Understanding the structural and functional differences between mouse thyrotropin-releasing hormone receptors 1 and 2

Laboratory of Biological Modeling, National Institute of Diabetes and Digestive, and Kidney Diseases, NIH, Bethesda, Maryland 20892-5646, USA.
Proteins Structure Function and Bioinformatics (Impact Factor: 2.63). 05/2008; 71(2):783-94. DOI: 10.1002/prot.21763
Source: PubMed


Multiple computational methods have been employed in a comparative study of thyrotropin-releasing hormone receptors 1 and 2 (TRH-R1 and TRH-R2) to explore the structural bases for the different functional properties of these G protein-coupled receptors. Three-dimensional models of both murine TRH receptors have been built and optimized by means of homology modeling based on the crystal structure of bovine rhodopsin, molecular dynamics simulations, and energy minimizations in a membrane-aqueous environment. The comparison between the two models showed a correlation between the higher flexibility and higher basal activity of TRH-R2 versus the lesser flexibility and lower basal activity of TRH-R1 and supported the involvement of the highly conserved W6.48 in the signaling process. A correlation between the level of basal activity and conformational changes of TM5 was detected also. Comparison between models of the wild type receptors and their W6.48A mutants, which have reversed basal activities compared with their respective wild types, further supported these correlations. A flexible molecular docking procedure revealed that TRH establishes a direct interaction with W6.48 in TRH-R2 but not in TRH-R1. We designed and performed new mutagenesis experiments that strongly supported these observations.

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    • "Despite this conservation in overall architecture, the orientation and length of the helices vary to some extent [14], [17] and considerable structural diversity is observed in the three intracellular and extracellular loops [24], [25] that connect the seven TMHs [26]. Furthermore, differences are also observed in the orientation of sidechains (including highly conserved amino acids) [18], [27] and the presence and extent of helical distortions (kinks and bulges) [28]. "
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    ABSTRACT: Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will help to produce more reliable three-dimensional models.
    PLoS ONE 09/2009; 4(9):e7011. DOI:10.1371/journal.pone.0007011 · 3.23 Impact Factor
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    • "This probably arises because GPCR models are always obtained from the rhodopsin X-ray structure, where TM7 is stabilized by retinal, its bound ligand. However, in a recently published paper, Deflorian and co-workers reported that in their MD simulations of thyrotropin-releasing hormone receptor models (THR-R1 and THR-R2), no restraints were required to preserve the α-helical secondary structure of the TM segments [32]. "
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    BMC Bioinformatics 02/2008; 9(1):263. DOI:10.1186/1471-2105-9-263 · 2.58 Impact Factor
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