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Thermodynamic Integration Networks and Their Application to Charge Transfer Reactions within the AauDyPI Fungal Peroxidase B
- Bauß, Anna, Langenmaier, Michael, Strittmatter, Eric, Plattner, Dietmar A., Koslowski, Thorsten
- The Journal of physical chemistry 2016 v.120 no.22 pp. 4937-4944
- Auricularia, computer simulation, fungi, least squares, molecular dynamics, peroxidase, thermodynamics
- We present a computer simulation study of the thermodynamics and kinetics of charge transfer reactions within the fungal peroxidase AauDyPI from Auricularia auriculae-judae. Driving forces and reorganization energies are obtained from a thermodynamic integration scheme based upon molecular dynamics simulations. To enhance the numerical accuracy, the free energies are analyzed within a least-squares scheme of a closely knit thermodynamic network. We identify Tyr147, Tyr229, and Trp105 as oxidative agents, and find Trp377 to be a long-lived reaction intermediate. The results are compared to recent experimental findings.