Advertisement

Topics

Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs.

07:00 EST 1st January 2019 | BioPortfolio

Summary of "Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs."

Rhodopsin is a light-driven G protein-coupled receptor mediating signal transduction in eyes. The molecular dynamics (MD) simulations are powerful computational tools to investigate molecular behavior of proteins and internal water molecules which are related to the function of proteins; however, the MD simulations of the rhodopsin require several technical setups for accurate calculations. This chapter discusses practical methods for setting up the MD simulations of the rhodopsin [preparation of initial systems, condition files for MD simulation package GROMACS, and data analysis]. The data analysis includes the root mean square deviation (RMSD) and mapping of accessibility of water molecules.

Affiliation

Journal Details

This article was published in the following journal.

Name: Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Pages: 21-30

Links

DeepDyve research library

PubMed Articles [23559 Associated PubMed Articles listed on BioPortfolio]

Atomistic Study of Dynamic Contact Angles in CO2-Water-Silica System.

The dynamic wetting for the CO2-water-silica system occurring in deep reservoirs is complex because of the interactions among multiple phases. This work aims to quantify the contact angle of CO2-water...

Thermophysical properties of glyceline-water mixtures investigated by molecular modelling.

The effect of water content on the static and dynamic properties of the deep eutectic solvent glyceline is studied using molecular dynamics (MD) simulations. Static properties are additionally calcula...

Assessment of Conformational State Transitions of Class B GPCRs Using Molecular Dynamics.

Class B G protein-coupled receptors (GPCRs) comprise a family of 15 peptide-binding members, which are crucial targets for endocrine, metabolic, and stress-related disorders. While their protein struc...

Multiscale simulations on human Frizzled and Taste2 GPCRs.

Recently, molecular dynamics simulations, from all atom and coarse grained to hybrid methods bridging the two scales, have provided exciting functional insights into class F (Frizzled and Taste2) GPCR...

The Duet of Acetate and Water at the Defects of Metal-organic Frameworks.

Metal-organic frameworks (MOFs) are porous crystalline materials with promising applications in molecular adsorption, separation and catalysis. It has been discovered recently that the existence of st...

Clinical Trials [4530 Associated Clinical Trials listed on BioPortfolio]

Validation Study of Multiple Probe Compounds for Drug Interaction Evaluation

The purpose of this study is to identify and validate a probe cocktail for use in future GSK drug-drug interaction studies. Cytochrome P450 enzymes and transport proteins play important r...

IMPLEMENTATION OF MOLECULAR DIAGNOSTIC PATHWAYS

Most neurological and neurodegenerative diseases have a multifactorial nature. For some of them it is documented a genetic component (sometimes described as Mendelian, other times as a mul...

The Impact of a Modified Probe Tip Design on Patient Perception of Discomfort on Probing and Clinical Parameters Using the Florida Probe® System

Patient perception of pain on periodontal probing using a controlled-force, electronic probe was not significantly affected by the use of a modified (ball-end) probe tip design except for ...

Trial of the Effects of Remote Preconditioning on the Tissue Metabolism During Exercise and Ischemia

Previously, the preconditioning signaling pathways have been studied on molecular level or in animal model. By using MR spectroscopy and imaging in a dynamic human model of preconditioning...

Collection of Samples From HIV-1 Infected Individuals for Evaluation of the Aptima HIV-1 Assay

The objective is to obtain plasma samples from Human Immunodeficiency Virus Type 1 (HIV-1) infected individuals that have viral loads across the dynamic range of the Aptima HIV-1 assay. Th...

Medical and Biotech [MESH] Definitions

The use of devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms.

Non-visual system arrestins that negatively regulate G-PROTEIN-COUPLED RECEPTORS (GPCRs) and may also function independently of GPCR signaling. They bind and recruit many different signaling factors, including MITOGEN-ACTIVATED PROTEIN KINASES; SRC-FAMILY-KINASES; and FILAMIN to GPCRs and may recognize different phosphorylation states of the receptors to determine the specificity of the cellular response to signaling.

A molecular probe technique that utilizes branched DNA (bDNA) as a means to amplify the hybridization signal. One end of the bDNA molecule is designed to bind a specific target, while the other end of the bDNA molecule contains many branches of DNA that are designed to bind a probe used for signal detection.

A type of scanning probe microscopy in which a probe systematically rides across the surface of a sample being scanned in a raster pattern. The vertical position is recorded as a spring attached to the probe rises and falls in response to peaks and valleys on the surface. These deflections produce a topographic map of the sample.

Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)

Advertisement
Quick Search
Advertisement
Advertisement

 


DeepDyve research library

Relevant Topics

Nutrition
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...

Ophthalmology
Ophthalmology is the branch of medicine that is devoted to the study and treatment of eye diseases. As well as mild visual defects correctable by lenses, ophthalmology is concerned with glaucoma, uveitis and other serious conditions affecting the eye, ...


Searches Linking to this Article