Homology modeling and docking study of diamondback moth ryanodine receptor reveals the mechanisms for channel activation, insecticide binding and resistance

2019 ◽  
Vol 76 (4) ◽  
pp. 1291-1303 ◽  
Author(s):  
Lianyun Lin ◽  
Zhiyuan Hao ◽  
Peng Cao ◽  
Zhiguang Yuchi
Keyword(s):  
Homology Modeling ◽  
Ryanodine Receptor ◽  
Diamondback Moth ◽  
Docking Study ◽  
Channel Activation

scholarly journals The N-Terminal Region of the Ryanodine Receptor Affects Channel Activation

2017 ◽  
Vol 8 ◽  
Author(s):  
Andrea Faltinova ◽  
Nataša Tomaskova ◽  
Marián Antalik ◽  
Jozef Sevcik ◽  
Alexandra Zahradnikova
Keyword(s):  
Ryanodine Receptor ◽  
Terminal Region ◽  
Channel Activation

Identification of potential agonist of human and mouse FFAR2 by homology modeling and molecular docking study approach

2020 ◽  
Vol 34 (S1) ◽  
pp. 1-1
Author(s):  
Prashantha Karunakar ◽  
Sidharth P. Mishra ◽  
Atefeh P. Razazan ◽  
Shailesh Sharma ◽  
Hariom Yadav
Keyword(s):  
Molecular Docking ◽  
Homology Modeling ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Study Approach ◽  
Human And Mouse

Spontaneous Ryanodine-Receptor-Dependent Ca2+-Activated K+ Currents and Hyperpolarizations in Rat Medial Preoptic Neurons

2010 ◽  
Vol 103 (5) ◽  
pp. 2900-2911 ◽  
Author(s):  
Göran Klement ◽  
Michael Druzin ◽  
David Haage ◽  
Evgenya Malinina ◽  
Peter Århem ◽  
...  
Keyword(s):  
Ryanodine Receptor ◽  
Ryanodine Receptors ◽  
Underlying Mechanism ◽  
Sk Channels ◽  
Patch Clamp Technique ◽  
Channel Activation ◽  
Impulse Generation ◽  
Outward Currents ◽  
Main Charge ◽  
Perforated Patch Clamp

The aim of the present study was to clarify the identity of slow spontaneous currents, the underlying mechanism and possible role for impulse generation in neurons of the rat medial preoptic nucleus (MPN). Acutely dissociated neurons were studied with the perforated patch-clamp technique. Spontaneous outward currents, at a frequency of ∼0.5 Hz and with a decay time constant of ∼200 ms, were frequently detected in neurons when voltage-clamped between approximately −70 and −30 mV. The dependence on extracellular K+ concentration was consistent with K+ as the main charge carrier. We concluded that the main characteristics were similar to those of spontaneous miniature outward currents (SMOCs), previously reported mainly for muscle fibers and peripheral nerve. From the dependence on voltage and from a pharmacological analysis, we concluded that the currents were carried through small-conductance Ca2+-activated (SK) channels, of the SK3 subtype. From experiments with ryanodine, xestospongin C, and caffeine, we concluded that the spontaneous currents were triggered by Ca2+ release from intracellular stores via ryanodine receptor channels. An apparent voltage dependence was explained by masking of the spontaneous currents as a consequence of steady SK-channel activation at membrane potentials > −30 mV. Under current-clamp conditions, corresponding transient hyperpolarizations occasionally exceeded 10 mV in amplitude and reduced the frequency of spontaneous impulses. In conclusion, MPN neurons display spontaneous hyperpolarizations triggered by Ca2+ release via ryanodine receptors and SK3-channel activation. Thus such events may affect impulse firing of MPN neurons.

scholarly journals Some novel insights into the binding of oseltamivir and zanamivir to H5N1 and N9 influenza virus neuraminidases: A homology modeling and flexible docking study

2009 ◽  
Vol 74 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Marija Mihajlovic ◽  
Petar Mitrasinovic
Keyword(s):  
Homology Modeling ◽  
Protein Structures ◽  
Three Dimensional ◽  
Docking Study ◽  
Energy Difference ◽  
Am1 Method ◽  
Free Energies ◽  
Flexible Docking ◽  
Three Dimensional Models ◽  
Binding Free Energies

In the context of the recent pandemic threat by the worldwide spread of H5N1 avian influenza, novel insights into the mechanism of ligand binding and interaction between various inhibitors (zanamivir - ZMV, oseltamivir - OTV, 2,3-didehydro-2-deoxy-N-acetylneuraminic acid - DANA, peramivir - PMV) and neuraminidases (NA) are of vital importance for the structure-based design of new anti-viral drugs. To address this issue, three-dimensional models of H5N1-NA and N9-NA were generated by homology modeling. Traditional residues within the active site throughout the family of NA protein structures were found to be highly conserved in H5N1-NA. A subtle variation between lipophilic and hydrophilic environments in H5N1-NA with respect to N9-NA was observed, thus shedding more light on the high resistance of some H5N1 strains to various NA inhibitors. Based on these models, an ArgusLab4/AScore flexible docking study was performed. The conformational differences between OTV bound to H5N1-NA and OTV bound to N9-NA were structurally identified and quantified. A slight difference of less than 1 kcal mol-1 between the OTV-N9 and OTV-N1 binding free energies is in agreement with the experimentally predicted free energy difference. The conformational differences between ZMV and OTV bound to either H5N1-NA or N9-NA were structurally identified. The binding free energies of the ZMV complexes, being slightly higher than those of OTV, are not in agreement with what was previously proposed using homology modeling. The differences between ZMV and OTV are suggested to be ascribed to the presence/absence of Asn166 in the active cavity of ZMV/OTV in H5N1-NA, and to the presence/absence of Ser165 in the binding site of ZMV/OTV in N9-NA. The charge distribution was evaluated using the semi-empirical AM1 method. The trends of the AM1 charges of the ZMV and OTV side chains in the complexes deviate from those previously reported.

Exploring the binding site of the human muscarinic M3 receptor: Homology modeling and docking study

2007 ◽  
Vol 107 (8) ◽  
pp. 1794-1802 ◽  
Author(s):  
Liliana Ostopovici ◽  
Maria Mracec ◽  
Mircea Mracec ◽  
Ana Borota
Keyword(s):  
Homology Modeling ◽  
Binding Site ◽  
Docking Study ◽  
M3 Receptor

scholarly journals The Predicted TM10 Transmembrane Sequence of the Cardiac Ca2+Release Channel (Ryanodine Receptor) Is Crucial for Channel Activation and Gating

2003 ◽  
Vol 279 (5) ◽  
pp. 3635-3642 ◽  
Author(s):  
Ruiwu Wang ◽  
Jeff Bolstad ◽  
Huihui Kong ◽  
Lin Zhang ◽  
Cindy Brown ◽  
...  
Keyword(s):  
Ryanodine Receptor ◽  
Release Channel ◽  
Channel Activation ◽  
Transmembrane Sequence

Exploring the resistance-developing mutations on Ryanodine receptor in diamondback moth and binding mechanism of its activators using computational study

2017 ◽  
Vol 121 ◽  
pp. 59-72 ◽  
Author(s):  
Thangaraj Sindhu ◽  
Thiruvengadam Venkatesan ◽  
Gandhi R. Gracy ◽  
Sushil Kumar Jalali ◽  
Anil Rai
Keyword(s):  
Ryanodine Receptor ◽  
Computational Study ◽  
Diamondback Moth ◽  
Binding Mechanism
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