Keyword search (3,448 papers available)


The antibacterial activity of p-tert-butylcalix[6]arene and its effect on a membrane model: molecular dynamics and Langmuir film studies.

Author(s): Wrobel EC, de Lara LS, do Carmo TAS, Castellen P, Lazzarotto M, de Lázaro SR, Camilo A, Caseli L, Schmidt R, DeWolf CE, Wohnrath K

Phys Chem Chem Phys. 2020 Mar 03;: Authors: Wrobel EC, de Lara LS, do Carmo TAS, Castellen P, Lazzarotto M, de Lázaro SR, Camilo A, Caseli L, Schmidt R, DeWolf CE, Wohnrath K

Article GUID: 32124897

Computational insight into hydrogen persulfide and a new additive model for chemical and biological simulations

Author(s): Orabi EA; Peslherbe GH;

S-Sulfhydration of cysteine to the Cys-SSH persulfide is an oxidative post-translational modification that plays an important regulatory role in many physiological systems. Though hydrogen persulfide (H2S2) has recently been established as a signaling and c...

Article GUID: 31297500

Expanding the range of binding energies and oxidizability of biologically relevant S-aromatic interactions: imidazolium and phenolate binding to sulfoxide and sulfone

Author(s): Orabi EA; English AM;

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 arom...

Article GUID: 31214677

Predicting structural and energetic changes in Met-aromatic motifs on methionine oxidation to the sulfoxide and sulfone

Author(s): Orabi EA; English AM;

Noncovalent interactions between Met and aromatic residues define a common Met-aromatic motif in proteins. Met oxidation to MetOn (n = 1 sulfoxide, n = 2 sulfone) alters protein stability and function. To predict the chemical and physical consequences of su...

Article GUID: 30168822

Structural organization and phase behaviour of meta-substituted dioctadecylaminobenzoquinones at the air/water interface.

Author(s): Behyan S, Gritzalis D, Schmidt R, Kebede E, Cuccia LA, DeWolf C

Phys Chem Chem Phys. 2019 Jan 30;21(5):2345-2350 Authors: Behyan S, Gritzalis D, Schmidt R, Kebede E, Cuccia LA, DeWolf C

Article GUID: 30657501


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
Category:Phys Chem Chem Phys
PMID:31214677
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.