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• Singlet oxygen quenching rate constants have been measured for oxidizable amino acid tripeptides.
• Singlet oxygen quenching rate constants have been measured for model proteins.
• The SASA for each oxidizable amino acid within the proteins has been calculated.
• Reaction rate constants in proteins can be modelled by the sum of the SASA values.
• Improved results were obtained using molecular dynamics simulated trajectories.
The singlet oxygen quenching rate constants were measured for three model proteins, bovine serum albumin, β-lactoglobulin and lysozyme. The results were analyzed by comparing them with the corresponding singlet oxygen quenching rate constants for a series of tripeptides with the basic formula GlyAAGly where the central amino acid (AA) was the oxidizable amino acid, tryptophan, tyrosine, methionine and histidine. It was found that the reaction rate constant in proteins can be satisfactorily modelled by the sum of the individual contributions of the oxidizable AA residues corrected for the solvent accessible surface area (SASA) effects. The best results were obtained when the SASA of the AA residues were determined by averaging over molecular dynamics simulated trajectories of the proteins. The limits of this geometrical correction of the AA residue reactivity are also discussed.
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Journal: Journal of Photochemistry and Photobiology B: Biology - Volume 159, June 2016, Pages 106–110