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TMKink: A method to predict transmembrane helix kinks
Author(s) -
Meruelo Alejandro D.,
Samish Ilan,
Bowie James U.
Publication year - 2011
Publication title -
protein science
Language(s) - Uncategorized
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.653
Subject(s) - transmembrane domain , helix (gastropod) , distortion (music) , sequence (biology) , transmembrane protein , sensitivity (control systems) , protein secondary structure , chemistry , computational biology , biology , computer science , membrane , genetics , biochemistry , engineering , ecology , amplifier , computer network , receptor , bandwidth (computing) , electronic engineering , snail
A hallmark of membrane protein structure is the large number of distorted transmembrane helices. Because of the prevalence of bends, it is important to not only understand how they are generated but also to learn how to predict their occurrence. Here, we find that there are local sequence preferences in kinked helices, most notably a higher abundance of proline, which can be exploited to identify bends from local sequence information. A neural network predictor identifies over two-thirds of all bends (sensitivity 0.70) with high reliability (specificity 0.89). It is likely that more structural data will allow for better helix distortion predictors with increased coverage in the future. The kink predictor, TMKink, is available at http://tmkinkpredictor.mbi.ucla.edu/.