scholarly journals Conformational and interface variability of bivalent RNF4-SIM diSUMO3 interaction

2021 ◽  
Author(s):  
Alexander Kotter ◽  
Henning D. Mootz ◽  
Andreas Heuer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Experimental Results ◽  
Conformational Freedom ◽  
Dynamics Simulations ◽  
The Individual ◽  
Chain Interaction ◽  
Disordered Regions

SUMO targeted ubiqutin ligases (STUbLs) like RNF4 or Arkadia/RNF111 recognize SUMO chains through multiple SUMO interacting motifs (SIMs). Typically, these are contained in disordered regions of these enzymes and also the individual SUMO domains of SUMO chains move relatively freely. It is assumed that binding the SIM region significantly restricts the conformational freedom of SUMO chains. Here, we present the results of extensive molecular dynamics simulations on the complex formed by the SIM2-SIM3 region of RNF4 and diSUMO3. Though our simulations highlight the importance of typical SIM-SUMO interfaces also in the multivalent situation, we observe that frequently other regions of the peptide than the canonical SIMs establish this interface. This variability regarding the individual interfaces leads to a conformationally highly flexible complex. Even though this is in contrast to previous models of the RNF4 SUMO chain interaction, we demonstrate that our simulations are clearly consistent with previous experimental results.

Mechanical Properties of Tubulin Molecules by Molecular Dynamics Simulations

2006 ◽  
Author(s):  
So̸ren Enemark ◽  
Marco A. Deriu ◽  
Monica Soncini
Keyword(s):  
Molecular Dynamics ◽  
Elastic Constant ◽  
Molecular Dynamics Simulations ◽  
Elastic Constants ◽  
Interaction Force ◽  
Basic Unit ◽  
Dynamics Simulations ◽  
The Individual ◽  
Explicit Water ◽  
Β Tubulin

The basic unit in microtubules is αβ-tubulin, a hetero-dimer consisting of an α- and a β-tubulin monomer. The mechanical characteristics of the dimer as well as of the individual monomers may be used to obtain new insight into the microtubule tensile properties. In the present work we evaluate the elastic constants of each of the monomers and the interaction force between them by means of molecular dynamics simulations. Molecular models of α-, β-, and αβ-tubulin were developed starting from the 1TUB.pdb structure from the RSCB database. Simulations were carried out in a solvated environment using explicit water molecules. In order to measure the monomers’ elastic constants, simulations were performed by mimicking experiments carried out with atomic force microscopy. A different approach was used to determine the interaction force between the α- and β-monomers using 8 different monomer configurations based on different inter-monomer distances. The obtained results show an elastic constant value for α-tubulin of 3.4–3.9 N/m, while for the β-tubulin the elastic constant was measured to be 1.8–2.4 N/m. The maximum interaction force between the monomers was estimated to be 11.2 nN. In perspective, these outcomes will allow exchanging atomic level description with key mechanical features enabling microtubule characterisation by continuum mechanics approach.

scholarly journals Effects of magnetic field gradients on the aggregation dynamics of colloidal magnetic nanoparticles

Soft Matter ◽  
2015 ◽  
Vol 11 (38) ◽  
pp. 7606-7616 ◽  
Author(s):  
D. Heinrich ◽  
A. R. Goñi ◽  
T. M. Osán ◽  
L. M. C. Cerioni ◽  
A. Smessaert ◽  
...  
Keyword(s):  
Magnetic Field ◽  
Molecular Dynamics ◽  
Magnetic Nanoparticles ◽  
Molecular Dynamics Simulations ◽  
Theoretical Models ◽  
Experimental Results ◽  
Field Gradients ◽  
Magnetic Field Gradients ◽  
Dynamics Simulations

We combined theoretical models, experimental results and molecular dynamics simulations to explain the aggregation dynamics of ferrofluids in the presence of magnetic field gradients.

scholarly journals Ion-induced damage and annealing of silicon. Molecular dynamics simulations

2002 ◽  
Vol 74 (3) ◽  
pp. 419-422 ◽  
Author(s):  
David Humbird ◽  
David B. Graves
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamic Balance ◽  
Silicon Surfaces ◽  
Ion Energy ◽  
Argon Ions ◽  
Dynamics Simulations ◽  
Disordered Regions

A study of the interactions of energetic argon ions with silicon surfaces using molecular dynamics simulations is reported. A dynamic balance between ion-induced damage and recrystallization of the surface is detected. By manipulating ion energy, argon ions are able to both create disordered regions near the surface, and recrystallize these disordered regions.

