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Proteins. 2012 Feb;80(2):421-32. doi: 10.1002/prot.23204. Epub 2011 Nov 17.

Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues.

Author information

1
Center for Bioinformatics, Saarland University, D-66041 Saarbrücken, Germany.

Abstract

Proteins containing concavities such as pockets, cavities, and tunnels or pores perform important functions in ligand-induced signal transduction, enzymatic catalysis, and in facilitating the permeation of small molecules through membranes. Computational algorithms for identifying such shapes are therefore of great use for studying the mechanisms of these reactions. We developed the novel toolkit PROPORES for pore identification and applied our program to the systems aquaporin, tryptophan synthase, leucine transporter, and acetylcholinesterase. As a novel feature, the program checks whether access to occluded ligand binding pockets or blocked channels can be achieved by systematically rotating side chains of the gating residues. In this way, we obtain a more flexible view of the putative structural adaptability of protein structures. For the four systems mentioned, the new method was able to identify connections between pores that are separated in the X-ray structures or to connect internal pores with the protein surrounding. The software is available from http://gepard.bioinformatik.uni-saarland.de/software/propores/.

KEYWORDS:

acetylcholinesterase; aquaporin; dead-end elimination; gating residue; leucine transporter; pore detection; protein cavity; tryptophan synthase

PMID:
22095919
DOI:
10.1002/prot.23204
[Indexed for MEDLINE]
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