Structure and dynamics of an amphiphilic peptide in a lipid bilayer: a molecular dynamics study
TLDR
A molecular dynamics simulation of a simple model membrane system composed of a single amphiphilic helical peptide in a fully hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayer indicated that residues 6 through 15 remain in a stable right-handed alpha-helical conformation, whereas both termini exhibit substantial fluctuations.About:
This article is published in Biophysical Journal.The article was published on 1997-12-01 and is currently open access. It has received 69 citations till now. The article focuses on the topics: Polyproline helix & Peptide plane flipping.read more
Citations
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Hydrophobic mismatch between proteins and lipids in membranes
TL;DR: It is concluded that hydrophobic mismatch can strongly affect protein and lipid organization, but that the precise consequences depend on the individual properties of the proteins and lipids.
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Mesoscopic models of biological membranes
TL;DR: In this article, the authors compare various strategies to coarse-grained simulation of a biological membrane and conclude that the results obtained by the various mesoscopic models are surprisingly consistent. But they do not discuss the effect of transmembrane peptides on the local structure of a membrane and the mechanism of vesicle fusion and fission.
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Protein–lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring (Review)
TL;DR: It is shown for phosphatidylcholine bilayers and for other model membranes that these peptides adapt a transmembrane topology without extensive peptide or lipid adaptations under conditions of hydrophobic matching, but that significant rearrangements can result from hydrophilic mismatch.
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Simulations of Ion Permeation Through a Potassium Channel: Molecular Dynamics of KcsA in a Phospholipid Bilayer
TL;DR: Multiple nanosecond-duration molecular dynamics simulations of a bacterial potassium channel embedded in a phospholipid bilayer reveal motions of ions, water, and protein that may form the molecular basis of channel gating.
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Infectious disease: Connecting innate immunity to biocidal polymers
TL;DR: This review attempts to bridge the research areas of natural host defense peptides (HDPs), a component of the innate immune system, and biocidal cationic polymers, and the arsenal of biophysical techniques available to study their mode of action and interactions with phospholipid membranes.
References
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Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.
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Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction
TL;DR: A backbone-dependent rotamer library for amino acid side-chains is developed and used for constructing protein side-chain conformations from the main-chain co-ordinates and it is evident from the results that a single protein does not adequately test a prediction scheme.
Book
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
TL;DR: In this article, the authors present an analysis of solvent influence on protein dynamics and demonstrate that solvent influences protein dynamics with respect to both Atom and Sidechain Motions and Rigid-Body Motions.
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Langevin dynamics of peptides: The frictional dependence of isomerization rates of N‐acetylalanyl‐N′‐methylamide
TL;DR: The rate constant for the transition between the equatorial and axial conformations of N‐acetylalanyl‐N′‐methylamide has been determined from Langevin dynamics simulations with no explicit solvent, indicating that both collisional energy transfer with solvent and vibrational energy transfer between internal modes are important in the dynamics of barrier crossing for this system.