scholarly journals An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guy G. Butcher ◽  
William S. Harwin ◽  
Chris I. Jones
Keyword(s):  
Molecular Dynamics ◽  
Alpha Helix ◽  
Interaction Force ◽  
Coiled Coils ◽  
Coarse Grained ◽  
Simulation Framework ◽  
Force Estimation ◽  
Model And Simulation ◽  
Target Force ◽  
Dynamics Simulations

AbstractThe alpha-helix coiled-coils within talin’s rod domain have mechanical and signalling functions through their unfolding and refolding dynamics. A better understanding of talin unfolding events and the forces that are involved should allow better prediction of talin signalling. To overcome the current limitations of force measuring in molecular dynamics simulations, a new simulation framework was developed which operated directly within the force domain. Along with a corresponding alpha-helix modelling method, the simulation framework was developed drawing on robotic kinematics to specifically target force interactions. Coordinate frames were used efficiently to compartmentalise the simulation structures and static analysis was applied to determine the propagation of forces and torques through the protein structure. The results of the electrostatic approximation using Coulomb’s law shows a simulated force interaction within the physiological relevant range of 5–40 pN for the rod sub-domains of talin. This covers the range of forces talin operates in and is 2–3 orders of magnitude closer to experimentally measured values than the compared all-atom and coarse-grained molecular dynamics. This targeted, force-based simulation is, therefore, able to produce more realistic forces values than previous simulation methods.

Multibody Molecular Dynamics I: Theoretical Development

2007 ◽  
Author(s):  
Rudranarayan M. Mukherjee ◽  
Kurt S. Anderson
Keyword(s):  
Molecular Dynamics ◽  
Multibody Dynamics ◽  
Temporal Integration ◽  
Interaction Force ◽  
Theoretical Development ◽  
Coarse Grained ◽  
Unified Framework ◽  
Multi Scale ◽  
Integration Schemes ◽  
Dynamics Simulations

This is the first paper in a series of two papers on using multibody dynamics algorithms and methods for coarse-grained molecular dynamics simulations. This paper presents the underlying framework for multi-scale modelling of biomolecules and polymers. In this framework, the system to be simulated is sub-structured into a hierarchy of multi-resolution models that are simulated using efficient multibody dynamics algorithms. The algorithms work in a unified framework, enabling efficient multi-scale (or multi-resolution) simulations. A discussion of the hierarchy of models with different resolutions along with the salient features of the appropriate multibody dynamics algorithms used for simulating them is presented. The unified scheme and the qualitative advantages of the method are discussed. Important implementation details such as boundary conditions, temporal integration schemes, interaction force field calculations and solvent models are also presented. In the next paper applications and results are discussed.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

scholarly journals Variation of Interaction Zone Size For The Target Design of 2D Supramolecular Networks

2021 ◽  
Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Zone Size ◽  
Interaction Zone ◽  
Supramolecular Networks ◽  
Dynamics Simulations ◽  
Target Design

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...

Adsorption-induced co-assembly of hairy and isotropic particles

2020 ◽  
Vol 22 (16) ◽  
pp. 8757-8767
Author(s):  
Tomasz Staszewski ◽  
Małgorzata Borówko
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

We use coarse-grained molecular dynamics simulations to study the behavior of polymer-tethered particles immersed in fluids of isotropic particles.

scholarly journals Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

2021 ◽  
Author(s):  
Hiroki Koide ◽  
Noriyuki Kodera ◽  
Shveta Bisht ◽  
Shoji Takada ◽  
Tsuyoshi Terakawa
Keyword(s):  
Molecular Dynamics ◽  
Atomic Force Microscopy ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Force Microscopy ◽  
Atomic Force ◽  
Dna Loop ◽  
Dynamics Simulations ◽  
Dsdna Binding ◽  
Hinge Domain

The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the so-called hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain contacts dsDNA has remained unknown, potentially due to its conformational plasticity. Here, we conducted atomic force microscopy imaging of the budding yeast condensin holo-complex and used this data as basis for coarse-grained molecular dynamics simulations to model the hinge structure in a transient open conformation. We then simulated the dsDNA binding to open and closed hinge conformations, predicting that dsDNA binds to the outside surface when closed and to the outside and inside surfaces when open. Our simulations also suggested that the hinge can close around dsDNA bound to the inside surface. The conformational change of the hinge domain might be essential for the dsDNA binding regulation and play important roles in condensin-mediated DNA-loop extrusion.

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