scholarly journals The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases

2015 ◽  
Vol 6 (2) ◽  
pp. 1167-1177 ◽  
Author(s):  
Javier Iglesias-Fernández ◽  
Lluís Raich ◽  
Albert Ardèvol ◽  
Carme Rovira
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Dynamics Simulations ◽  
Conformational Free Energy

Ab initio conformational free energy landscapes, together with molecular dynamics simulations, enable to predict the catalytic itineraries of β-xylanase enzymes.

scholarly journals Free Energy Landscapes and Residue Network Analysis for Six SARS-CoV-2 Targets in Complex with Plausible Phytochemical Inhibitors from Withania Somnifera: 1 µS Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Pratap Kumar Parida ◽  
Dipak Paul ◽  
Debamitra Chakravorty
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Withania Somnifera ◽  
Minimum Energy ◽  
Interaction Network ◽  
Energy Landscapes ◽  
Residue Interaction ◽  
Free Energy Landscapes ◽  
Dynamics Simulations

The pandemic is here to stay- evident from the second wave that is severely affecting global population. Though vaccination is now available, the population size restricts its efficacy, especially in the third world countries. Therefore, to avoid a third wave, natural preventive therapeutics are the need of the hour. In this work the efficiency of phytochemicals from <i>Withania somnifera</i> to bind to a total of six SARS-CoV-2 targets have been shown.1 µs molecular dynamics simulations and essential dynamic analyses shed light on the changes induced by the phytochemicals and highlights their multipotent capabilities- 27-Hydroxywithanolide B was able to bind to three targets. Relative free energy of binding for all the phytochemicals were calculated by MM/PBSA. Minimum energy structures were extracted from their free energy landscapes and were subjected to PSN-ENM-NMA and network centrality analysis. Results showed that the phytochemical binding changes the residue-residue interaction network. Network communities increase while hubs and links decrease. Metapath rewiring occurs through residues Phe456 in spike protein, Thr26 and Tyr118 in main protease, Val49 and Phe156 in NSP3, Leu98 in NSP9, Leu4345 in NSP10, Phe440 and Phe843 in NSP12. This work tries to understand the mechanism of possible inhibition by the phytochemicals to combat SARS-CoV-2 with their capability of targeting multiple proteins. The insight from this study can be of great relevance to explore the changes in network properties induced by reported potential inhibitors against SARS-CoV-2 targets.

scholarly journals Free Energy Landscapes and Residue Network Analysis for Six SARS-CoV-2 Targets in Complex with Plausible Phytochemical Inhibitors from Withania Somnifera: 1 µS Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Pratap Kumar Parida ◽  
Dipak Paul ◽  
Debamitra Chakravorty
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Withania Somnifera ◽  
Minimum Energy ◽  
Interaction Network ◽  
Energy Landscapes ◽  
Residue Interaction ◽  
Free Energy Landscapes ◽  
Dynamics Simulations

The pandemic is here to stay- evident from the second wave that is severely affecting global population. Though vaccination is now available, the population size restricts its efficacy, especially in the third world countries. Therefore, to avoid a third wave, natural preventive therapeutics are the need of the hour. In this work the efficiency of phytochemicals from <i>Withania somnifera</i> to bind to a total of six SARS-CoV-2 targets have been shown.1 µs molecular dynamics simulations and essential dynamic analyses shed light on the changes induced by the phytochemicals and highlights their multipotent capabilities- 27-Hydroxywithanolide B was able to bind to three targets. Relative free energy of binding for all the phytochemicals were calculated by MM/PBSA. Minimum energy structures were extracted from their free energy landscapes and were subjected to PSN-ENM-NMA and network centrality analysis. Results showed that the phytochemical binding changes the residue-residue interaction network. Network communities increase while hubs and links decrease. Metapath rewiring occurs through residues Phe456 in spike protein, Thr26 and Tyr118 in main protease, Val49 and Phe156 in NSP3, Leu98 in NSP9, Leu4345 in NSP10, Phe440 and Phe843 in NSP12. This work tries to understand the mechanism of possible inhibition by the phytochemicals to combat SARS-CoV-2 with their capability of targeting multiple proteins. The insight from this study can be of great relevance to explore the changes in network properties induced by reported potential inhibitors against SARS-CoV-2 targets.

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