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Ab initio computational modeling of long loops in G-protein coupled receptors

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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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Acknowledgements

Computational support was provided by the National Science Foundation Terascale Computing System at the Pittsburgh Supercomputing Center. The authors also acknowledge access to the computer facilities at the Institute of Computational Biomedicine (ICB) of Weill Medical College of Cornell University. Support of the work by NIH Grants R01-DA15170, R01-MH063162 and P01-DA012923 is gratefully acknowledged.

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Author notes

  1. Sandhya Kortagere

    Present address: Department of Pharmacology, UMDNJ - Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ, 08854, USA

Authors and Affiliations

  1. Department of Physiology and Biophysics, Weill-Cornell Medical College, 1300 York Avenue, New York, 10021, USA

    Sandhya Kortagere, Amitava Roy & Ernest L. Mehler

Authors
  1. Sandhya Kortagere
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  2. Amitava Roy
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  3. Ernest L. Mehler
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Correspondence to Ernest L. Mehler.

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Kortagere, S., Roy, A. & Mehler, E.L. Ab initio computational modeling of long loops in G-protein coupled receptors. J Comput Aided Mol Des 20, 427–436 (2006). https://doi.org/10.1007/s10822-006-9056-0

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  • DOI: https://doi.org/10.1007/s10822-006-9056-0

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