scholarly journals Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly

Structure ◽  
2008 ◽  
Vol 16 (4) ◽  
pp. 621-630 ◽  
Author(s):  
Kathryn A. Scott ◽  
Peter J. Bond ◽  
Anthony Ivetac ◽  
Alan P. Chetwynd ◽  
Syma Khalid ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Self Assembly ◽  
Md Simulations ◽  
Coarse Grained

Simulation studies of the interactions between membrane proteins and detergents

2005 ◽  
Vol 33 (5) ◽  
pp. 910-912 ◽  
Author(s):  
P.J. Bond ◽  
J. Cuthbertson ◽  
M.S.P. Sansom
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Self Assembly ◽  
Kinetic Mechanism ◽  
Coarse Grained ◽  
Simulation Studies ◽  
High Resolution Data ◽  
Biologically Relevant ◽  
Structure And Dynamics ◽  
Detergent Interactions

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.

scholarly journals Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile

2021 ◽  
Vol 11 (5) ◽  
pp. 2357
Author(s):  
Ruixin Li ◽  
Haorong Chen ◽  
Hyeongwoon Lee ◽  
Jong Hyun Choi
Keyword(s):  
Self Assembly ◽  
Mechanical Energy ◽  
Single Layer ◽  
Md Simulations ◽  
Dna Origami ◽  
Coarse Grained ◽  
Initial Curvature ◽  
Coarse Grained Model ◽  
Reconfigurable Structures ◽  
Computational Platform

DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn, which is slightly different from that of native B-form DNA (~10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.

scholarly journals Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile

2021 ◽  
Author(s):  
Ruixin Li ◽  
Haorong Chen ◽  
Hyeongwoon Lee ◽  
Jong Hyun Choi
Keyword(s):  
Self Assembly ◽  
Mechanical Energy ◽  
Single Layer ◽  
Md Simulations ◽  
Dna Origami ◽  
Coarse Grained ◽  
Initial Curvature ◽  
Coarse Grained Model ◽  
Reconfigurable Structures ◽  
Computational Platform

ABSTRACTDNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn which is slightly different from that of native B-form DNA (10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.

Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations

2012 ◽  
Vol 8 (5) ◽  
pp. 1556-1569 ◽  
Author(s):  
Johan F. Kraft ◽  
Mikkel Vestergaard ◽  
Birgit Schiøtt ◽  
Lea Thøgersen
Keyword(s):  
Self Assembly ◽  
Md Simulations ◽  
The Self ◽  
Atomic Resolution ◽  
Coarse Grained

scholarly journals Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations

2021 ◽  
Author(s):  
T. Bertie Ansell ◽  
Luke Curran ◽  
Michael R Horrell ◽  
Tanadet Pipatpolkai ◽  
Suzanne C Letham ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Specific Interaction ◽  
Protein Structures ◽  
Md Simulations ◽  
Lipid Binding ◽  
Coarse Grained ◽  
Binding Affinities ◽  
Interaction Sites

Specific interactions of lipids with membrane proteins contribute to protein stability and function. Multiple lipid interactions surrounding a membrane protein are often identified in molecular dynamics (MD) simulations and are, increasingly, resolved in cryo-EM densities. Determining the relative importance of specific interaction sites is aided by determination of lipid binding affinities by experimental or simulation methods. Here, we develop a method for determining protein-lipid binding affinities from equilibrium coarse-grained MD simulations using binding saturation curves, designed to mimic experimental protocols. We apply this method to directly obtain affinities for cholesterol binding to multiple sites on a range of membrane proteins and compare our results with free energies obtained from density-based equilibrium methods and with potential of mean force calculations, getting good agreement with respect to the ranking of affinities for different sites. Thus, our binding saturation method provides a robust, high-throughput alternative for determining the relative consequence of individual sites seen in e.g. cryo-EM derived membrane protein structures surrounded by a plethora of ancillary lipid densities.

scholarly journals Aggregation of Lipid A Variants: a Hybrid Particle-Field Model

2019 ◽  
Author(s):  
Antonio De Nicola ◽  
Thereza A. Soares ◽  
Sigbjørn Løland Bore ◽  
G. J. Agur Sevink ◽  
Michele Cascella ◽  
...  
Keyword(s):  
Self Assembly ◽  
Electrostatic Interactions ◽  
Lipid A ◽  
Md Simulations ◽  
Coarse Grained ◽  
Water Mixture ◽  
Particle Field ◽  
Hybrid Particle ◽  
Acyl Chains ◽  
The Stability

