Modeling lipid-protein interactions for coarse-grained lipid and Cα protein models

2021 ◽  
Author(s):  
Diego Renato Ugarte La Torre ◽  
Shoji Takada
Keyword(s):  
Protein Interactions ◽  
Coarse Grained ◽  
Lipid Protein Interactions ◽  
Protein Models

scholarly journals Lipid-mediated Association of the Slg1 Transmembrane Domains in Yeast Plasma Membranes

2021 ◽  
Author(s):  
Azadeh Alavizargar ◽  
Annegret Eltig ◽  
Roland Wedlich Soeldner ◽  
Andreas Heuer
Keyword(s):  
Plasma Membrane ◽  
Protein Interactions ◽  
Plasma Membranes ◽  
Acyl Chain ◽  
Md Simulations ◽  
Receptor Activation ◽  
Transmembrane Domains ◽  
Coarse Grained ◽  
Self Association ◽  
Lipid Protein Interactions

Clustering of transmembrane proteins underlies a multitude of fundamental biological processes at the plasma membrane such as receptor activation, lateral domain formation and mechanotransduction. The self-association of the respective transmembrane domains (TMD) has also been suggested to be responsible for the micron-scaled patterns seen for integral membrane proteins in the budding yeast plasma membrane (PM). However, the underlying interplay between local lipid composition and TMD identity is still not mechanistically understood. In this work we have used coarse-grained molecular dynamics (MD) simulations as well as microscopy experiments (TIRFM) to analyze the behavior of a representative helical yeast TMD (Slg1) within different lipid environments. Via the simulations we evaluated the effect of acyl chain saturation and the presence of anionic lipids head groups on the association of TMDs via simulations. Our simulations revealed that weak lipid-protein interactions significantly affect the configuration of TMD dimers and the free energy of association. Increased amounts of unsaturated phospholipids strongly reduced helix-helix interaction and the presence of phosphatidylserine (PS) lipids only slightly affected the dimer. Experimentally, the network factor, characterizing the association strength on a mesoscopic level, was measured in the presence and absence of PS lipids. Consistently with the simulations, no significant effect was observed. We also found that formation of TMD dimers in turn increased the order parameter of the surrounding lipids and induced long-range perturbations in lipid organization, shedding new light on the lipid-mediated dimerization of TMDs in complex lipid mixtures.

scholarly journals CG2AT2: An Enhanced Fragment-based approach for Serial Multi-scale Molecular Dynamics simulations

2021 ◽  
Author(s):  
Owen N. Vickery ◽  
Phillip J. Stansfeld
Keyword(s):  
Molecular Dynamics ◽  
Protein Interactions ◽  
Integral Membrane Protein ◽  
Phospholipid Bilayer ◽  
Coarse Grained ◽  
Macromolecular Complex ◽  
Macromolecular Complexes ◽  
Lipid Dynamics ◽  
Lipid Protein Interactions ◽  
Dynamics Simulations

AbstractCoarse-grained molecular dynamics provides a means for simulating the assembly and interactions of macromolecular complexes at a reduced level of representation, thereby allowing both longer timescale and larger sized simulations. Here, we describe an enhanced fragment-based protocol for converting macromolecular complexes from coarse-grained to atomistic resolution, for further refinement and analysis. While the focus is upon systems that comprise an integral membrane protein embedded in a phospholipid bilayer, the technique is also suitable for e.g. membrane-anchored and soluble protein/nucleotide complexes. Overall, this provides a method for generating an accurate and well equilibrated atomic-level description of a macromolecular complex. The approach is evaluated using a diverse test set of eleven system configurations of vary size and complexity. Simulations are assessed in terms of protein stereochemistry, conformational drift, lipid/protein interactions, and lipid dynamics.

Lipid-protein Interactions in Crystals of Plant Light-harvesting Complex

1993 ◽  
Vol 234 (2) ◽  
pp. 347-356 ◽  
Author(s):  
Stephan Nußberger ◽  
Karoline Dörr ◽  
Da Neng Wang ◽  
Werner Kühlbrandt
Keyword(s):  
Protein Interactions ◽  
Light Harvesting ◽  
Light Harvesting Complex ◽  
Lipid Protein Interactions
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