scholarly journals Coarse-Grained Model of the SNARE Complex Shows that Quick Zippering Requires Partial Assembly

2018 ◽  
Author(s):  
N. Fortoul ◽  
M. Bykhovskaia ◽  
A. Jagota
Keyword(s):  
Single Molecule ◽  
Time Scale ◽  
Membrane Vesicles ◽  
Vesicle Fusion ◽  
Separation Distance ◽  
Snare Complex ◽  
Coarse Grained ◽  
Complex Needs ◽  
Coarse Grained Model ◽  
Dynamics Simulations

ABSTRACTNeuronal transmitters are released from nerve terminals via the fusion of synaptic vesicles with the presynaptic membrane. Vesicles become attached to the membrane via the SNARE complex. The SNARE complex comprises the vesicle associate protein Synaptobrevin (Syb), the membrane associated protein syntaxin (Syx), and the cytosolic protein SNAP25, which together form a four-helical bundle. The full assembly of Syb onto the core SNARE bundle promotes vesicle fusion. We investigated SNARE assembly using a coarse-grained model of the SNARE complex. The model retains chemical specificity, and was calibrated using single molecule experiments and all-atom molecular dynamics simulations. Steered force-control simulations of SNARE unzippering by peeling off Syb were used to set up initial disassembled states of the SNARE complex. From these states, the assembly process was simulated. We found that if Syb is in helical form, then the SNARE complex assembles rapidly, on a sub-microsecond time-scale. We found that assembly times grow exponentially with separation distance between Syb and Syx C-termni. The formation of helical turns is likely to substantially decelerate the assembly, consistent with single molecule force experiments that show SNARE assembly duration on the time-scale of hundreds of ms. Since synaptic vesicle fusion occurs at a sub-millisecond time-scale, our results indicate that for biologically relevant rapid assembly the SNARE complex needs to be partially zippered and its constituent helices brought into proximity, possibly by means of molecular chaperones.

A coil-to-globule transition capable coarse-grained model for poly(N-isopropylacrylamide)

2020 ◽  
Vol 22 (32) ◽  
pp. 17913-17921
Author(s):  
H. A. Pérez-Ramírez ◽  
G. Odriozola
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Isopropyl Acrylamide ◽  
Dynamics Simulations

We present a model for mesoscopic molecular dynamics simulations of poly(N-isopropyl-acrylamide) (pNIPAM).

A Finite Element-Based Coarse-Grained Model for Cell–Nanomaterial Interactions by Combining Absolute Nodal Coordinate Formula and Brownian Dynamics

2020 ◽  
Vol 88 (4) ◽  
Author(s):  
Teng Ma ◽  
Yuanpeng Liu ◽  
Guochang Lin ◽  
Changguo Wang ◽  
Huifeng Tan
Keyword(s):  
Finite Element ◽  
Brownian Dynamics ◽  
Lipid Membrane ◽  
Contact Region ◽  
Detection Algorithm ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Absolute Nodal Coordinate ◽  
Coarse Grained Model ◽  
Dynamics Simulations

Abstract A fundamental understanding of the interactions between one-dimensional nanomaterials and the cell membrane is of great importance for assessing the hazardous effects of viruses and improving the performance of drug delivery. Here, we propose a finite element-based coarse-grained model to describe the cell entry of nanomaterials based on an absolute nodal coordinate formula and Brownian dynamics. The interactions between nanoparticles and lipid membrane are described by the Lennard–Jones potential, and a contact detection algorithm is used to determine the contact region. Compared with the theoretical and published experimental results, the correctness of the model has been verified. We take two examples to test the robustness of the model: the endocytosis of nanorods grafted with polymer chains and simultaneous entry of multiple nanorods into a lipid membrane. It shows that the model can not only capture the effect of ligand–receptor binding on the penetration but also accurately characterize the cooperative or separate entry of multiple nanorods. This coarse-grained model is computationally highly efficient and will be powerful in combination with molecular dynamics simulations to provide an understanding of cell–nanomaterial interactions.

scholarly journals Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Astrid F. Brandner ◽  
Stepan Timr ◽  
Simone Melchionna ◽  
Philippe Derreumaux ◽  
Marc Baaden ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Lattice Boltzmann ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Mesoscopic Scale ◽  
Coarse Grained Model ◽  
Dynamics Simulations ◽  
Cellular Compartments ◽  
Biological Entities

Abstract In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. After validating the implementation of the model, we explored several systems where the action of a perturbing fluid plays an important role. Namely, we investigated the role of an external shear flow on the dynamics of a vesicle, the dynamics of substrate release under shear, and inquired the dynamics of proteins and substrates confined inside the core of a vesicle. Our methodology enables future exploration of a large variety of biological entities and processes involving lipid systems at the mesoscopic scale where hydrodynamics plays an essential role, e.g. by modulating the migration of proteins in the proximity of membranes, the dynamics of vesicle-based drug delivery systems, or, more generally, the behaviour of proteins in cellular compartments.

scholarly journals Coarse-Grained Model of the Snare Complex Determines the Number of Snares Required for Docking

2015 ◽  
Vol 108 (2) ◽  
pp. 154a ◽  
Author(s):  
Nicole Fortoul ◽  
Pankaj Singh ◽  
Chung-Yuen Hui ◽  
Maria Bykhovskaia ◽  
Anand Jagota
Keyword(s):  
Snare Complex ◽  
Coarse Grained ◽  
Coarse Grained Model
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