scholarly journals α-Helix in Cystathionine β-Synthase Enzyme Acts as Electron Reservoir

2021 ◽  
Author(s):  
Aashish Bhatt ◽  
Aritra Mukhopadhyaya ◽  
Md. Ehesan Ali
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Real Space ◽  
Hydrogen Bond Network ◽  
Catalytic Center ◽  
Density Analysis ◽  
Density Delocalization ◽  
Bond Network ◽  
Α Helix ◽  
Determining Factor

The modulation of electron density at the Pyridoxal 5-phosphate (PLP) catalytic center, due to charge transfer across the α-Helix-PLP interface, is the determining factor for the enzymatic activities in the human Cystathionine β-Synthase (hCBS) enzyme. Applying density-based first-principle calculations in conjunction with the real space density analysis, we investigated the charge density delocalization across the entire Heme-α-Helix-PLP electron communication channels. The hydrogen bonds at the interfaces, i.e. Heme-α-Helix and α-Helix-PLP interfaces, are found to play the pivotal role in bi-directional electron transfer towards the α-Helix. Moreover, the internal hydrogen bonds of α-Helix that are crucial for its secondary structure also actively participate in the electron redistribution through the structured hydrogen bond network. α-Helix is found to accumulate the electron density at the ground state from both the cofactors and behaves as an electron reservoir for catalytic reaction at the electrophilic center of PLP.

scholarly journals Docking of Platinum Compounds on Cube Rhombellane Functionalized Homeomorphs

Symmetry ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 749
Author(s):  
Beata Szefler ◽  
Przemysław Czeleń
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Binding Affinity ◽  
Fullerene C60 ◽  
C60 Fullerene ◽  
Binding Affinities ◽  
Hydrogen Bond Network ◽  
Platinum Compounds ◽  
Anti Cancer ◽  
Bond Network

Platinum compounds are anti-cancer drugs and can bind to canonical purine bases, mainly guanine, found within double helical DNA. Platinum compounds can be transferred directly to pathologically altered sites in a specific and site-oriented manner by nanocarriers as potential nanocarriers for carboplatin. Two types of nanostructures were used as potential nanocarriers for carboplatin, the first were functionalized C60 fullerene molecules and the second were rhombellanes. The analyzed nanostructures show considerable symmetry, which affects the affinity of the studied nanocarriers and ligands. Thus symmetry of nanostructures affects the distribution of binding groups on their surface. After the docking procedure, analysis of structural properties revealed many interesting features. In all described cases, binding affinities of complexes of platinum compounds with functionalized fullerene C60 are higher compared with affinities of complexes of platinum compounds with rhombellane structures. All platinum compounds easily create complexes with functionalized fullerene C60, CID_16156307, and at the same time show the highest binding affinity. The binding affinities of lobaplatin and heptaplatin are higher compared with oxaliplatin and nedaplatin. The high value of binding affinity and equilibrium constant K is correlated with creation of strong and medium hydrogen bonds or is correlated with forming a hydrogen bond network. The performed investigations enabled finding nanocarriers for lobaplatin, heptaplatin, oxaliplatin and nedaplatin molecules.

Insights into the binding of dorzagliatin with glucokinase: A molecular dynamics simulation

2020 ◽  
Vol 19 (07) ◽  
pp. 2050027
Author(s):  
Wei Liu ◽  
Chenhui Yao ◽  
Qian Shang ◽  
Yuqiang Liu ◽  
Changying Liu ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Metabolic Diseases ◽  
Tight Binding ◽  
Simulation Method ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Phase Iii ◽  
Hydrogen Bond Network ◽  
Phase Iii Clinical Trial ◽  
Bond Network

Human glucokinase (GK) is a potentially attractive target for diabetes, playing a prominent role in the control of glucose homeostasis. Dorzagliatin is the first GK activator (GKA) to enter phase III clinical trial. In this study, the possible binding mode of dorzagliatin with GK was investigated via the molecular simulation method. Two other systems in the absence of dorzagliatin and glucose were also studied to disclose the roles of dorzagliatin and glucose. The outcomes revealed that dorzagliatin can create the characteristic hydrogen bonds of GKA with Arg63, and Arg63 can form hydrogen bonds with nearby residues, making a tight binding hydrogen bond network around dorzagliatin. The presence of dorzagliatin can stabilize glucokinase for a period of time, and the binding of glucose may prevent the GK conformational change to a certain extent. Our results may be beneficial to mechanism understanding of GKA, and will be useful in design of novel GKAs for treating metabolic diseases.

