scholarly journals Self-assembled Structure of Amphiphiles by Coarse-grained Molecular Model

2010 ◽  
Vol 50 (5) ◽  
pp. 232-235
Author(s):  
Wataru SHINODA
Keyword(s):  
Molecular Model ◽  
Coarse Grained ◽  
Self Assembled

scholarly journals FOLDING ELASTIC TRANSMEMBRANE HELICES TO FIT IN A LOW-RESOLUTION IMAGE BY ELECTRON MICROSCOPY

2011 ◽  
Vol 09 (supp01) ◽  
pp. 37-50 ◽  
Author(s):  
YUTAKA UENO ◽  
KAZUNORI KAWASAKI ◽  
OSAMU SAITO ◽  
MASAFUMI ARAI ◽  
MAKIKO SUWA
Keyword(s):  
Membrane Proteins ◽  
Structure Prediction ◽  
Molecular Model ◽  
Imaging Techniques ◽  
Transmembrane Helix ◽  
Prediction Method ◽  
Molecular Shape ◽  
Coarse Grained ◽  
Transmembrane Helices ◽  
Low Resolution

Structure prediction of membrane proteins could be constrained and thereby improved by introducing data of the observed molecular shape. We studied a coarse-grained molecular model that relied on residue-based dummy atoms to fold the transmembrane helices of a protein in the observed molecular shape. Based on the inter-residue potential, the α-helices were folded to contact each other in a simulated annealing protocol to search optimized conformation. Fitting the model into a three-dimensional volume was tested for proteins with known structures and resulted in a fairly reasonable arrangement of helices. In addition, the constraint to the packing transmembrane helix with the two-dimensional region was tested and found to work as a very similar folding guide. The obtained models nicely represented α-helices with the desired slight bend. Our structure prediction method for membrane proteins well demonstrated reasonable folding results using a low-resolution structural constraint introduced from recent cell-surface imaging techniques.

scholarly journals Formation of adhesion domains in stressed and confined membranes

Soft Matter ◽  
2015 ◽  
Vol 11 (19) ◽  
pp. 3780-3785 ◽  
Author(s):  
Nadiv Dharan ◽  
Oded Farago
Keyword(s):  
Surface Tension ◽  
Lipid Bilayers ◽  
Computer Simulations ◽  
Molecular Model ◽  
Coarse Grained ◽  
Supported Lipid Bilayers

We use computer simulations of a coarse-grained molecular model of supported lipid bilayers to study the formation of adhesion domains in confined membranes, and in membranes subjected to a non-vanishing surface tension. When the membrane is subjected to compression, the condensation of the adhesion domains triggers membrane buckling.

scholarly journals Modelling fibrillogenesis of collagen-mimetic molecules

2020 ◽  
Author(s):  
A. E. Hafner ◽  
N. G. Gyori ◽  
C. A. Bench ◽  
L. K. Davis ◽  
A. Šarić
Keyword(s):  
Extracellular Matrix ◽  
Electrostatic Interactions ◽  
Collagen Type ◽  
Collagen Type I ◽  
Coarse Grained ◽  
Cell Phenotype ◽  
Type I ◽  
Collagen Scaffolds ◽  
Crucial Component ◽  
Self Assembled

One of the most robust examples of self-assembly in living organisms is the formation of collagen architectures. Collagen type I molecules are a crucial component of the extracellular-matrix where they self-assemble into fibrils of well defined striped patterns. This striped fibrilar pattern is preserved across the animal kingdom and is important for the determination of cell phenotype, cell adhesion, and tissue regulation and signalling. The understanding of the physical processes that determine such a robust morphology of self-assembled collagen fibrils is currently almost completely missing. Here we develop a minimal coarse-grained computational model to identify the physical principles of the assembly of collagen-mimetic molecules. We find that screened electrostatic interactions can drive the formation of collagen-like filaments of well-defined striped morphologies. The fibril pattern is determined solely by the distribution of charges on the molecule and is robust to the changes in protein concentration, monomer rigidity, and environmental conditions. We show that the fibril pattern cannot be easily predicted from the interactions between two monomers, but is an emergent result of multi-body interactions. Our results can help address collagen remodelling in diseases and ageing, and guide the design of collagen scaffolds for biotechnological applications.Statement of SignificanceCollagen type I protein is the most abundant protein in mammals. It is a crucial component of the extracellular-matrix where it robustly self-assembles into fibrils of specific striped architectures that are crucial for the correct collagen function. The molecular features that determine such robust fibril architectures are currently not well understood. Here we develop a minimal coarse-grained model to connect the design of collagen-like molecules to the architecture of the resulting self-assembled fibrils. We find that the pattern of charged residues on the surface of molecules can drive the formation of collagen-like fibrils and fully control their architectures. Our findings can help understand changes in collagen architectures observed in diseases and guide the design of synthetic collagen scaffolds.

