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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:Predicting structural and energetic changes in Met-aromatic motifs on methionine oxidation to the sulfoxide and sulfone
Authors:Orabi EAEnglish AM
Link:https://pubmed.ncbi.nlm.nih.gov/30168822/
DOI:10.1039/c8cp03277g
Category:Phys Chem Chem Phys
PMID:30168822
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:

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 such oxidations, we modeled the chemistry and redox properties of MetOn-aromatic complexes in depth for comparison with our Met-aromatic models (E. A. Orabi and A. M. English, J. Phys. Chem. B, 2018, 122, 3760). We describe here ab initio quantum mechanical calculations at the MP2(full)/6-311++G(d,p) level of theory on complexes of MetOn (n = 1, 2; modeled by Me2SO and Me2SO2) with models of the side-chains of Phe (benzene, toluene), Trp (indole, 3-methylindole), Tyr (phenol, 4-methylphenol) and His (imidazole, 4-methylimidazole). Binding energies of the global minimum conformers (-3.4 to -11.9 kcal mol-1) indicate that the gas-phase Me2SOn-aromatics are 40-115% more stable than the Me2S-aromatics. Binding of S between the edge and face of the aromatic ring is favored in most complexes as it accommodates both robust s- and p-type H-bonding. Interactions involving the s-holes on the S atoms (s-holepar and s-holeNar/Oar), as well as Sp interactions in the sulfoxides, contribute to complex stability. Complexation modulates the ionization potential (IP) of the interacting fragments with the binding geometry dictating the center oxidized in the Me2SO-aromatics whereas the aromatic is oxidized in the Me2SO2 complexes because of the sulfone's high IP. Potentials of mean force reveal binding free energies of -0.2 to -0.7 kcal mol-1 in bulk water, which indicates that the Me2SOn-aromatics are up to 80% less stable than the corresponding aqueous Me2S-aromatics. Molecular dynamics simulations predict that Me2SOn preferentially interacts with the ring face and expose the dominance of p- vs. s-type H-bonding in the hydrated complexes as found for the Me2S-aromatics. Our modeling will inform how Met/MetOn-aromatic motifs are determinants of redox-induced changes in proteins.