New representatives of solid acid conductors: CsmHn((HSO4),(H2PO4))m+n

2014 ◽  
Vol 70 (a1) ◽  
pp. C65-C65 ◽  
Author(s):  
Irina Makarova ◽  
Vadim Grebenev ◽  
Elena Dmitricheva ◽  
Vladimir Komornikov
Keyword(s):  
Hydrogen Bond ◽  
Phase Transitions ◽  
High Temperature ◽  
Hydrogen Bonds ◽  
Functional Materials ◽  
Proton Conductors ◽  
Hydrogen Bond Network ◽  
Outward Diffusion ◽  
Bond Network ◽  
Superprotonic Phase

Crystals - superprotonics are extensively studied with the goal of elucidating the influence of the hydrogen subsystem on the physicochemical properties and designing new functional materials. As opposed to other hydrogen-containing compounds, phase transitions in these crystals are accompanied by a hydrogen-bond network rearrangement, resulting in radical changes of their properties, in particular, in the appearance of proton conductivity about 10–1 Ω–1 cm–1. These crystals are unique in the class of proton conductors, since the superprotonic conductivity is related to the structural features of these compounds rather than to the presence of doping additives. The occurrence of high superprotonic conductivity in the Me3H(XO4)2 (Me = K, Rb, Cs, NH4; X = S, Se, P, As) crystals is associated with the formation of a qualitatively new and dynamically disordered hydrogen-bond system [1]. In K9H7(SO4)8·N2O crystals, the only known representative of the Me9H7(XO4)8·xN2O family, the occurrence of high conductivity is associated with the outward diffusion of water molecules, the hydrogen-bond network rearrangement, and the formation of channels for the possible motion of K+ ions [2]. The hydrogen-bond rearrangement and the hindered back diffusion of water to the crystal bulk stabilize the high-temperature crystal structure and ensure its supercooling to low temperatures. The new crystals of Cs3(HSO4)2(H2PO4), Cs4(HSO4)3(H2PO4) and Cs6H(HSO4)3(H2PO4)4 were grown up in the CsHSO4–CsH2PO4-H2O system - enough big, with good optic quality [3]. The thermal and optical properties of crystals as well as their conductivity have been investigated in the temperature range 295 – 445 K. It was observed superprotonic phase transitions at 409, 411 and 365 K correspondingly. The distinction in the properties of Cs3(HSO4)2(H2PO4) and Cs4(HSO4)3(H2PO4) (sp. gr. C2/c at 295 K) is related to differences in nets of hydrogen bonds formed between different-occupied XO4 tetrahedra. Cs6H(HSO4)3(H2PO4)4 srystals (sp. gr. I-43d at 295 K) have the net of hydrogen bonds which is completely different. After cooling the high-temperature superprotonic phase preserves long enough without essential decrease in conductivity. This study was supported by the Russian Foundation for Basic Research (projects 13-03-12216 and 13-02-92693).

Study of the Hydrogen Bond Network in sub-and supercritical Water by Molecular Dynamics Simulations

2001 ◽  
Vol 56 (8) ◽  
pp. 579-584 ◽  
Author(s):  
S. Krishtal ◽  
M. Kiselev ◽  
Y. Puhovski ◽  
T. Kerdcharoen ◽  
S. Hannongbua ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Critical Point ◽  
Supercritical Water ◽  
Diffusion Coefficients ◽  
Md Simulations ◽  
Saturation Curve ◽  
Hydrogen Bond Network ◽  
Self Diffusion ◽  
Bond Network ◽  
Dynamics Simulations

