How does the protein environment optimize the thermodynamics of thiol sulfenylation? Insights from model systems to QM/MM calculations on human 2-Cys peroxiredoxin.
Protein thiol/sulfenic acid oxidation potentials provide a tool to select specific oxidation agents, but are experimentally difficult to obtain. Here, insights into the thiol sulfenylation thermodynamics are obtained from model calculations on small systems and from a quantum mechanics/molecular mechanics (QM/MM) analysis on human 2-Cys peroxiredoxin thioredoxin peroxidase B (Tpx-B). To study thiol sulfenylation in Tpx-B, our recently developed computational method to determine reduction potentials relatively compared to a reference system and based on reaction energies reduction potential from electronic energies is updated. Tpx-B forms a sulfenic acid (R-SO(-)) on one of its active site cysteines during reactive oxygen scavenging. The observed effect of the conserved active site residues is consistent with the observed hydrogen bond interactions in the QM/MM optimized Tpx-B structures and with free energy calculations on small model systems. The ligand effect could be linked to the complexation energies of ligand L with CH3S(-) and CH3SO(-). Compared to QM only calculations on Tpx-B's active site, the QM/MM calculations give an improved understanding of sulfenylation thermodynamics by showing that other residues from the protein environment other than the active site residues can play an important role.
a Department of Inorganic and Analytical Chemistry , Budapest University of Technology and Economics , H-1111 Budapest, Gellért tér 4 , Hungary.
Julianna
J
Oláh
Laura
L
van Bergen
Frank
F
De Proft
Goedele
G
Roos
D020134:Catalytic Domain; D003545:Cysteine / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D010084:Oxidation-Reduction; D054464:Peroxiredoxins / Q000737:chemistry*; D011789:Quantum Theory; D013816:Thermodynamics
C086065:PRDX2 protein, human; D054464:Peroxiredoxins; D003545:Cysteine
QM/MM; ligand effect; peroxiredoxin; redox chemistry; sulfenylation