Keyword search (4,163 papers available)

"Orabi EA" Authored Publications:

Title Authors PubMed ID
1 Modeling CH sub 3 /sub SOH-aromatic complexes to probe cysteine sulfenic acid-aromatic interactions in proteins Orabi EA; English AM; 40994121
CHEMBIOCHEM
2 Modeling predicts facile release of nitrite but not nitric oxide from the thionitrate CH3SNO2 with relevance to nitroglycerin bioactivation Parmar V; Orabi EA; English AM; Peslherbe GH; 39738238
CERMM
3 Ammonium transporters achieve charge transfer by fragmenting their substrate Wang S; Orabi EA; Baday S; Bernèche S; Lamoureux G; 22631217
CERMM
4 New Megastigmane and Polyphenolic Components of Henna Leaves and Their Tumor-Specific Cytotoxicity on Human Oral Squamous Carcinoma Cell Lines Orabi MAA; Orabi EA; Awadh AAA; Alshahrani MM; Abdel-Wahab BA; Sakagami H; Hatano T; 38001804
CHEMBIOCHEM
5 Structural determination and anticholinesterase assay of C-glycosidic ellagitannins from Lawsonia inermis leaves: A study supported by DFT calculations and molecular docking Orabi MAA; Orabi EA; Abdel-Sattar ES; English AM; Hatano T; Elimam H; 36423882
CHEMBIOCHEM
6 Modeling Shows that Rotation about the Peroxide O-O Bond Assists Protein and Lipid Functional Groups in Discriminating between H2O2 and H2O Orabi EA; English AM; 33356279
CHEMBIOCHEM
7 Drude polarizable force field for cation-π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains Orabi EA; Davis RL; Lamoureux G; 31652004
CERMM
8 Computational insight into hydrogen persulfide and a new additive model for chemical and biological simulations Orabi EA; Peslherbe GH; 31297500
CHEMBIOCHEM
9 Expanding the range of binding energies and oxidizability of biologically relevant S-aromatic interactions: imidazolium and phenolate binding to sulfoxide and sulfone Orabi EA; English AM; 31214677
CHEMBIOCHEM
10 Predicting structural and energetic changes in Met-aromatic motifs on methionine oxidation to the sulfoxide and sulfone Orabi EA; English AM; 30168822
CHEMBIOCHEM

 

Title:Expanding the range of binding energies and oxidizability of biologically relevant S-aromatic interactions: imidazolium and phenolate binding to sulfoxide and sulfone
Authors:Orabi EAEnglish AM
Link:https://pubmed.ncbi.nlm.nih.gov/31214677/
DOI:10.1039/c9cp02332a
Publication:Physical chemistry chemical physics : PCCP
Keywords:
PMID:31214677 Category:Phys Chem Chem Phys Date Added:2019-06-20
Dept Affiliation: CHEMBIOCHEM
1 Center for Research in Molecular Modeling (CERMM), Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada. ann.english@concordia.ca.

Description:

Oxidation and protonation/deprotonation strongly impact intermolecular noncovalent interactions. For example, S-aromatic interactions are stabilized up to three-fold in the gas phase on oxidation of the sulfur ligand or protonation/deprotonation of the aromatic. To probe if such stabilizing effects are additive and to model interactions of oxidized methionine (MetOn) with protonated histidine and deprotonated tyrosine residues in proteins, we examined Me2SOn (n = 1, 2) binding to imidazolium, phenolate and their 4-methylated forms. Ab initio MP2(full)/6-311++G(d,p) gas-phase calculations reveal that the Me2SOn-imidazolium complexes adopt edge-on geometry with s-type (N/C-HarO) H-bonding and interaction energies of -17.2 to -31.1 kcal mol-1. The less stable (-13.8 to -21.0 kcal mol-1) Me2SOn-phenolates possess en-face geometry stabilized by p-type (C-Hpar) H-bonding. Comparing these energies with those reported for the Me2S-neutral aromatics affirms the additive effects of ligand protonation/deprotonation and oxidation on gas-phase stability. However, this is not the case in water although the aqueous complexes retain their preferred gas-phase s- and p-type H-bonded structures. Binding free energies (kcal mol-1) calculated from molecular dynamics simulations in bulk water (preceded by CHARMM36 force field calibration where necessary) reveal that Me2SO-imidazolium (-4.4) is more stable than Me2SO-phenolate (-2.4) but Me2SO2-imidazolium (-0.6) is less stable than Me2SO2-phenolate (-3.8). Vertical ionization potentials (IPV) calculated for the gas-phase complexes indicate that the Me2SOn-phenolates, but not the Me2SOn-imidazoles, are oxidizable under biological conditions. Charge transfer from the phenolate increases its IPV by ~20%, decreasing its susceptibility to oxidation. Overall, this work provides fundamental data to predict the behaviour of protein-based MetOn-aromatic-ion interactions.





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