Abstract For 12 points along the tangent to the saturation curve at the critical point the temperature dependen­cies of the heights of the first maximum in the 0 -0 RDF, the average number of hydrogen bonds, and the self-diffusion coefficients have been calculated from MD simulations. The curves of these three properties show an inflection near the critical point. To improve the understanding of these changes in going from subcritical to supercritical water the librational spectra and the change in the fractions of wa­ter molecules with a given number of hydrogen bonds as a function of temperature have been derived from the simulations, additionally.

scholarly journals Crystal structure of (±)-[trans-cyclohexane-1,2-diylbis(azanediyl)]diphosphonium dibromide dichloromethane disolvate

2016 ◽  
Vol 72 (4) ◽  
pp. 559-562
Author(s):  
Aurora Rodríguez Álvarez ◽  
Hugo Tlahuext ◽  
Jean-Michel Grévy
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Rotation Axis ◽  
Chair Conformation ◽  
Chain Structure ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
A Chain

The cation of the title solvated salt, C42H42N2P22+·2Br−·2CH2Cl2, lies on a crystallographic twofold rotation axis. The 1,2-diaminocyclohexane fragment has a chair conformation with two N atoms in atransoidconformation [N—C—C—N = 163.4 (2)°]. In the crystal, the cations are linked to the anions by N—H...Br and C—H...Br hydrogen bonds, forming a chain structure along thecaxis. The dichloromethane molecule takes part in the hydrogen-bond network through C—H...π and C—H...Br interactions.

Disentangling steric and electronic factors in monomeric bis(2-bromo-4-chloro-6-{[(2-hydroxyethyl)imino]methyl}phenolato-κ2N,O)copper(II)

2014 ◽  
Vol 70 (7) ◽  
pp. 659-661 ◽  
Author(s):  
Piotr Zabierowski ◽  
Janusz Szklarzewicz ◽  
Wojciech Nitek
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Substituent Effects ◽  
Two Dimensional ◽  
Hydrogen Bond Network ◽  
Intermolecular Hydrogen Bonds ◽  
Square Planar ◽  
Bond Network ◽  
Hydroxyethyl Group

The title compound, [Cu(C9H8BrClNO2)2], is a square-planar complex. The potentially tridentate dibasic 2-bromo-4-chloro-6-{[(2-hydroxyethyl)imino]methyl}phenolate ligand coordinates in atrans-bis fashion to the CuIIcentreviathe imine N and phenolate O atoms. The CuIIatom lies on the centre of inversion of the molecule. The potentially coordinating hydroxyethyl group remains protonated and uncoordinated, taking part in intermolecular hydrogen bonds with vicinal groups, leading to the formation of a two-dimensional hydrogen-bond network with sheets parallel to the (10\overline{1}) plane. Substituent effects on the crystal packing and coordination modes of the ligand are discussed.

Competition between hydrogen bonds and van der Waals forces in intermolecular structure formation of protonated branched-chain alcohol clusters

2018 ◽  
Vol 20 (39) ◽  
pp. 25482-25494 ◽  
Author(s):  
Natsuko Sugawara ◽  
Po-Jen Hsu ◽  
Asuka Fujii ◽  
Jer-Lai Kuo
Keyword(s):  
Hydrogen Bond ◽  
Ir Spectroscopy ◽  
Hydrogen Bonds ◽  
Temperature Dependence ◽  
Structure Formation ◽  
Hydrogen Bond Network ◽  
Chain Alcohol ◽  
Bond Network ◽  
Dft Simulations ◽  
Branched Chain

Temperature dependence of hydrogen bond network structures of protonated bulky alcohol clusters is explored by IR spectroscopy and DFT simulations.

QTAIM Study of an α-Helix Hydrogen Bond Network

2009 ◽  
Vol 113 (31) ◽  
pp. 10957-10964 ◽  
Author(s):  
Shenna M. LaPointe ◽  
Sarah Farrag ◽  
Hugo J. Bohórquez ◽  
Russell J. Boyd
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Α Helix
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