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Dissecting Methionine Oxidation by Hydrogen Peroxide in Proteins: Thermodynamics, Kinetics, and Susceptibility Descriptors.
J Chem Inf Model
January 2025
Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy.
The oxidation of Met residues in proteins is a complex process, where protein-specific structural and dynamical features play a relevant role in determining the reaction kinetics. Aiming to a full-side perspective, we report here a comprehensive characterization of Met oxidation kinetics by hydrogen peroxide in a leptin protein case study. To do that, we estimated the reaction-free energy profile of the Met oxidation via a QM/MM approach, while the kinetics of the formation of the reactive species were calculated using classical molecular dynamics (MD) simulations.
View Article and Find Full Text PDFLeveraging Cryptic Ligand Envelopes through Enhanced Molecular Simulations.
J Phys Chem Lett
January 2025
Molecular Ocean Lab, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Carrer de Jordi Girona 18-26, 08034 Barcelona, Spain.
Protein-bound ligands can adopt a range of different conformations, collectively defining a ligand envelope that has proven to be crucial for the design of potent and selective drugs. Yet, the cryptic nature of this ligand envelope makes it difficult to visualize, characterize, and ultimately exploit for drug design. Using enhanced molecular dynamics simulations, here, we provide a general framework to reconstruct the cryptic ligand envelope that is dynamically accessible by protein-bound small molecules in solution.
View Article and Find Full Text PDFPrednisolone pharmacokinetics in dogs with protein-losing enteropathy.
J Vet Intern Med
December 2024
Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA.
Background: It is unknown if glucocorticoid malabsorption contributes to the approximate 50% treatment failure rate in dogs with protein-losing enteropathy (PLE).
Objective: To compare pharmacokinetics (PK) of orally administered prednisolone in dogs with PLE vs healthy controls.
Animals: Fourteen dogs with well-characterized PLE and 7 control dogs.
Water Encapsulated [(FeSe)Se] Clusters in [Na(HO)][FeSe].
Inorg Chem
December 2024
Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 9-13 (D), 81377 München, Germany.
[Na(HO)][FeSe] was synthesized using hydrothermal methods and characterized by single-crystal X-ray diffraction, Fe Mössbauer spectroscopy, magnetization, and muon spin resonance (μSR) measurements. The cubic crystal structure (space group 23, = 11.785 Å, = 2) contains heterocubane-type clusters with symmetry.
View Article and Find Full Text PDFSynthesis and structural characterization of the heavy tricysteinylpnictines, models of protein-bound As(III), Sb(III), and Bi(III).
Dalton Trans
December 2024
Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, USA.
The heavier group 15 elements As, Sb, and Bi are more restricted in their biochemistry than the nearly ubiquitous lighter congeners N and P, but organisms do encounter compounds of these elements as environmental toxins, starting materials for secondary metabolite biosynthesis, substrates for primary metabolism, or exogenously applied medicines. Under many physiological conditions, these compounds are transformed into pnictogen(III) species, the soft Lewis acidic character of which leads them to interact strongly with biologically relevant soft Lewis bases such as small-molecule thiols or cysteine residues of proteins and peptides. The archetypal complexes As(Cys), Sb(Cys), and Bi(Cys) have been studied in the past but a lack of detailed information about their molecular structures has hampered the analysis of protein structures featuring As(III), Sb(III), and Bi(III) bound to cysteine thiolate residues.
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