Atomistic account of structural and dynamical changes induced by small binders in the double helix of a short DNA

2014 ◽  
Vol 16 (27) ◽  
pp. 14070-14082 ◽  
Author(s):  
Barbara Fresch ◽  
F. Remacle
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Double Helix ◽  
Drug Molecules ◽  
Conformational Freedom ◽  
Dna Fragment ◽  
Dynamics Simulations

How drug molecules perturb the conformational freedom of a helical DNA fragment is investigated by molecular dynamics simulations.

Simulation by classical molecular dynamics of the influence of radiation effects on the fracture behavior of simplified nuclear glasses

2012 ◽  
Vol 1475 ◽  
Author(s):  
Le-Hai Kieu ◽  
Jean-Marc Delaye ◽  
Claude Stolz
Keyword(s):  
Molecular Dynamics ◽  
Fracture Toughness ◽  
Molecular Dynamics Simulations ◽  
Radiation Effects ◽  
Fracture Behavior ◽  
Elastic Limit ◽  
Experimental Results ◽  
Displacement Cascades ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

ABSTRACTClassical molecular dynamics simulations were used to compare the fracture behavior of pristine and disordered specimens of a simplified nuclear glass. The disordered specimen is prepared in order to mimic the effects of accumulating displacement cascades. It is characterized by a decreasing Boron coordination and an increasing Na concentration in a modifying role. We observe an enhancement of the plasticity of the disordered glass and a decrease of the elastic limit, resulting in greater fracture toughness. The simulation findings are consistent with experimental results.

Advances in Molecular Dynamics Simulations of Nanotribology

2008 ◽  
Author(s):  
Michael Chandross
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
State Of The Art ◽  
Simulation Method ◽  
Detailed Understanding ◽  
The Past ◽  
Simulation Techniques ◽  
Dynamics Simulations ◽  
The Individual ◽  
Made In

Molecular dynamics is the simulation method that is most amenable to the length and time scales of nanotribological experiments. The ability to track the individual motion of every atom in simulations has led to a detailed understanding of the underlying physics that is difficult to extract from experiment. While significant progress has been made in simulations over the past two decades, computational issues still limit the types of problems that can be approached, and the detailed understanding that results. Here we discuss recent advances in molecular dynamics simulations that push the bounds of simulation size, velocity, and chemistry. These state of the art simulation techniques have made great strides in allowing detailed comparisons to experimental results. These advances will be placed in context by addressing the barriers that remain and where future progress lies.

Influence of Adsorbate Monolayer on the Nano-Mechanics of TIP-Substrate Interactions

1991 ◽  
Vol 239 ◽  
Author(s):  
H. Rafii-Tabar ◽  
J. B. Pethica ◽  
A. P. Sutton
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Plastic Flow ◽  
Constant Temperature ◽  
Three Dimensional ◽  
Experimental Results ◽  
Work Of Adhesion ◽  
Substrate Interactions ◽  
Complete Cycle ◽  
Dynamics Simulations

ABSTRACTWe employ constant temperature molecular dynamics simulations to study, at the atomistic level, the interactions of an Ir tip with a Pb substrate. We have considered the complete cycle of approach.contact, indentation and retraction of the tip from the substrate. We have observed the wetting of the tip by the substrate atoms, and the formation of atomic necking between the tip and the substrate.We have carried out further simulations to study the interactions of an Ir tip with an Ir substrate covered with an adsorbate monolayer of Pb film. We show that the introduction of the adsorbate considerably reduces the work of adhesion and the extent of plastic flow, in agreement with experimental results.Three-dimensional geometries have been generated on computer and used for the animation of the simulation runs.

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