A Theoretical Study of Benzhydroxamic Acid Binding Modes in Horseradish Peroxidase

1998 ◽  
Vol 120 (21) ◽  
pp. 5168-5178 ◽  
Author(s):  
Yan-Tyng Chang ◽  
Nigel C. Veitch ◽  
Gilda H. Loew
Keyword(s):  
Horseradish Peroxidase ◽  
Theoretical Study ◽  
Binding Modes ◽  
Benzhydroxamic Acid

THEORETICAL STUDY ON POTENCY AND SELECTIVITY OF NOVEL NONPEPTIDE INHIBITORS OF MATRIX METALLOPROTEINASES MMP-2 AND MMP-9

2009 ◽  
Vol 08 (03) ◽  
pp. 491-506 ◽  
Author(s):  
DAI-LIN LI ◽  
QING-CHUAN ZHENG ◽  
XUE-XUN FANG ◽  
HAI-TAO JI ◽  
JIN-GANG YANG ◽  
...  
Keyword(s):  
Inhibitory Activity ◽  
Density Functional ◽  
Theoretical Study ◽  
Zinc Binding ◽  
Hydroxyl Group ◽  
Interaction Energies ◽  
Binding Modes ◽  
Functional Theory ◽  
Total Interaction ◽  
Binding Affinity Calculations

Two novel matrix metalloproteinase (MMP) inhibitors, myricetin (m) and kaempferol (k), were found and the inhibitory activity is both in decreased order towards MMP-2 and MMP-9. To understand the mechanism during the processes when inhibitors bind to MMP-2 and MMP-9, molecular modeling, docking, and density functional theory (DFT) calculations were performed. The calculated results indicated that the hydroxyls on benzene ring of the inhibitors control the binding modes between inhibitors and MMPs, thus play an important role on the potency and selectivity. Besides coordinating with the N atoms of three His residues, Zn also interacts with a hydroxyl group of inhibitors by O – Zn distances of 2.66–2.78 Å in all of the docked complexes, so that the hydroxyl acts as a weak zinc binding group (ZBG). The DFT calculated results support the above analysis. The binding affinity calculations between inhibitors and MMPs present the total interaction energies in the m-MMP < k-MMP order and the solvation energy of myricetin is less than that of kaempferol, which reflect the experimental inhibitory activity.

Theoretical study of the binding profile of an allosteric modulator NS-1738 with a chimera structure of the α7 nicotinic acetylcholine receptor

2016 ◽  
Vol 18 (40) ◽  
pp. 28003-28009 ◽  
Author(s):  
Guanglin Kuang ◽  
Xu Wang ◽  
Christer Halldin ◽  
Agneta Nordberg ◽  
Bengt Långström ◽  
...  
Keyword(s):  
Acetylcholine Receptor ◽  
Nicotinic Acetylcholine Receptor ◽  
Theoretical Study ◽  
Allosteric Modulator ◽  
Simulation Methods ◽  
Binding Modes ◽  
Free Energies ◽  
Α7 Nicotinic Acetylcholine Receptor ◽  
Nicotinic Acetylcholine ◽  
Binding Free Energies

The binding modes and binding free energies of the allosteric modulator NS-1738 with a chimera structure of the α7 nicotinic acetylcholine receptor have been studied by molecular simulation methods.

Theoretical Study on the Catalytic Oxidation of p ‐Iodophenol by Horseradish Peroxidase in a Chemiluminescent System

2018 ◽  
Vol 3 (42) ◽  
pp. 11749-11757
Author(s):  
Jian Liu ◽  
Jiahui Lai ◽  
Liguo Qi ◽  
Xiumei Liu ◽  
Lili Zhang ◽  
...  
Keyword(s):  
Horseradish Peroxidase ◽  
Catalytic Oxidation ◽  
Theoretical Study

Combined Experimental and Theoretical Study on the Reactivity of Compounds I and II in Horseradish Peroxidase Biomimetics

2014 ◽  
Vol 20 (44) ◽  
pp. 14437-14450 ◽  
Author(s):  
Li Ji ◽  
Alicja Franke ◽  
Małgorzata Brindell ◽  
Maria Oszajca ◽  
Achim Zahl ◽  
...  
Keyword(s):  
Horseradish Peroxidase ◽  
Theoretical Study

scholarly journals Theoretical Study of Sequence Selectivity and Preferred Binding Mode of Psoralen with DNA

2007 ◽  
Vol 2007 ◽  
pp. 1-5 ◽  
Author(s):  
Patricia Saenz-Méndez ◽  
Rita C. Guedes ◽  
Daniel J. V. A. dos Santos ◽  
Leif A. Eriksson
Keyword(s):  
Molecular Dynamics ◽  
Theoretical Study ◽  
Binding Mode ◽  
Minor Groove Binding ◽  
Binding Modes ◽  
Groove Binding ◽  
Base Pairs ◽  
Sequence Selectivity ◽  
Molecular Dynamics Methods ◽  
Low Efficiency

Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand. We found that both binding modes are possible, explaining the low efficiency for monoadduct formation from intercalated ligands. A comparison between the interaction energy for intercalation between different base pairs suggests that the observed sequence selectivity is due to favorable intercalation in 5′-TpA in (AT)n sequences.

Haem-linked interactions in horseradish peroxidase revealed by spectroscopic analysis of the Phe-221→Met mutant

2001 ◽  
Vol 353 (2) ◽  
pp. 181-191 ◽  
Author(s):  
Barry D. HOWES ◽  
Nigel C. VEITCH ◽  
Andrew T. SMITH ◽  
Christopher G. WHITE ◽  
Giulietta SMULEVICH
Keyword(s):  
Horseradish Peroxidase ◽  
Enzyme Stability ◽  
Solvent Accessibility ◽  
Imidazole Ring ◽  
Axial Ligand ◽  
Wild Type ◽  
Gene Encoding ◽  
Alkaline Transition ◽  
In The Wild ◽  
Benzhydroxamic Acid

A gene encoding a Phe-221-to-Met substitution in the haem enzyme horseradish peroxidase has been constructed and expressed in Escherichia coli. In the wild-type enzyme the side chain of Phe-221 is tightly stacked against the imidazole ring of His-170, which provides the only axial ligand to the haem iron atom. The Phe-221 → Met enzyme is active, and forms characteristic complexes with typical peroxidase ligands (CO, cyanide, fluoride), and with benzhydroxamic acid. Significant differences between the mutant and wild-type enzymes can be detected spectroscopically. These include a change in the Fe(III) resting state of the enzyme to an unusual quantum mechanically mixed-spin haem species, a marked decrease in the pKa of the alkaline transition and a reduction in enzyme stability at alkaline pH for both Fe(III) and Fe(II) forms. The perturbation of the haem pocket in the mutant can be attributed to several factors, including the increased steric freedom and solvent accessibility of the His-170 ligand, as indicated by 1H-NMR data, and the loss of the πŐπ interaction between His-170 and Phe-221.

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