Discovery and identification of Cdc37-derived peptides targeting the Hsp90–Cdc37 protein–protein interaction

RSC Advances ◽  
2015 ◽  
Vol 5 (116) ◽  
pp. 96138-96145 ◽  
Author(s):  
Lei Wang ◽  
Qi-Chao Bao ◽  
Xiao-Li Xu ◽  
Fen Jiang ◽  
Kai Gu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Protein Interaction ◽  
Peptide Inhibitors ◽  
Dynamics Simulation ◽  
Protein Protein Interaction ◽  
Binding Interface ◽  
Combined Strategy ◽  
Key Residues

In order to explore the key residues of the Hsp90–Cdc37 binding interface for further design of peptide inhibitors, a combined strategy of molecular dynamics simulation and MM-PBSA analysis was performed.

scholarly journals Molecular Dynamics Simulations for Biological Systems

2017 ◽  
pp. 1044-1071 ◽  
Author(s):  
Prerna Priya ◽  
Minu Kesheri ◽  
Rajeshwar P. Sinha ◽  
Swarna Kanchan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Ligand Docking ◽  
Protein Protein Interaction ◽  
Dynamics Simulations

Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.

scholarly journals Residues R1075, D1090, R1095, and C1130 Are Critical in ADAMTS13 TSP8-Spacer Interaction Predicted by Molecular Dynamics Simulation

Molecules ◽  
2021 ◽  
Vol 26 (24) ◽  
pp. 7525
Author(s):  
Zhiwei Wu ◽  
Junxian Yang ◽  
Xubin Xie ◽  
Guangjian Liu ◽  
Ying Fang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Homology Modelling ◽  
Microvascular Disease ◽  
Dynamics Simulation ◽  
Salt Bridges ◽  
Key Residues ◽  
Von Willebrand ◽  
Willebrand Factor

ADAMTS13 (A Disintegrin and Metalloprotease with Thrombospondin type 1 repeats, member 13) cleaves von Willebrand Factor (VWF) multimers to limit the prothrombotic function of VWF. The deficiency of ADAMTS13 causes a lethal thrombotic microvascular disease, thrombotic thrombocytopenic purpura (TTP). ADAMTS13 circulates in a “closed” conformation with the distal domain associating the Spacer domain to avoid off-target proteolysis or recognition by auto-antibodies. However, the interactions of the distal TSP8 domain and the Spacer domain remain elusive. Here, we constructed the TSP8-Spacer complex by a combination of homology modelling and flexible docking. Molecular dynamics simulation was applied to map the binding sites on the TSP8 or Spacer domain. The results predicted that R1075, D1090, R1095, and C1130 on the TSP8 domain were key residues that interacted with the Spacer domain. R1075 and R1095 bound exosite-4 tightly, D1090 formed multiple hydrogen bonds and salt bridges with exosite-3, and C1130 interacted with both exosite-3 and exosite-4. Specific mutations of exosite-3 (R568K/F592Y/R660K/Y661F/Y665F) or the four key residues (R1075A/D1090A/R1095A/C1130A) impaired the binding of the TSP8 domain to the Spacer domain. These results shed new light on the understanding of the auto-inhibition of ADAMTS13.

Molecular Dynamics Simulations for Biological Systems

2016 ◽  
pp. 286-313 ◽  
Author(s):  
Prerna Priya ◽  
Minu Kesheri ◽  
Rajeshwar P. Sinha ◽  
Swarna Kanchan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Ligand Docking ◽  
Protein Protein Interaction ◽  
Dynamics Simulations

Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.

Identification of potential CCR5 inhibitors through pharmacophore-based virtual screening, molecular dynamics simulation and binding free energy analysis

2016 ◽  
Vol 12 (11) ◽  
pp. 3396-3406 ◽  
Author(s):  
Juan Wang ◽  
Mao Shu ◽  
Yuanqiang Wang ◽  
Yong Hu ◽  
Yuanliang Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Energy Analysis ◽  
Binding Free Energy ◽  
Rational Drug Design ◽  
Dynamics Simulation ◽  
Rational Drug ◽  
Combined Strategy ◽  
Free Energy Analysis

Employing the combined strategy to identify novel CCR5 inhibitors and provide a basis for rational drug design.

