Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

Unfolding of intrinsically unstructured full-length LEA proteins in a differentially crowded environment can be modeled by 30 ns MD simulations in accordance with experimental data.

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Mechanism of stacking fault annihilation in 3C-SiC epitaxially grown on Si(001) by molecular dynamics simulations

CrystEngComm ◽

10.1039/d0ce01613f ◽

2021 ◽

Author(s):

Andrey Sarikov ◽

Anna Marzegalli ◽

Luca Barbisan ◽

Massimo Zimbone ◽

Corrado Bongiorno ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Stacking Faults ◽

Md Simulations ◽

Stacking Fault ◽

Dynamics Simulations

In this work, annihilation mechanism of stacking faults (SFs) in epitaxial 3C-SiC layers grown on Si(001) substrates is studied by molecular dynamics (MD) simulations. The evolution of SFs located in...

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Local Structuring of Diketopyrrolopyrrole (DPP)-based Oligomers from Molecular Dynamics Simulations

Physical Chemistry Chemical Physics ◽

10.1039/d1cp03257g ◽

2021 ◽

Author(s):

Maryam Reisjalali ◽

J. Javier Burgos-Marmol ◽

Rex Manurung ◽

Alessandro Troisi

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

High Mobility ◽

Semiconducting Polymers ◽

Microscopic Structure ◽

Dynamics Simulations

The microscopic structure of high mobility semiconducting polymers is known to be essential for their performance but it cannot be easily deduced from the available experimental data. A series of...

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Structural stability of CmTin microclusters and nanoparticles: Molecular–dynamics simulations

Computing Letters ◽

10.1163/157404005776611321 ◽

2005 ◽

Vol 1 (4) ◽

pp. 204-209

Author(s):

O.B. Malcıoğlu ◽

Ş. Erkoç

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Binary Systems ◽

Minimum Energy ◽

Potential Energy Function ◽

Md Simulations ◽

Atomic Interactions ◽

Dynamics Simulations ◽

Three Body ◽

Initial Geometry

The minimum energy structures of CmTin microclusters and nanoparticles have been investigated theoretically by performing molecular–dynamics (MD) simulations. Selected crystalline and completely random initial geometries are considered. The potential energy function (PEF) used in the calculations includes two– and three–body atomic interactions for C-Ti binary systems. Molecular–dynamics simulations have been performed at 1 K and 300 K. It has been found that initial geometry has a very strong influence on relaxed geometry

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Tight-Binding Molecular Dynamics Study of Liquid and Amorphous Carbon

MRS Proceedings ◽

10.1557/proc-291-177 ◽

1992 ◽

Vol 291 ◽

Cited By ~ 1

Author(s):

C. Z. Wang ◽

K. M. Ho ◽

C. T. Chan

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Amorphous Carbon ◽

Simulation Study ◽

Tight Binding ◽

Sufficient Accuracy ◽

Complex Carbon ◽

Dynamics Simulations

ABSTRACTTight-binding molecular-dynamics simulations are performed to study the structure of liquid and amorphous carbon. Comparisons of our results with ab initiomolecular dynamics (Car-Parrinello) results and experimental data show that the scheme has sufficient accuracy and efficiency for realistic simulation study of the structural properties of complex carbon systems.

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An Integrative Approach to Single-Molecule FRET Spectroscopy and Molecular Dynamics Simulations for the Study of Intrinsically Disordered Proteins

Biophysical Journal ◽

10.1016/j.bpj.2019.11.906 ◽

2020 ◽

Vol 118 (3) ◽

pp. 143a

Author(s):

Mahmoud Moradi

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Single Molecule ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Integrative Approach ◽

Intrinsically Disordered ◽

Single Molecule Fret ◽

Dynamics Simulations

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Optimization of Molecular Dynamics Simulations of c-MYC1-88—An Intrinsically Disordered System

Life ◽

10.3390/life10070109 ◽

2020 ◽

Vol 10 (7) ◽

pp. 109 ◽

Cited By ~ 2

Author(s):

Sandra S. Sullivan ◽

Robert O.J. Weinzierl

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Proliferation And Apoptosis ◽

Conventional Structure ◽

Experimental Approaches ◽

Dynamics Simulations

Many of the proteins involved in key cellular regulatory events contain extensive intrinsically disordered regions that are not readily amenable to conventional structure/function dissection. The oncoprotein c-MYC plays a key role in controlling cell proliferation and apoptosis and more than 70% of the primary sequence is disordered. Computational approaches that shed light on the range of secondary and tertiary structural conformations therefore provide the only realistic chance to study such proteins. Here, we describe the results of several tests of force fields and water models employed in molecular dynamics simulations for the N-terminal 88 amino acids of c-MYC. Comparisons of the simulation data with experimental secondary structure assignments obtained by NMR establish a particular implicit solvation approach as highly congruent. The results provide insights into the structural dynamics of c-MYC1-88, which will be useful for guiding future experimental approaches. The protocols for trajectory analysis described here will be applicable for the analysis of a variety of computational simulations of intrinsically disordered proteins.

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Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

Physical Chemistry Chemical Physics ◽

10.1039/d0cp00435a ◽

2020 ◽

Vol 22 (12) ◽

pp. 6690-6697 ◽

Cited By ~ 3

Author(s):

Aman Jindal ◽

Sukumaran Vasudevan

Keyword(s):

Molecular Dynamics ◽

Hydrogen Bonding ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Liquid State ◽

Crystalline State ◽

Md Simulations ◽

Ab Initio Molecular Dynamics ◽

Linear Alcohols ◽

Dynamics Simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

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