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Student > Doctoral Student | 7 | 5% |
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Unknown | 29 | 21% |