Underlying mechanisms of cyclic peptide inhibitors interrupting the interaction of CK2α/CK2β: comparative molecular dynamics simulation studies

2016 ◽  
Vol 18 (13) ◽  
pp. 9202-9210 ◽  
Author(s):  
Yue Zhou ◽  
Na Zhang ◽  
Wenjuan Chen ◽  
Lijiao Zhao ◽  
Rugang Zhong
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Cyclic Peptide ◽  
Peptide Inhibitors ◽  
Dynamics Simulation ◽  
Simulation Methods ◽  
Simulation Studies ◽  
Underlying Mechanisms ◽  
Structural Mechanisms

The structural mechanisms of cyclic peptide inhibitors disrupting CK2α/CK2β interaction have been deeply studied by means of comparative molecular dynamics simulation methods.

scholarly journals Interactive Visualization of Molecular Dynamics Simulation Data

2020 ◽  
Author(s):  
◽  
Naif Alharbi
Keyword(s):  
Molecular Dynamics ◽  
Protein Interaction ◽  
User Study ◽  
Visual Analysis ◽  
Interaction Space ◽  
Time Dependent ◽  
Dynamics Simulation ◽  
Simulation Data ◽  
Protein Protein Interaction ◽  
Lipid Interaction

Molecular Dynamics Simulations (MD) plays an essential role in the field of computational biology. The simulations produce extensive high-dimensional, spatio-temporal data describ-ing the motion of atoms and molecules. A central challenge in the field is the extraction and visualization of useful behavioral patterns from these simulations. Throughout this thesis, I collaborated with a computational biologist who works on Molecular Dynamics (MD) Simu-lation data. For the sake of exploration, I was provided with a large and complex membrane simulation. I contributed solutions to his data challenges by developing a set of novel visual-ization tools to help him get a better understanding of his simulation data. I employed both scientific and information visualization, and applied concepts of abstraction and dimensions projection in the proposed solutions. The first solution enables the user to interactively fil-ter and highlight dynamic and complex trajectory constituted by motions of molecules. The molecular dynamic trajectories are identified based on path length, edge length, curvature, and normalized curvature, and their combinations. The tool exploits new interactive visual-ization techniques and provides a combination of 2D-3D path rendering in a dual dimension representation to highlight differences arising from the 2D projection on a plane. The sec-ond solution introduces a novel abstract interaction space for Protein-Lipid interaction. The proposed solution addresses the challenge of visualizing complex, time-dependent interactions between protein and lipid molecules. It also proposes a fast GPU-based implementation that maps lipid-constituents involved in the interaction onto the abstract protein interaction space. I also introduced two abstract level-of-detail (LoD) representations with six levels of detail for lipid molecules and protein interaction. Finally, I proposed a novel framework consisting of four linked views: A time-dependent 3D view, a novel hybrid view, a clustering timeline, and a details-on-demand window. The framework exploits abstraction and projection to enable the user to study the molecular interaction and the behavior of the protein-protein interaction and clusters. I introduced a selection of visual designs to convey the behavior of protein-lipid interaction and protein-protein interaction through a unified coordinate system. Abstraction is used to present proteins in hybrid 2D space, and a projected tiled space is used to present both Protein-Lipid Interaction (PLI) and Protein-Protein Interaction (PPI) at the particle level in a heat-map style visual design. Glyphs are used to represent PPI at the molecular level. I coupled visually separable visual designs in a unified coordinate space. The result lets the user study both PLI and PPI separately, or together in a unified visual analysis framework.

Molecular dynamics simulation studies of a protein–RNA complex with a selectively modified binding interface

Biopolymers ◽  
2006 ◽  
Vol 81 (4) ◽  
pp. 256-269 ◽  
Author(s):  
Ying Zhao ◽  
Bethany L. Kormos ◽  
David L. Beveridge ◽  
Anne M. Baranger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Binding Interface ◽  
Rna Complex
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