Using Molecular Dynamics Simulations To Provide New Insights into Protein Structure on the Nanosecond Timescale:  Comparison with Experimental Data and Biological Inferences for the Hyaluronan-Binding Link Module of TSG-6

2006 ◽  
Vol 3 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Andrew Almond ◽  
Charles D. Blundell ◽  
Victoria A. Higman ◽  
Alexander D. MacKerell, ◽  
Anthony J. Day
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Protein Structure ◽  
Molecular Dynamics Simulations ◽  
Link Module ◽  
Dynamics Simulations ◽  
Hyaluronan Binding ◽  
Comparison With Experimental Data

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

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...

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

2016 ◽  
Vol 18 (37) ◽  
pp. 25806-25816 ◽  
Author(s):  
Carlos Navarro-Retamal ◽  
Anne Bremer ◽  
Jans Alzate-Morales ◽  
Julio Caballero ◽  
Dirk K. Hincha ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Arabidopsis Thaliana ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Cd Spectroscopy ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Dynamics Simulations ◽  
Crowded Environment

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.

Tight-Binding Molecular Dynamics Study of Liquid and Amorphous Carbon

1992 ◽  
Vol 291 ◽  
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.

scholarly journals SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations

2021 ◽  
Author(s):  
Markus Schneider ◽  
Iris Antes
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Molecular Dynamics Simulations ◽  
Network Models ◽  
Local Environment ◽  
Future Application ◽  
Analysis Tool ◽  
Innovative Drug ◽  
Nmr Structures ◽  
Dynamics Simulations

Computational methods play a key role for investigating allosteric mechanisms in proteins, with the potential of generating valuable insights for innovative drug design. Here we present the SenseNet ("Structure ENSEmble NETworks") framework for analysis of protein structure networks, which differs from established network models by focusing on interaction timelines obtained by molecular dynamics simulations. This approach is evaluated by predicting allosteric residues reported by NMR experiments in the PDZ2 domain of hPTP1e, a reference system for which previous computational predictions have shown considerable variance. We applied two models based on the mutual information between interaction timelines to estimate the conformational influence of each residue on its local environment. In terms of accuracy our prediction model is comparable to the top performing model published for this system, but by contrast benefits from its independence from NMR structures. Our results are complementary to experimental data and the consensus of previous predictions, demonstrating the potential of our new analysis tool SenseNet. Biochemical interpretation of our model suggests that allosteric residues in the PDZ2 domain form two distinct clusters of contiguous sidechain surfaces. SenseNet is provided as a plugin for the network analysis software Cytoscape, allowing for ease of future application and contributing to a system of compatible tools bridging the fields of system and structural biology.

scholarly journals Impact of deep eutectic solvents (DESs) and individual DES components on alcohol dehydrogenase catalysis: Connecting experimental data and molecular dynamics simulations

2021 ◽  
Author(s):  
Jan Philipp Bittner ◽  
Ningning Zhang ◽  
Lei Huang ◽  
Pablo Dominguez de Maria ◽  
Sven Jakobtorweihen ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Alcohol Dehydrogenase ◽  
Molecular Dynamics Simulations ◽  
Enzyme Catalysis ◽  
Deep Eutectic Solvents ◽  
Knowledge Based ◽  
Dynamics Simulations ◽  
The Impact ◽  
Knowledge Based Design

For a knowledge-based design of enzyme catalysis in deep eutectic solvents (DESs), the influence of the DESs properties (e.g., water activity, viscosity), and the impact of DESs and their individual...

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