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Biochim Biophys Acta. 2016 Jul;1864(7):747-54. doi: 10.1016/j.bbapap.2016.03.015. Epub 2016 Apr 9.

MBPpred: Proteome-wide detection of membrane lipid-binding proteins using profile Hidden Markov Models.

Author information

1
Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15701, Greece.
2
Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15701, Greece. Electronic address: shamodr@biol.uoa.gr.

Abstract

A large number of modular domains that exhibit specific lipid binding properties are present in many membrane proteins involved in trafficking and signal transduction. These domains are present in either eukaryotic peripheral membrane or transmembrane proteins and are responsible for the non-covalent interactions of these proteins with membrane lipids. Here we report a profile Hidden Markov Model based method capable of detecting Membrane Binding Proteins (MBPs) from information encoded in their amino acid sequence, called MBPpred. The method identifies MBPs that contain one or more of the Membrane Binding Domains (MBDs) that have been described to date, and further classifies these proteins based on their position in respect to the membrane, either as peripheral or transmembrane. MBPpred is available online at http://bioinformatics.biol.uoa.gr/MBPpred. This method was applied in selected eukaryotic proteomes, in order to examine the characteristics they exhibit in various eukaryotic kingdoms and phyla.

KEYWORDS:

Membrane Binding Domains; Membrane Binding Proteins; Membrane lipids; Peripheral membrane proteins; Profile Hidden Markov Models

PMID:
27048983
DOI:
10.1016/j.bbapap.2016.03.015
[Indexed for MEDLINE]

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