MD simulation studies on the effect of the temperature and protonation state on the imide-linked amino acid-based dendrimers

2018 ◽  
Vol 151 ◽  
pp. 124-131 ◽  
Author(s):  
Rahim Ghadari ◽  
Yousef Mohammadzadeh
Keyword(s):  
Amino Acid ◽  
Md Simulation ◽  
Simulation Studies ◽  
Protonation State

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

Combined DFT and MD simulation studies of protein stability on imidazolium–water (ImH+Wn) clusters with aromatic amino acids

2020 ◽  
Vol 44 (41) ◽  
pp. 17912-17923
Author(s):  
Kandhan Palanisamy ◽  
Muthuramalingam Prakash ◽  
Varatharaj Rajapandian
Keyword(s):  
Amino Acids ◽  
Protein Stability ◽  
Md Simulation ◽  
Protein Denaturation ◽  
Aromatic Amino Acids ◽  
Simulation Studies ◽  
Π Stacking ◽  
Hydrated Clusters

The hydrated clusters of protonated imidazole (ImH+) can induce protein denaturation through various kinds of monovalent interactions such as cation···π (stacking), N–H⋯π (T-shaped) and water-mediated O–H⋯O H-bonds.

Desorption of water from hydrophilic MCM-41 mesopores: positron annihilation, FTIR and MD simulation studies

2016 ◽  
Vol 29 (5) ◽  
pp. 055003 ◽  
Author(s):  
Priya Maheshwari ◽  
D Dutta ◽  
T Muthulakshmi ◽  
B Chakraborty ◽  
N Raje ◽  
...  
Keyword(s):  
Positron Annihilation ◽  
Md Simulation ◽  
Simulation Studies ◽  
Mcm 41

scholarly journals Chemical mechanism of D-amino acid oxidase from Rhodotorula gracilis: pH dependence of kinetic parameters

1998 ◽  
Vol 330 (1) ◽  
pp. 311-314 ◽  
Author(s):  
F. RAMÓN ◽  
M. P. CASTILLÓN ◽  
I. DE LA MATA ◽  
C. ACEBAL
Keyword(s):  
Amino Acid ◽  
Kinetic Parameters ◽  
Ph Dependence ◽  
Competitive Inhibitor ◽  
Chemical Mechanism ◽  
Acid Oxidase ◽  
Protonation State ◽  
Amino Acid Oxidase ◽  
Basic Group ◽  
Rhodotorula Gracilis

The variation of kinetic parameters of D-amino acid oxidase from Rhodotorula gracilis with pH was used to gain information about the chemical mechanism of the oxidation of D-amino acids catalysed by this flavoenzyme. D-Alanine was the substrate used. The pH dependence of Vmax and Vmax/Km for alanine as substrate showed that a group with a pK value of 6.26-7.95 (pK1) must be unprotonated and a group with a pK of 10.8-9.90 (pK2) must be protonated for activity. The lower pK value corresponded to a group on the enzyme involved in catalysis and whose protonation state was not important for binding. The higher pK value was assumed to be the amino group of the substrate. Profiles of pKi for D-aspartate as competitive inhibitor showed that binding is prevented when a group on the enzyme with a pK value of 8.4 becomes unprotonated; this basic group was not detected in Vmax/Km profiles suggesting its involvement in binding of the β-carboxylic group of the inhibitor.

scholarly journals SERS and MD simulation studies of a kinase inhibitor demonstrate the emergence of a potential drug discovery tool

2014 ◽  
Vol 111 (29) ◽  
pp. 10416-10421 ◽  
Author(s):  
D. Karthigeyan ◽  
S. Siddhanta ◽  
A. H. Kishore ◽  
S. S. R. R. Perumal ◽  
H. Agren ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Md Simulation ◽  
Kinase Inhibitor ◽  
Simulation Studies ◽  
Potential Drug
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