Analysis of the RGD sequence in protein structures: comparison to the conformations of the RGDW and D RGDW peptides determined by molecular dynamics simulations

2001 ◽  
Vol 106 (1-2) ◽  
pp. 128-136 ◽  
Author(s):  
Roland H. Stote
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Structures ◽  
Rgd Sequence ◽  
Dynamics Simulations

scholarly journals A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

Soft Matter ◽  
2021 ◽  
Author(s):  
Rakesh K Vaiwala ◽  
Ganapathy Ayappa
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Native Protein ◽  
Dynamics Simulations

A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by...

scholarly journals Molecular Dynamics Simulations of resistin and RELMβ proteins: Insight into structural dynamics

2021 ◽  
Author(s):  
L. América Chi Uluac ◽  
M. Cristina Vargas González
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulations ◽  
Structural Dynamics ◽  
Protein Structures ◽  
Globular Domain ◽  
The Family ◽  
Network Of Hydrogen Bonds ◽  
Dynamics Simulations ◽  
Metabolic Dysfunctions

Diabetes mellitus and high levels of resistin are risk factors for COVID-19, suggest- ing a shared mechanism for their contribution to the increased severity of COVID-19. Resistin belongs to the family of resistin-like molecules (RELMs) whose implications for inflammatory and metabolic dysfunctions warrant its study in order to shed light on the etiology of these concerning pathologies. In this work, our objective is to char- acterize the structural dynamics of the reported crystallized resistin-like molecules. We performed molecular dynamics simulations of all-atom solvated protein at physiological and high temperatures for the three mouse structures reported so far. We found that in all the structures studied, there is a loss of helicity as a first step of protein denat- uration. There is a high stability of the globular β-sheet domain in resistin protein structures that is not conserved for RELMβ. At high temperature, we found a partial interconversion of α-helices into β-sheets in all proteins, indicating that this propensity is not only found during aggregation but also heating. We had been able to identify a largely persistent hydrogen-bond network shared by all the proteins in the interchain globular domain at room temperature. This network of hydrogen bonds is conserved considerably at high temperature in resistin structures, but not in RELMβ. These findings may guide future studies to increase our understanding of the different and shared mechanisms of action of RELMs.

scholarly journals PBxplore: a tool to analyze local protein structure and deformability with protein Blocks

2017 ◽  
Author(s):  
Jonathan Barnoud ◽  
Hubert Santuz ◽  
Pierrick Craveur ◽  
Agnel Praveen Joseph ◽  
Vincent Jallu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Molecular Dynamics Simulations ◽  
Open Source ◽  
Local Structure ◽  
Protein Structures ◽  
Local Protein Structure ◽  
Dynamics Simulations ◽  
Protein Blocks ◽  
Local Protein

ABSTRACTProteins are highly dynamic macromolecules. A classical way to analyze their inner flexibility is to perform molecular dynamics simulations. In this context, we present the advantage to use small structural prototypes, namely the Protein Blocks (PBs). PBs give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, they allow analyzes of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is a suite of tools to analyze the dynamics and deformability of protein structures using PBs. It is able to process large amount of data such as those produced by molecular dynamics simulations. It produces various outputs with text and graphics, such as frequencies, entropy and information logo. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.

scholarly journals Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

2017 ◽  
Vol 3 (7) ◽  
pp. e1700479 ◽  
Author(s):  
Nicholas I. Brodie ◽  
Konstantin I. Popov ◽  
Evgeniy V. Petrotchenko ◽  
Nikolay V. Dokholyan ◽  
Christoph H. Borchers
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Short Distance ◽  
Protein Structures ◽  
Cross Linking ◽  
Discrete Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Selection of Near-Native Protein Structures by Means of Molecular Dynamics Simulations

2010 ◽  
Vol 98 (3) ◽  
pp. 196a
Author(s):  
Bogdan Barz ◽  
Qingguo Wang ◽  
Jingfen Zhang ◽  
Zhiquan He ◽  
Dong Xu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Structures ◽  
Native Protein ◽  
Dynamics Simulations ◽  
Selection Of

scholarly journals PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4013 ◽  
Author(s):  
Jonathan Barnoud ◽  
Hubert Santuz ◽  
Pierrick Craveur ◽  
Agnel Praveen Joseph ◽  
Vincent Jallu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Molecular Dynamics Simulations ◽  
Open Source ◽  
Local Structure ◽  
Protein Structures ◽  
Local Protein Structure ◽  
Dynamics Simulations ◽  
Protein Blocks ◽  
Local Protein

This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.

scholarly journals Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction

2021 ◽  
Vol 8 ◽  
Author(s):  
Ennys Gheyouche ◽  
Matthias Bagueneau ◽  
Gervaise Loirand ◽  
Bernard Offmann ◽  
Stéphane Téletchéa
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Interface Design ◽  
Protein Structures ◽  
Binding Mode ◽  
Protein Docking ◽  
Protein Interface ◽  
Nucleotide Exchange ◽  
Protein Protein Interaction ◽  
Dynamics Simulations

The interaction between two proteins may involve local movements, such as small side-chains re-positioning or more global allosteric movements, such as domain rearrangement. We studied how one can build a precise and detailed protein-protein interface using existing protein-protein docking methods, and how it can be possible to enhance the initial structures using molecular dynamics simulations and data-driven human inspection. We present how this strategy was applied to the modeling of RHOA-ARHGEF1 interaction using similar complexes of RHOA bound to other members of the Rho guanine nucleotide exchange factor family for comparative assessment. In parallel, a more crude approach based on structural superimposition and molecular replacement was also assessed. Both models were then successfully refined using molecular dynamics simulations leading to protein structures where the major data from scientific literature could be recovered. We expect that the detailed strategy used in this work will prove useful for other protein-protein interface design. The RHOA-ARHGEF1 interface modeled here will be extremely useful for the design of inhibitors targeting this protein-protein interaction (PPI).

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