scholarly journals Length of Mucin-Like Domains Enhance Cell-Ebola Virus Adhesion by Increasing Binding Probability

2020 ◽  
Author(s):  
X. Cui ◽  
N. Lapinski ◽  
X. Zhang ◽  
A. Jagota
Keyword(s):  
Ebola Virus ◽  
Molecular Model ◽  
Persistence Length ◽  
Experimental Studies ◽  
Coarse Grained ◽  
Physiological Processes ◽  
Initial Adhesion ◽  
Binding Probability ◽  
A Cell ◽  
Coated Surface

AbstractThe Ebola virus (EBOV) hijacks normal physiological processes by apoptotic mimicry in order to be taken up by the cell it infects. The initial adhesion of the virus to the cell is based on the interaction between T-cell immunoglobulin and mucin domain protein, TIM, on the cell-surface and phosphatidylserine (PS) on the viral outer surface. Therefore, it is important to understand the interaction between EBOV/PS and TIM, with selective blocking of the interaction as a potential therapy. Recent experimental studies have shown that for TIM-dependent EBOV entry, a Mucin-like Domain (MLD) with a length of at least 120 amino acids is required, possibly due to the increase of area of the PS-coated surface sampled. We examine this hypothesis by modeling the process of TIM-PS adhesion using a coarse-grained molecular model. We find that the strength of bound PS−TIM pairs is essentially independent of TIM length. TIMs with longer MLDs have higher average binding strengths because of an increase in the probability of binding between EBOV and TIM proteins. Similarly, we find that for larger persistence length (less flexible) the average binding force decreases, again because of a reduction in the probability of binding.Statement of SignificanceThis work studies the mechanism of TIM-dependent adhesion of the Ebola virus to a cell. Through coarse grained modeling we show that longer TIM stalks adhere more easily as they can sample a larger area, thus offering a mechanistic interpretation of an experimental finding. Better mechanistic understanding can lead to therapeutic ideas for blocking adhesion.

scholarly journals A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion

2020 ◽  
Author(s):  
Alvin Yu ◽  
Alexander J. Pak ◽  
Peng He ◽  
Viviana Monje-Galvan ◽  
Lorenzo Casalino ◽  
...  
Keyword(s):  
Large Scale ◽  
Molecular Model ◽  
Structural Data ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Current Status ◽  
Multiscale Approach ◽  
X Ray Crystallography ◽  
Coarse Grained Model ◽  
Viral Particles

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations, however, are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and on-going development of a largely “bottom-up” coarse-grained (CG) model of the SARS-CoV-2 virion. Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data becomes publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.Significance StatementThis study reports the construction of a molecular model for the SARS-CoV-2 virion and details our multiscale approach towards model refinement. The resulting model and methods can be applied to and enable the simulation of SARS-CoV-2 virions.

Self-assembly of spheroidal triblock Janus nanoparticle solutions in nanotubes

2019 ◽  
Vol 4 (1) ◽  
pp. 122-132 ◽  
Author(s):  
Yusei Kobayashi ◽  
Takuya Inokuchi ◽  
Atushi Nishimoto ◽  
Noriyoshi Arai
Keyword(s):  
Phase Diagrams ◽  
Self Assembly ◽  
Molecular Simulations ◽  
Coarse Grained ◽  
Janus Nanoparticles ◽  
Self Assembled

We have performed coarse-grained molecular simulations to investigate the morphologies and phase diagrams of self-assembled spheroidal triblock Janus nanoparticles (JNPs) confined in nanotubes.

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