Journal article
Ab initio computational modeling of long loops in G-protein coupled receptors
Journal of computer-aided molecular design, v 20(7), pp 427-436
Aug 2006
PMID: 16972169
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
A newly developed approach for predicting the structure of segments that connect known elements of secondary structure in proteins has been applied to some of the longer loops in the G-protein coupled receptors (GPCRs) rhodopsin and the dopamine receptor D2R. The algorithm uses Monte Carlo (MC) simulation in a temperature annealing protocol combined with a scaled collective variables (SCV) technique to search conformation space for loop structures that could belong to the native ensemble. Except for rhodopsin, structural information is only available for the transmembrane helices (TMHs), and therefore the usual approach of finding a single conformation of lowest energy has to be abandoned. Instead the MC search aims to find the ensemble located at the absolute minimum free energy, i.e., the native ensemble. It is assumed that structures in the native ensemble can be found by an MC search starting from any conformation in the native funnel. The hypothesis is that native structures are trapped in this part of conformational space because of the high-energy barriers that surround the native funnel. In this work it is shown that the crystal structure of the second extracellular loop (e2) of rhodopsin is a member of this loop’s native ensemble. In contrast, the crystal structure of the third intracellular loop is quite different in the different crystal structures that have been reported. Our calculations indicate, that of three crystal structures examined, two show features characteristic of native ensembles while the other one does not. Finally the protocol is used to calculate the structure of the e2 loop in D2R. Here, the crystal structure is not known, but it is shown that several side chains that are involved in interaction with a class of substituted benzamides assume conformations that point into the active site. Thus, they are poised to interact with the incoming ligand.
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Details
- Title
- Ab initio computational modeling of long loops in G-protein coupled receptors
- Creators
- Sandhya Kortagere - Department of Physiology and Biophysics Weill-Cornell Medical College 1300 York Avenue New York 10021 USAAmitava Roy - Department of Physiology and Biophysics Weill-Cornell Medical College 1300 York Avenue New York 10021 USAErnest Mehler - Department of Physiology and Biophysics Weill-Cornell Medical College 1300 York Avenue New York 10021 USA
- Publication Details
- Journal of computer-aided molecular design, v 20(7), pp 427-436
- Publisher
- Kluwer Academic Publishers; Dordrecht
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Microbiology and Immunology
- Web of Science ID
- WOS:000242326100003
- Scopus ID
- 2-s2.0-34548394107
- Other Identifier
- 991014878316704721
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InCites Highlights
Data related to this publication, from InCites Benchmarking & Analytics tool:
- Web of Science research areas
- Biochemistry & Molecular Biology
- Biophysics
- Computer Science, Interdisciplinary Applications