scholarly journals MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics

2019 ◽  
Vol 47 (W1) ◽  
pp. W456-W461 ◽  
Author(s):  
Mangesh Damre ◽  
Alessandro Marchetto ◽  
Alejandro Giorgetti
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Dynamics ◽  
Conformational Changes ◽  
Coarse Grained ◽  
Computational Power ◽  
Molecular Features ◽  
Molecular Events ◽  
Membrane Protein Dynamics

Abstract Atomistic molecular dynamics simulations of membrane proteins have been shown to be extremely useful for characterizing the molecular features underlying their function, but require high computational power, limiting the understanding of complex events in membrane proteins, e.g. ion channels gating, GPCRs activation. To overcome this issue, it has been shown that coarse-grained approaches, although requiring less computational power, are still capable of correctly describing molecular events underlying big conformational changes in biological systems. Here, we present the Martini coarse-grained membrane protein dynamics (MERMAID), a publicly available web interface that allows the user to prepare and run coarse-grained molecular dynamics (CGMD) simulations and to analyse the trajectories.

scholarly journals Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations

2021 ◽  
Author(s):  
T. Bertie Ansell ◽  
Luke Curran ◽  
Michael R Horrell ◽  
Tanadet Pipatpolkai ◽  
Suzanne C Letham ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Specific Interaction ◽  
Protein Structures ◽  
Md Simulations ◽  
Lipid Binding ◽  
Coarse Grained ◽  
Binding Affinities ◽  
Interaction Sites

Specific interactions of lipids with membrane proteins contribute to protein stability and function. Multiple lipid interactions surrounding a membrane protein are often identified in molecular dynamics (MD) simulations and are, increasingly, resolved in cryo-EM densities. Determining the relative importance of specific interaction sites is aided by determination of lipid binding affinities by experimental or simulation methods. Here, we develop a method for determining protein-lipid binding affinities from equilibrium coarse-grained MD simulations using binding saturation curves, designed to mimic experimental protocols. We apply this method to directly obtain affinities for cholesterol binding to multiple sites on a range of membrane proteins and compare our results with free energies obtained from density-based equilibrium methods and with potential of mean force calculations, getting good agreement with respect to the ranking of affinities for different sites. Thus, our binding saturation method provides a robust, high-throughput alternative for determining the relative consequence of individual sites seen in e.g. cryo-EM derived membrane protein structures surrounded by a plethora of ancillary lipid densities.

scholarly journals Fat SIRAH: Coarse-Grained Phospholipids To Explore Membrane–Protein Dynamics

2019 ◽  
Vol 15 (10) ◽  
pp. 5674-5688 ◽  
Author(s):  
Exequiel E. Barrera ◽  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Membrane Protein ◽  
Protein Dynamics ◽  
Coarse Grained ◽  
Membrane Protein Dynamics

Simulation studies of the interactions between membrane proteins and detergents

2005 ◽  
Vol 33 (5) ◽  
pp. 910-912 ◽  
Author(s):  
P.J. Bond ◽  
J. Cuthbertson ◽  
M.S.P. Sansom
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Self Assembly ◽  
Kinetic Mechanism ◽  
Coarse Grained ◽  
Simulation Studies ◽  
High Resolution Data ◽  
Biologically Relevant ◽  
Structure And Dynamics ◽  
Detergent Interactions

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.

scholarly journals EXPRESS: Single-Molecule Fluorescence Techniques for Membrane Protein Dynamics Analysis

2021 ◽  
pp. 000370282110099
Author(s):  
Ziyu Yang ◽  
Haiqi Xu ◽  
Jiayu Wang ◽  
Wei Chen ◽  
Meiping Zhao
Keyword(s):  
Membrane Protein ◽  
Protein Dynamics ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Correlation Spectroscopy ◽  
Membrane Receptors ◽  
Biological Macromolecules ◽  
Dynamics Analysis ◽  
Single Molecule Fluorescence ◽  
Membrane Protein Dynamics

Fluorescence-based single molecule techniques, mainly including fluorescence correlation spectroscopy (FCS) and single-molecule fluorescence resonance energy transfer (smFRET), are able to analyze the conformational dynamics and diversity of biological macromolecules. They have been applied to analysis of the dynamics of membrane proteins, such as membrane receptors and membrane transport proteins, due to their superior ability in resolving spatio-temporal heterogeneity and the demand of trace amounts of analytes. In this review, we first introduced the basic principle involved in FCS and smFRET. Then we summarized the labelling and immobilization strategies of membrane protein molecules, the confocal-based and TIRF-based instrumental configuration, and the data processing methods. The applications to membrane protein dynamics analysis are described in detail with the focus on how to select suitable fluorophores, labelling sites, experimental setup and analysis methods. In the last part, the remaining challenges to be addressed and further development in this field are also briefly discussed.

Hyperspectral image correlation for monitoring membrane protein dynamics in living cells

2009 ◽  
Author(s):  
Ryan W. Davis ◽  
Bryan Carson ◽  
Howland D. T. Jones ◽  
Michael B. Sinclair
Keyword(s):  
Membrane Protein ◽  
Protein Dynamics ◽  
Hyperspectral Image ◽  
Living Cells ◽  
Image Correlation ◽  
Membrane Protein Dynamics
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