Organization and Dynamics of Receptor Proteins in a Plasma Membrane

Koldsø, Heidi; Sansom, Mark S. P.

doi:10.1021/jacs.5b08048

Cited by 95 publications

(163 citation statements)

References 74 publications

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“…Their results showed that the extent of peptide solvation within bicelles and nanodiscs is strongly dependent upon location of the peptide within the membrane mimetic environment and that dynamics of membrane mimetics can be rather different when proteins are embedded compared to the protein-free environment. This observation is in agreement with other molecular dynamics simulations studies, which have also revealed the complex interplay between proteins and lipids 52,53 .…”

Section: Opportunity For Use In Molecular Simulationsupporting

confidence: 93%

Encapsulated membrane proteins: A simplified system for molecular simulation

Lee¹,

Khalid²,

Pollock³

et al. 2016

Biochimica et Biophysica Acta (BBA) - Biomembranes

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A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT 2Over the past 50 years there has been considerable progress in our understanding of biomolecular interactions at an atomic level. This in turn has allowed molecular simulation methods employing full atomistic modeling at ever larger scales to develop. However, some challenging areas still remain where there is either a lack of atomic resolution structures or where the simulation system is inherentlycomplex.An area where both challenges are present is that of membranes containing membrane proteins. In this review we analyse a new practical approach to membrane protein study that offers a potential new route to high resolution structures and the possibility to simplify simulations.These new approaches collectively recognise that preservation of the interaction between the membrane protein and the lipid bilayer is often essential to maintain structure and function. The new methods preserve these interactions by producing nano-scale disc shaped particles that include bilayer and the chosen protein. Currently two approaches lead in this area: the MSP system that relies on peptides to stabilise the discs, and SMALPs where an amphipathic styrene maleic acid copolymer is used. Both methods greatly enable protein production and hence have the potential to accelerate atomic resolution structure determination as well as providing a simplified format for simulations of membrane protein dynamics.

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Section: Opportunity For Use In Molecular Simulationsupporting

confidence: 93%

Encapsulated membrane proteins: A simplified system for molecular simulation

Lee¹,

Khalid²,

Pollock³

et al. 2016

Biochimica et Biophysica Acta (BBA) - Biomembranes

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show abstract

“…By its very nature CG models may not be suited to the study of ligand binding in highly specific pockets where packing of ligand and protein is tight. However, as described above, binding of lipid molecules to membrane protein surfaces is generally less structurally specific than binding at a typical ligand binding site [14], and the CG approach has been used to study lipid-protein interactions at annular (boundary) lipid binding sites for a wide range of lipid molecules, including cholesterol [11,[25][26][27][28][29][30]. Hydrogen bonds are not modelled explicitly in most force fields used in molecular dynamic simulations, and in the Martini force fields used in CG simulations are present implicitly in the non-bonded interaction potentials between the beads [25].…”

mentioning

confidence: 99%

G protein coupled receptor interactions with cholesterol deep in the membrane

Genheden

Essex

Lee

2017

Biochimica et Biophysica Acta (BBA) - Biomembranes

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“…Key examples are multi-component lipid mixtures that model the plasma membrane (Flinner and Schleiff, 2015;Ingólfsson et al, 2014b;Koldsø and Sansom, 2015;Koldsø et al, 2014;van Eerden et al, 2015) and the dynamic model of an entire virion membrane (Reddy et al, 2015).…”

Section: Coarse-grain Resolutionmentioning

confidence: 99%

Computational ‘microscopy’ of cellular membranes

Ingólfsson

Arnarez²,

Periole³

et al. 2016

Journal of Cell Science

136

120

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Computational 'microscopy' refers to the use of computational resources to simulate the dynamics of a molecular system. Tuned to cell membranes, this computational 'microscopy' technique is able to capture the interplay between lipids and proteins at a spatiotemporal resolution that is unmatched by other methods. Recent advances allow us to zoom out from individual atoms and molecules to supramolecular complexes and subcellular compartments that contain tens of millions of particles, and to capture the complexity of the crowded environment of real cell membranes. This Commentary gives an overview of the main concepts of computational 'microscopy' and describes the state-of-the-art methods used to model cell membrane processes. We illustrate the power of computational modelling approaches by providing a few in-depth examples of largescale simulations that move up from molecular descriptions into the subcellular arena. We end with an outlook towards modelling a complete cell in silico.

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Organization and Dynamics of Receptor Proteins in a Plasma Membrane

Cited by 95 publications

References 74 publications

Encapsulated membrane proteins: A simplified system for molecular simulation

Encapsulated membrane proteins: A simplified system for molecular simulation

G protein coupled receptor interactions with cholesterol deep in the membrane

Computational ‘microscopy’ of cellular membranes

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