Molecular modeling and MD-simulation studies: Fast and reliable tool to study the role of low-redox bacterial laccases in the decolorization of various commercial dyes

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.

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

Computers in Biology and Medicine ◽

10.1016/j.compbiomed.2013.09.021 ◽

2013 ◽

Vol 43 (12) ◽

pp. 2063-2070 ◽

Cited By ~ 26

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

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Molecular modeling and molecular dynamics simulation studies on thyroid hormone receptor from Rattus norvegicus: role of conserved water molecules

Journal of Molecular Modeling ◽

10.1007/s00894-021-04740-1 ◽

2021 ◽

Vol 27 (5) ◽

Author(s):

Soumita Mukherjee ◽

Subrata Dasgupta ◽

Utpal Adhikari ◽

Sujit Sankar Panja

Keyword(s):

Molecular Dynamics ◽

Molecular Modeling ◽

Molecular Dynamics Simulation ◽

Rattus Norvegicus ◽

Thyroid Hormone Receptor ◽

Dynamics Simulation ◽

Water Molecules ◽

Simulation Studies ◽

Conserved Water Molecules

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Experimental and simulation studies on the role of fluid velocity during particle separation in a liquid–solid fluidized bed

International Journal of Mineral Processing ◽

10.1016/j.minpro.2006.11.006 ◽

2007 ◽

Vol 82 (4) ◽

pp. 211-221 ◽

Cited By ~ 21

Author(s):

A.K. Mukherjee ◽

B.K. Mishra

Keyword(s):

Fluidized Bed ◽

Fluid Velocity ◽

Particle Separation ◽

Simulation Studies

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Molecular modulation of calcium oxalate crystallization

AJP Renal Physiology ◽

10.1152/ajprenal.00136.2006 ◽

2006 ◽

Vol 291 (6) ◽

pp. F1123-F1132 ◽

Cited By ~ 57

Author(s):

James J. De Yoreo ◽

S. Roger Qiu ◽

John R. Hoyer

Keyword(s):

Molecular Modeling ◽

Calcium Oxalate ◽

Stone Formation ◽

Energy Levels ◽

Critical Role ◽

Specific Interactions ◽

Crystal Surfaces ◽

Site Specific

Calcium oxalate monohydrate (COM) is the primary constituent of the majority of renal stones. Osteopontin (OPN), an aspartic acid-rich urinary protein, and citrate, a much smaller molecule, are potent inhibitors of COM crystallization at levels present in normal urine. Current concepts of the role of site-specific interactions in crystallization derived from studies of biomineralization are reviewed to provide a context for understanding modulation of COM growth at a molecular level. Results from in situ atomic force microscopy (AFM) analyses of the effects of citrate and OPN on growth verified the critical role of site-specific interactions between these growth modulators and individual steps on COM crystal surfaces. Molecular modeling investigations of interactions of citrate with steps and faces on COM crystal surfaces provided links between the stereochemistry of interaction and the binding energy levels that underlie mechanisms of growth modification and changes in overall crystal morphology. The combination of in situ AFM and molecular modeling provides new knowledge that will aid rationale design of therapeutic agents for inhibition of stone formation.

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