Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics

Wang, Yi; Markwick, Phineus R. L.; Oliveira, César Augusto F. de; McCammon, J. Andrew

doi:10.1021/ct200430c

Cited by 64 publications

(61 citation statements)

References 57 publications

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“…Wang et al examined acceleration of lateral diffusion and mixing of two lipid components by using the aMD method [85]. In their method, the dihedral potential was boosted, which enhances trans-gauche isomerization of lipid acyl chains during the simulation.…”

Section: Recent Membrane and Membrane Protein Simulations Using Enmentioning

confidence: 99%

“…To illustrate the accuracy and efficiency of different molecular models and enhanced sampling algorithms, we review recent simulations of glycophorin A (GpA) [72-75], phospholamban (PLN) [76-80], amyloid precursor protein (APP) [81-84], and mixed lipid bilayers [85-87]. In the simulations of GpA, PLN, and APP, REMD and REUS using implicit membrane models were mostly used to determine their conformational ensembles in membranes.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

Mori

Miyashita²,

et al. 2016

Biochimica et Biophysica Acta (BBA) - Biomembranes

128

108

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This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov.

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Section: Recent Membrane and Membrane Protein Simulations Using Enmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

Mori

Miyashita²,

et al. 2016

Biochimica et Biophysica Acta (BBA) - Biomembranes

128

108

View full text Add to dashboard Cite

show abstract

“…The same group also presented the first application of the accelerated molecular dynamics (aMD) method to lipid membranes. It was found that the aMD simulations produce 2-3 fold speedups in lipid lateral diffusion versus those in conventional AAMD simulations 153,154 . However, neither the above AAMD simulations have produced a complete phase separation from a randomly mixed lipid (and cholesterol) mixtures.…”

Section: Computational Studies Of Cross-layer Couplingmentioning

confidence: 99%

Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes

Nickels

Smith

Cheng

2015

Chemistry and Physics of Lipids

108

115

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Understanding of cell membrane organization has evolved significantly from the classic fluid mosaic model. It is now recognized that biological membranes are highly organized structures, with differences in lipid compositions between inner and outer leaflets and in lateral structures within the bilayer plane, known as lipid rafts. These organizing principles are important for protein localization and function as well as cellular signaling. However, the mechanisms and biophysical basis of lipid raft formation, structure, dynamics and function are not clearly understood. One key question, which we focus on in this review, is how lateral organization and leaflet compositional asymmetry are coupled. Detailed information elucidating this question has been sparse because of the small size and transient nature of rafts and the experimental challenges in constructing asymmetric bilayers. Resolving this mystery will require advances in both experimentation and modeling. We discuss here the preparation of model systems along with experimental and computational approaches that have been applied in efforts to address this key question in membrane biology. We seek to place recent and future advances in experimental and computational techniques in context, providing insight into in-plane and transverse organization of biological membranes.

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“…For example, aMD simulations provide significant speed-up of the peptide conformational transitions[56, 99, 100], lipid diffusion and mixing[101], conformational transitions in proteins[89, 102–105], protein folding[106, 107] and protein-ligand binding[108]. Notably, hundreds-of-nanosecond aMD simulations are to capture millisecond-timescale events in both globular and membrane proteins[109–112].…”

Section: Unconstrained Enhanced Sampling Methodsmentioning

confidence: 99%

Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

Miao

McCammon

2016

Molecular Simulation

Self Cite

154

128

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Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.

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Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics

Cited by 64 publications

References 57 publications

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes

Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

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