Strategies for modeling the interactions of transmembrane helices of G protein-coupled receptors by geometric complementarity using the GRAMM computer algorithm

2002 ◽  
pp. 313-328 ◽  
Author(s):  
Ilya A. Vakser ◽  
Sulin Jiang
Keyword(s):  
G Protein ◽  
G Protein Coupled Receptors ◽  
Computer Algorithm ◽  
Transmembrane Helices ◽  
G Protein Coupled

scholarly journals patGPCR: A Multitemplate Approach for Improving 3D Structure Prediction of Transmembrane Helices of G-Protein-Coupled Receptors

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Hongjie Wu ◽  
Qiang Lü ◽  
Lijun Quan ◽  
Peide Qian ◽  
Xiaoyan Xia
Keyword(s):  
G Protein ◽  
Structure Prediction ◽  
Transmembrane Helix ◽  
3D Structure ◽  
G Protein Coupled Receptors ◽  
Ligand Docking ◽  
Molecular Function ◽  
Transmembrane Helices ◽  
G Protein Coupled ◽  
Multiple Template

The structures of the seven transmembrane helices of G-protein-coupled receptors are critically involved in many aspects of these receptors, such as receptor stability, ligand docking, and molecular function. Most of the previous multitemplate approaches have built a “super” template with very little merging of aligned fragments from different templates. Here, we present a parallelized multitemplate approach, patGPCR, to predict the 3D structures of transmembrane helices of G-protein-coupled receptors. patGPCR, which employs a bundle-packing related energy function that extends on the RosettaMem energy, parallelizes eight pipelines for transmembrane helix refinement and exchanges the optimized helix structures from multiple templates. We have investigated the performance of patGPCR on a test set containing eight determined G-protein-coupled receptors. The results indicate that patGPCR improves the TM RMSD of the predicted models by 33.64% on average against a single-template method. Compared with other homology approaches, the best models for five of the eight targets built by patGPCR had a lower TM RMSD than that obtained from SWISS-MODEL; patGPCR also showed lower average TM RMSD than single-template and multiple-template MODELLER.

The structure of bacteriorhodopsin and its relevance to the visual opsins and other seven-helix G-protein coupled receptors

1990 ◽  
Vol 326 (1236) ◽  
pp. 379-389 ◽  
Keyword(s):  
G Protein ◽  
Chloride Ion ◽  
G Protein Coupled Receptors ◽  
Three Dimensions ◽  
Ion Pump ◽  
Direct Sequence ◽  
Transmembrane Helices ◽  
Visual Transduction ◽  
Receptor Proteins ◽  
G Protein Coupled

Bacteriorhodopsin is a light-driven hydrogen-ion pump whose structure is known to about 6.0 Å in three dimensions and 2.8 Å in projection. It consists of seven transmembrane helices surrounding the chromophore, retinal. Halorhodopsin is a second member of the same family of membrane proteins, both of them from the cell membrane of halobacteria. Halorhodopsin is a light-driven chloride-ion pump but has very close homology to bacteriorhodopsin, especially around the retinal. In contrast, the visual opsins that are responsible for the primary step in visual transduction in all eukaryotes from Drosophila upwards, form a separate family with no direct sequence homology to the bacteriorhodopsin family. The visual opsin family now includes about 15 other receptor proteins, all of which activate G-protein cascades, including the β-adrenergic receptor as well as several others. Despite the lack of clear relations at the level of amino acid sequence, there are topographical similarities between the bacteriorhodopsin and the visual opsin families in the nature and site of chromophore attachment, the number of transmembrane helices and the positions of the amino and carboxyl termini in the membrane. These suggest that if the two were at one time closely related, they have diverged too far to have sequences that are detectably similar.

scholarly journals Engineering Salt Bridge Networks between Transmembrane Helices Confers Thermostability in G-Protein-Coupled Receptors

2018 ◽  
Vol 14 (12) ◽  
pp. 6574-6585 ◽  
Author(s):  
Soumadwip Ghosh ◽  
Tobias Bierig ◽  
Sangbae Lee ◽  
Suvamay Jana ◽  
Adelheid Löhle ◽  
...  
Keyword(s):  
G Protein ◽  
Salt Bridge ◽  
G Protein Coupled Receptors ◽  
Transmembrane Helices ◽  
Bridge Networks ◽  
G Protein Coupled

The third extracellular loop of G-protein-coupled receptors: more than just a linker between two important transmembrane helices

2004 ◽  
Vol 32 (6) ◽  
pp. 1048-1050 ◽  
Author(s):  
Z. Lawson ◽  
M. Wheatley
Keyword(s):  
G Protein ◽  
Tertiary Structure ◽  
Large Family ◽  
Receptor Activation ◽  
G Protein Coupled Receptors ◽  
Transmembrane Helices ◽  
Ligand Selectivity ◽  
Interaction Sites ◽  
Amine Neurotransmitters ◽  
G Protein Coupled

GPCRs (G-protein-coupled receptors) are a large family of structurally related proteins, which mediate their effects by coupling with G-proteins. Despite responding to a range of very diverse stimuli, these receptors exhibit a conserved tertiary structure comprising a bundle of seven TM (transmembrane) helices linked by alternating ECLs (extracellular loops) and ICLs (intracellular loops). The hydrophobic environment formed by the cluster of TM helices is functionally important. For example, the 11-cis retinal chromophore of rhodopsin forms a protonated Schiff base linkage to a lysine in TM7, deep within the helical bundle, and small ligands, such as amine neurotransmitters and non-peptide analogues of peptide hormones, also bind within the corresponding region of their cognate receptors. In addition, activation of GPCRs involves relative movement of TM helices to present G-protein interaction sites across the intracellular face of the receptor. Consequently, it might be assumed that the ECLs of the GPCR are inert peptide linkers that merely connect important TM helices. Focusing on ECL3 (third ECL), it is becoming increasingly apparent that this extracellular domain can fulfil a range of important roles with respect to GPCR signalling, including agonist binding, ligand selectivity and receptor activation.

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