An overview of recent developments in GPCR modelling: methods and validation
- Chemistry, BiologyExpert opinion on drug discovery
In this review the most common HM computational steps are reported and discussed together with the most recent alternative approaches and main validation methods.
Molecular modeling of adenosine receptors: new results and trends
- Biology, ChemistryMedicinal research reviews
The publication of the first high‐resolution crystal structure for bovine rhodopsin (bRh), a GPCR superfamily member, provides the option of utilizing HM to generate 3D models based on detailed structural information.
Molecular Modeling of Vasopressin V2 Receptor Tetramer in Hydrated Lipid Membrane
- Biology, Chemistry
This is the first Molecular Dynamics simulation of the tetramer model of a GPCR other than rhodopsin, and the optimal adjusting of monomers in lipid membrane surrounding was the purpose of simulation.
Alpha-Bulges in G Protein-Coupled Receptors
- BiologyInternational journal of molecular sciences
The role of these α-bulges in ligand and G-protein binding, as well as their role in several aspects of the mobility associated with GPCR activation, are drawn attention.
Comparative Sequence and Structural Analyses of G-Protein-Coupled Receptor Crystal Structures and Implications for Molecular Models
- BiologyPloS one
A systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for G PCR homology modelling that will help to produce more reliable three-dimensional models are provided.
How a small change in retinal leads to G‐protein activation: Initial events suggested by molecular dynamics calculations
- Biology, ChemistryProteins
This study creates an energetically unstable retinal in the light activated state and uses molecular dynamics simulations to examine the types of compensation, relaxation, and conformational changes that occur following the cis–trans light activation of Rhodopsin.
Data integration in the life sciences. A protein family-based approach.
The GPCRDB is a data source that holds a large amount of heterogeneous data in a well-organized and easily accessible form that facilitates inferring new information using a wide spectrum of bioinformatics techniques.
GPCRs: Past, present, and future
This chapter provides an overview of the major developments in the GPCR field since the 19th century, and sheds some light on some of the questions that are relevant now and those that need to be answered in the future regarding G PCR structure and function.
SHOWING 1-10 OF 74 REFERENCES
Prediction of structure and function of G protein-coupled receptors
- Biology, ChemistryProceedings of the National Academy of Sciences of the United States of America
It is found that the predicted structure of β1-adrenergic receptor leads to a binding site for epinephrine that agrees well with the mutation experiments, and the predicted binding sites and affinities for endothelial differential gene 6, mouse and rat I7 olfactory receptors, and human sweet receptor are consistent with the available experimental data.
GPCRDB: an information system for G protein-coupled receptors.
- BiologyNucleic acids research
The GPCRDB is a G protein-coupled receptor (GPCR) database system aimed at the collection and dissemination of GPCR related data. It holds sequences, mutant data and ligand binding constants as…
Modeling and Docking of the Three-Dimensional Structure of the Human Melanocortin 4 Receptor
- BiologyJournal of protein chemistry
The model constructed here might provide a structural framework for making rational predictions in relevant fields and was found that the ligand is located among transmembrane regions TM3, TM4, TM5, and TM6 of hMC4R.
Organization of the G Protein-coupled Receptors Rhodopsin and Opsin in Native Membranes*
- BiologyJournal of Biological Chemistry
This is the first semi-empirical model of a higher order structure of a GPCR in native membranes, and it has profound implications for the understanding of how this receptor interacts with partner proteins.
Arrangement of rhodopsin transmembrane α-helices
Rhodopsins, the photoreceptors in rod cells, are G-protein-coupled receptors with seven hydrophobic segments containing characteristic conserved sequence patterns that define a large family,. Members…
Arrangement of rhodopsin transmembrane alpha-helices.
Rhodopsins, the photoreceptors in rod cells, are G-protein-coupled receptors with seven hydrophobic segments containing characteristic conserved sequence patterns that define a large family. Members…
The probable arrangement of the helices in G protein‐coupled receptors.
- BiologyThe EMBO journal
The structural constraints for the receptors are used to allocate particular helices to the peaks in the recently published projection map of rhodopsin and to propose a tentative three‐dimensional arrangement of the helices in G protein‐coupled receptors.
Structural mimicry in G protein-coupled receptors: implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors.
- Biology, ChemistryMolecular pharmacology
It is proposed that the overall structures of rhodopsin and of amine receptors are very similar, although there are also localized regions where the structure of these receptors may diverge.
A common motif in G-protein-coupled seven transmembrane helix receptors
- BiologyJ. Comput. Aided Mol. Des.
A number of residues in the helices and in the cytosolic loops that might be important in the signal transduction pathway in subfamilies of this receptor family are revealed.
Key issues in the computational simulation of GPCR function: representation of loop domains
- BiologyJ. Comput. Aided Mol. Des.
It is shown that in the case where a given loop from two different GPCRs has approximately the same length and some degree of sequence identity, the fold adopted by the loops can be similar, and in such special cases homology modeling might be used to obtain initial structures of these loops.