scholarly journals Exploring GPCR–Lipid Interactions by Molecular Dynamics Simulations: Excitements, Challenges, and the Way Forward

2018 ◽  
Vol 122 (22) ◽  
pp. 5727-5737 ◽  
Author(s):  
Durba Sengupta ◽  
Xavier Prasanna ◽  
Madhura Mohole ◽  
Amitabha Chattopadhyay
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Interactions ◽  
Dynamics Simulations ◽  
The Way

scholarly journals Molecular Dynamics Simulations of G-Protein Coupled Receptor Lipid Interactions

2017 ◽  
Vol 112 (3) ◽  
pp. 386a
Author(s):  
George Hedger ◽  
Hsin-Yung Yen ◽  
Idlir Liko ◽  
Carol V. Robinson ◽  
Christian Siebold ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
G Protein ◽  
G Protein Coupled Receptor ◽  
Lipid Interactions ◽  
Dynamics Simulations ◽  
G Protein Coupled

scholarly journals Interactions of the designed antimicrobial peptide MB21 and truncated dermaseptin S3 with lipid bilayers: molecular-dynamics simulations

2003 ◽  
Vol 370 (1) ◽  
pp. 233-243 ◽  
Author(s):  
Craig M. SHEPHERD ◽  
Hans J. VOGEL ◽  
D. Peter TIELEMAN
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptide ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Helical Conformation ◽  
Constraint Forces ◽  
Surface Binding ◽  
Lipid Interactions ◽  
Area Per Lipid ◽  
Dynamics Simulations

Molecular-dynamics simulations covering 30ns of both a natural and a synthetic antimicrobial peptide in the presence of a zwitterionic lipid bilayer were performed. In both simulations, copies of the peptides were placed in an α-helical conformation on either side of the bilayer about 10Å (1Å = 0.1nm) from the interface, with either the hydrophobic or the positively charged face of the helix directed toward the bilayer surface. The degree of peptide—lipid interaction was dependent on the starting configuration: surface binding and subsequent penetration of the bilayer was observed for the hydrophobically oriented peptides, while the charge-oriented peptides demonstrated at most partial surface binding. Aromatic residues near the N-termini of the peptides appear to play an important role in driving peptide—lipid interactions. A correlation between the extent of peptide—lipid interactions and helical stability was observed in the simulations. Insertion of the peptides into the bilayer caused a dramatic increase in the lateral area per lipid and decrease in the bilayer thickness, resulting in substantial disordering of the lipid chains. Results from the simulations are consistent with early stages of proposed mechanisms for the lytic activity of antimicrobial peptides. In addition to these ‘free’ simulations, 25ns simulations were carried out with the peptides constrained at three different distances relative to the bilayer interface. The constraint forces are in agreement with the extent of peptide—bilayer insertion observed in the free simulations.

scholarly journals PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations

2021 ◽  
Author(s):  
Wanling Song ◽  
Robin A. Corey ◽  
Bertie Ansell ◽  
Keith Cassidy ◽  
Michael Horrell ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Molecular Dynamics Simulations ◽  
Binding Sites ◽  
Objective Assessment ◽  
Source Distribution ◽  
Lipid Interactions ◽  
Dynamics Simulations ◽  
Python Package

Lipids play important modulatory and structural roles for membrane proteins. Molecular dynamics simulations are frequently used to provide insights into the nature of these protein-lipid interactions. Systematic comparative analysis requires tools that provide algorithms for objective assessment of such interactions. We introduce PyLipID, a python package for the identification and characterization of specific lipid interactions and binding sites on membrane proteins from molecular dynamics simulations. PyLipID uses a community analysis approach for binding site detection, calculating lipid residence times for both the individual protein residues and the detected binding sites. To assist structural analysis, PyLipID produces representative bound lipid poses from simulation data, using a density-based scoring function. To estimate residue contacts robustly, PyLipID uses a dual-cutoff scheme to differentiate between lipid conformational rearrangements whilst bound from full dissociation events. In addition to the characterization of protein-lipid interactions, PyLipID is applicable to analysis of the interactions of membrane proteins with other ligands. By combining automated analysis, efficient algorithms, and open-source distribution, PyLipID facilitates the systematic analysis of lipid interactions from large simulation datasets of multiple species of membrane proteins.

scholarly journals Selectivity of pyoverdine recognition by the FpvA receptor of Pseudomonas aeruginosa from molecular dynamics simulations

2015 ◽  
Vol 17 (27) ◽  
pp. 18022-18034 ◽  
Author(s):  
Benjamin Bouvier ◽  
Christine Cézard ◽  
Pascal Sonnet
Keyword(s):  
Molecular Dynamics ◽  
Pseudomonas Aeruginosa ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Novel Antibiotics ◽  
The Way

Understanding the patterns of pyoverdine recognition by the bacterial FpvA receptor paves the way for the design of novel antibiotics.

The Viscous Coefficient Comparison between 2-D and 3-D Fluid Models in Molecular Dynamics Simulations

2011 ◽  
Vol 415-417 ◽  
pp. 62-65
Author(s):  
Dong Yu Xia ◽  
Xi Shan Sun ◽  
Mei Fen Wang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Periodic Boundary ◽  
Dynamics Simulation ◽  
Fluid Models ◽  
Dynamics Simulations ◽  
D Model ◽  
The Way

Abstract: In this paper，2-D and 3-D fluid models are calculated using equilibrium molecular dynamics simulation, the viscous coefficient and pressure are obtained under periodic boundary. By comparing and analyzing the differences of viscous coefficient and pressure curves between 2-D and 3-D fluid models, the way for how to use 2-D model to get the accurate viscous coefficient is found, the feasibility of 2-D model is discussed.

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