A two-entropies analysis to identify functional positions in the transmembrane region of class A G protein-coupled receptors

Proteins
Kai YeAdriaan P Ijzerman

Abstract

Residues in the transmembrane region of G protein-coupled receptors (GPCRs) are important for ligand binding and activation, but the function of individual positions is poorly understood. Using a sequence alignment of class A GPCRs (grouped in subfamilies), we propose a so-called "two-entropies analysis" to determine the potential role of individual positions in the transmembrane region of class A GPCRs. In our approach, such positions appear scattered, while largely clustered according to their biological function. Our method appears superior when compared to other bioinformatics approaches, such as the evolutionary trace method, entropy-variability plot, and correlated mutation analysis, both qualitatively and quantitatively.

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Citations

Aug 27, 2011·Journal of Chemical Information and Modeling·Marijn P A SandersJan P G Klomp
Jun 1, 2013·Journal of Chemical Information and Modeling·Akira ShiraishiYasushi Okuno
Feb 29, 2008·Bioinformatics·Kai YeAdriaan P IJzerman
Nov 30, 2006·Nucleic Acids Research·Walter PirovanoJaap Heringa
Jun 23, 2007·Nucleic Acids Research·K Anton FeenstraJaap Heringa
Nov 4, 2010·Nucleic Acids Research·Bas VrolingGert Vriend
Nov 9, 2011·Nucleic Acids Research·Bas VrolingGert Vriend
Jun 13, 2012·Nucleic Acids Research·Abhijit ChakrabortySaikat Chakrabarti
Jan 15, 2014·Briefings in Bioinformatics·Abhijit Chakraborty, Saikat Chakrabarti
Mar 18, 2008·Bioorganic & Medicinal Chemistry·Angel GonzalezTomas Perez-Acle
Feb 23, 2018·PloS One·Tom BrownElliott J Stollar
Feb 14, 2018·PLoS Computational Biology·Raju KalaivaniNarayanaswamy Srinivasan
Dec 1, 2020·Clinical and Translational Medicine·Yue WangBingyin Shi
Jul 2, 2021·Frontiers in Molecular Biosciences·Tülay KarakulakEzgi Karaca
Jul 26, 2012·Journal of Medicinal Chemistry·Gerard J P van WestenAndreas Bender

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