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How to Choose the Suitable Template for Homology Modelling of GPCRs: 5‐HT 7 Receptor as a Test Case
Author(s) -
Shahaf Nir,
Pappalardo Matteo,
Basile Livia,
Guccione Salvatore,
Rayan Anwar
Publication year - 2016
Publication title -
molecular informatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.481
H-Index - 68
eISSN - 1868-1751
pISSN - 1868-1743
DOI - 10.1002/minf.201501029
Subject(s) - g protein coupled receptor , homology modeling , rhodopsin , computational biology , receptor , docking (animal) , homology (biology) , sequence homology , template , bioinformatics , computer science , biology , peptide sequence , biochemistry , medicine , gene , retinal , nursing , programming language , enzyme
G protein‐coupled receptors (GPCRs) are a super‐family of membrane proteins that attract great pharmaceutical interest due to their involvement in almost every physiological activity, including extracellular stimuli, neurotransmission, and hormone regulation. Currently, structural information on many GPCRs is mainly obtained by the techniques of computer modelling in general and by homology modelling in particular. Based on a quantitative analysis of eighteen antagonist‐bound, resolved structures of rhodopsin family “A” receptors – also used as templates to build 153 homology models – it was concluded that a higher sequence identity between two receptors does not guarantee a lower RMSD between their structures, especially when their pair‐wise sequence identity (within trans‐membrane domain and/or in binding pocket) lies between 25 % and 40 %. This study suggests that we should consider all template receptors having a sequence identity ≤50 % with the query receptor. In fact, most of the GPCRs, compared to the currently available resolved structures of GPCRs, fall within this range and lack a correlation between structure and sequence. When testing suitability for structure‐based drug design, it was found that choosing as a template the most similar resolved protein, based on sequence resemblance only, led to unsound results in many cases. Molecular docking analyses were carried out, and enrichment factors as well as attrition rates were utilized as criteria for assessing suitability for structure‐based drug design.