Homology modeling, molecular docking and MD simulation studies to investigate role of cysteine protease from Xanthomonas campestris in degradation of Aβ peptide

2013 ◽  
Vol 43 (12) ◽  
pp. 2063-2070 ◽  
Author(s):  
Maruti J. Dhanavade ◽  
Chidambar B. Jalkute ◽  
Sagar H. Barage ◽  
Kailas D. Sonawane
Keyword(s):  
Molecular Docking ◽  
Homology Modeling ◽  
Cysteine Protease ◽  
Xanthomonas Campestris ◽  
Md Simulation ◽  
Aβ Peptide ◽  
Simulation Studies

scholarly journals Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Sensen Zhang ◽  
Baolei Yuan ◽  
Jordy Homing Lam ◽  
Jun Zhou ◽  
Xuan Zhou ◽  
...  
Keyword(s):  
Md Simulation ◽  
Potential Role ◽  
Md Simulations ◽  
Full Length ◽  
Inflammasome Activation ◽  
Simulation Studies ◽  
Cryo Electron Microscopy ◽  
Gating Mechanism ◽  
Atp Efflux

AbstractPannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, we show that in human macrophages PANX1 expression is upregulated by diverse stimuli that promote pyroptosis, which is reminiscent of the previously reported lipopolysaccharide-induced upregulation of PANX1 during inflammasome activation. To further elucidate the function of PANX1, we propose the full-length human Pannexin1 (hPANX1) model through cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulation studies, establishing hPANX1 as a homo-heptamer and revealing that both the N-termini and C-termini protrude deeply into the channel pore funnel. MD simulations also elucidate key energetic features governing the channel that lay a foundation to understand the channel gating mechanism. Structural analyses, functional characterizations, and computational studies support the current hPANX1-MD model, suggesting the potential role of hPANX1 in pyroptosis during immune responses.

2/3D-QSAR, molecular docking and MD simulation studies of FtsZ protein targeting benzimidazoles derivatives

2019 ◽  
Vol 78 ◽  
pp. 398-413 ◽  
Author(s):  
Shahzaib Ahamad ◽  
Asimul Islam ◽  
Faizan Ahmad ◽  
Neeraj Dwivedi ◽  
Md. Imtaiyaz Hassan
Keyword(s):  
Molecular Docking ◽  
Md Simulation ◽  
Protein Targeting ◽  
3D Qsar ◽  
Simulation Studies ◽  
Ftsz Protein

Molecular insight into binding behavior of polyphenol (rutin) with beta lactoglobulin: Spectroscopic, molecular docking and MD simulation studies

2018 ◽  
Vol 269 ◽  
pp. 511-520 ◽  
Author(s):  
Nasser Abdulatif Al-Shabib ◽  
Javed Masood Khan ◽  
Ajamaluddin Malik ◽  
Mohammad A. Alsenaidy ◽  
Md Tabish Rehman ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Md Simulation ◽  
Simulation Studies ◽  
Binding Behavior ◽  
Beta Lactoglobulin ◽  
Insight Into

scholarly journals Screening of potential drug from Azadirachta Indica (Neem) extracts for SARS-CoV-2: An insight from molecular docking and MD-simulation studies

2021 ◽  
Vol 1227 ◽  
pp. 129390
Author(s):  
Nabajyoti Baildya ◽  
Abdul Ashik Khan ◽  
Narendra Nath Ghosh ◽  
Tanmoy Dutta ◽  
Asoke P. Chattopadhyay
Keyword(s):  
Molecular Docking ◽  
Azadirachta Indica ◽  
Md Simulation ◽  
Simulation Studies ◽  
Potential Drug

scholarly journals A Role of Newly Found Auxiliary Site in Phospholipase A1 from Thai Banded Tiger Wasp (Vespa affinis) in Its Enzymatic Enhancement: In Silico Homology Modeling and Molecular Dynamics Insights

Toxins ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 510
Author(s):  
Withan Teajaroen ◽  
Suphaporn Phimwapi ◽  
Jureerut Daduang ◽  
Sompong Klaynongsruang ◽  
Varomyalin Tipmanee ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Homology Modeling ◽  
Binding Site ◽  
Lipid Binding ◽  
Surface Lipid ◽  
Phospholipase A1 ◽  
Enzymatic Function ◽  
Vespa Affinis ◽  
Lipid Binding Site

Phospholipase A1 from Thai banded tiger wasp (Vespa affinis) venom also known as Ves a 1 plays an essential role in fatal vespid allergy. Ves a 1 becomes an important therapeutic target for toxin remedy. However, established Ves a 1 structure or a mechanism of Ves a 1 function were not well documented. This circumstance has prevented efficient design of a potential phospholipase A1 inhibitor. In our study, we successfully recruited homology modeling and molecular dynamic (MD) simulation to model Ves a 1 three-dimensional structure. The Ves a 1 structure along with dynamic behaviors were visualized and explained. In addition, we performed molecular docking of Ves a 1 with 1,2-Dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid to assess a possible lipid binding site. Interestingly, molecular docking predicted another lipid binding region apart from its corresponding catalytic site, suggesting an auxiliary role of the alternative site at the Ves a 1 surface. The new molecular mechanism related to the surface lipid binding site (auxiliary site) provided better understanding of how phospholipase A1 structure facilitates its enzymatic function. This auxiliary site, conserved among Hymenoptera species as well as some mammalian lipases, could be a guide for interaction-based design of a novel phospholipase A1 inhibitor.

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