Journal
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
Volume 70, Issue -, Pages 140-152Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2016.10.004
Keywords
Homology modeling; Sequence alignment; G protein-coupled receptors; GPCRs; beta(2) adrenergic receptor
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Funding
- National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) [R15GM119084]
- American University
- Schwartz Fellowship of the Chemistry Department
- Mathias Fellowship of the College of Arts and Sciences
- National Science Foundation [BCS-1039497]
- Sardinia Regional Government
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With the present work we quantitatively studied the modellability of the inactive state of Class A G protein-coupled receptors (GPCRs). Specifically, we constructed models of one of the Class A GPCRs for which structures solved in the inactive state are available, namely the beta(2) AR, using as templates each of the other class members for which structures solved in the inactive state are also available. Our results showed a detectable linear correlation between model accuracy and model/template sequence identity. This suggests that the likely accuracy of the homology models that can be built for a given receptor can be generally forecasted on the basis of the available templates. We also probed whether sequence alignments that allow for the presence of gaps within the transmembrane domains to account for structural irregularities afford better models than the classical alignment procedures that do not allow for the presence of gaps within such domains. As our results indicated, although the overall differences are very subtle, the inclusion of internal gaps within the transmembrane domains has a noticeable a beneficial effect on the local structural accuracy of the domain in question. (C) 2016 Elsevier Inc. All rights reserved.
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