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

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 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

scholarly journals Membrane protein dynamics in different environments: simulation study of the outer membrane protein X in a lipid bilayer and in a micelle

2010 ◽  
Vol 40 (1) ◽  
pp. 39-58 ◽  
Author(s):  
Alexandra Choutko ◽  
Alice Glättli ◽  
César Fernández ◽  
Christian Hilty ◽  
Kurt Wüthrich ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Outer Membrane ◽  
Protein Dynamics ◽  
Lipid Bilayer ◽  
Simulation Study ◽  
Outer Membrane Protein ◽  
Protein X ◽  
Membrane Protein Dynamics

Exploring membrane protein dynamics by multicolor single quantum dot imaging using wide field, TIRF, and hyperspectral microscopy

2007 ◽  
Author(s):  
Diane S. Lidke ◽  
Nicholas L. Andrews ◽  
Janet R. Pfeiffer ◽  
Howland D.T. Jones ◽  
Michael B. Sinclair ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Quantum Dot ◽  
Protein Dynamics ◽  
Wide Field ◽  
Single Quantum ◽  
Single Quantum Dot ◽  
Membrane Protein Dynamics
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