<p>Lipid A is one of three components of bacterial lipopolysaccharides (constituting the outer membrane of Gram-negative bacteria) and is recognized to have an important biological role in inflammatory response of the immune system. Its biological activity is modulated by the number of acyl-chains and from the electrostatic interactions with the different counter-ions. In this paper we report a coarse-grained model of poly-acyl Lipid A based on the hybrid particle field molecular dynamics approach (hPF-MD). In particular, we investigate the stability of Lipid A bilayer with two different acyl-chains, hexa- and tetra-. We find a good agreement of the particle distribution along the cross-section of bilayer by comparing the density profiles calculated from hPF-MD simulations with respect to reference all-atom. Moreover, we validate the model simulating the self-assembly of lamellar phase from an initial random distribution of Lipid A/N<sup>2+</sup>molecules in water. Finally, we test the stability of a vesicle composed of hexa-acylated Lipid A in water. The proposed model is able to maintain stable bilayer aggregates and spherical vesicle, and to correctly reproduce the phase behavior of Lipid A/Ca<sup>2+</sup>/Water mixture.</p>

Self-Assembled Morphologies of Diblock Copolymers Confined in Multiwalled Carbon Nanotubes

2013 ◽  
Vol 815 ◽  
pp. 512-515
Author(s):  
Yu Xin Zuo ◽  
Guo Qing Wang ◽  
Ying Yu ◽  
Chun Cheng Zuo ◽  
Yi Rui Wang
Keyword(s):  
Carbon Nanotubes ◽  
Multiwalled Carbon Nanotubes ◽  
Self Assembly ◽  
Diblock Copolymers ◽  
Three Dimensional ◽  
Md Simulations ◽  
Surface Interactions ◽  
Coarse Grained ◽  
Multiwalled Carbon ◽  
Self Assembled

Self-assembly of symmetric diblock copolymers (DCP) confined in multiwalled carbon nanotubes (MWCNTs) is studied using coarse-grained molecular dynamic (MD) simulations. The dependence of the self-assembled morphologies on the strength of the surface interactions is examined systematically. A rich variety of novel morphologies under the three-dimensional confinement have been revealed. The adsorption energy and cohesive energy have been discussed qualitatively and used to account for the appearance of the complex morphological transition.

Self assembly of peptides near or within membranes using coarse grained MD simulations

2009 ◽  
Vol 358 (1-2) ◽  
pp. 161-170 ◽  
Author(s):  
A. Khalfa ◽  
W. Treptow ◽  
B. Maigret ◽  
M. Tarek
Keyword(s):  
Self Assembly ◽  
Md Simulations ◽  
Coarse Grained

scholarly journals Auxetic Two-Dimensional Nanostructures from DNA

2020 ◽  
Author(s):  
Ruixin Li ◽  
Haorong Chen ◽  
Jong Hyun Choi
Keyword(s):  
Self Assembly ◽  
Md Simulations ◽  
Dna Origami ◽  
Coarse Grained ◽  
Two Dimensional ◽  
Materials Chemistry ◽  
Dna Nanostructures ◽  
Unit Cells ◽  
Materials Used ◽  
Architectured Materials

ABSTRACTArchitectured materials exhibit negative Poisson’s ratios and enhanced mechanical properties compared with regular materials. Their auxetic behaviors should emerge from periodic cellular structures regardless of the materials used. The majority of such metamaterials are constructed by top-down approaches and macroscopic with unit cells of microns or larger. On the other extreme, there are molecular-scale auxetics including naturally-occurring crystals which are not designable. There is a gap from few nanometers to microns, which may be filled by bottom-up biomolecular self-assembly. Here we demonstrate two-dimensional auxetic nanostructures using DNA origami. Structural reconfiguration experiments are performed by strand displacement and complemented by mechanical deformation studies using coarse-grained molecular dynamics (MD) simulations. We find that the auxetic properties of DNA nanostructures are mostly defined by geometrical designs, yet materials’ chemistry also plays an important role. From elasticity theory, we introduce a set of design principles for auxetic DNA metamaterials, which should find diverse applications.

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