Conformational H-bonding modulation of the iron active site cysteine ligand of superoxide reductase: absorption and resonance Raman studies

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

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Alkylation of Escherichia coli Thioredoxin by S-(2-Chloroethyl)glutathione and Identification of the Adduct on the Active Site Cysteine-32 by Mass Spectrometry

Chemical Research in Toxicology ◽

10.1021/tx00049a006 ◽

1995 ◽

Vol 8 (7) ◽

pp. 934-941 ◽

Cited By ~ 8

Author(s):

John C. L. Erve ◽

Elisabeth Barofsky ◽

Douglas F. Barofsky ◽

Max L. Deinzer ◽

Donald J. Reed

Keyword(s):

Mass Spectrometry ◽

Escherichia Coli ◽

Active Site ◽

Active Site Cysteine

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Redox regulation of Ca2+/calmodulin-dependent protein kinase IV via oxidation of its active-site cysteine residue

Free Radical Biology and Medicine ◽

10.1016/j.freeradbiomed.2018.10.440 ◽

2019 ◽

Vol 130 ◽

pp. 99-106 ◽

Cited By ~ 5

Author(s):

Tsuyoshi Takata ◽

Jun Kimura ◽

Hideshi Ihara ◽

Naoya Hatano ◽

Yukihiro Tsuchiya ◽

...

Keyword(s):

Protein Kinase ◽

Active Site ◽

Redox Regulation ◽

Cysteine Residue ◽

Dependent Protein Kinase ◽

Active Site Cysteine ◽

Dependent Protein ◽

Active Site Cysteine Residue

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Redshift or Adduct Stabilization—A Computational Study of Hydrogen Bonding in Adducts of Protonated Carboxylic Acids

European Journal of Mass Spectrometry ◽

10.1255/ejms.970 ◽

2009 ◽

Vol 15 (2) ◽

pp. 239-248 ◽

Cited By ~ 4

Author(s):

Solveig Gaarn Olesen ◽

Steen Hammerum

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Bond Strength ◽

Bond Length ◽

Carboxylic Acids ◽

Computational Study ◽

Proton Affinities ◽

Oh Groups ◽

Hydrogen Bond Strength ◽

Length Changes

It is generally expected that the hydrogen bond strength in a D–H•••A adduct is predicted by the difference between the proton affinities (Δ PA) of D and A, measured by the adduct stabilization, and demonstrated by the infrared (IR) redshift of the D–H bond stretching vibrational frequency. These criteria do not always yield consistent predictions, as illustrated by the hydrogen bonds formed by the E and Z OH groups of protonated carboxylic acids. The Δ PA and the stabilization of a series of hydrogen bonded adducts indicate that the E OH group forms the stronger hydrogen bonds, whereas the bond length changes and the redshift favor the Z OH group, matching the results of NBO and AIM calculations. This reflects that the thermochemistry of adduct formation is not a good measure of the hydrogen bond strength in charged adducts, and that the ionic interactions in the E and Z adducts of protonated carboxylic acids are different. The OH bond length and IR redshift afford the better measure of hydrogen bond strength.

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