Examining the Mechanism of Phosphite Dehydrogenase with Quantum Mechanical/Molecular Mechanical Free Energy Simulations

Assessing the effect of a series of mutations on the dynamic behavior of phosphite dehydrogenase using molecular docking, molecular dynamics and quantum mechanics/molecular mechanics simulations

Discovered in Pseudomonas stutzeri, phosphite dehydrogenase (PTDH) is an enzyme that catalyzes the oxidation of phosphite to phosphate while simultaneously reducing NAD⁺ to NADH. Despite several investigations into the mechanism of reaction and cofactor regeneration, only a few studies have focused on improving the activity and stability of PTDH. In this study, we combine molecular docking, molecular dynamics (MD) simulation, and Quantum Mechanics/Molecular Mechanics (QM/MM) to identify the impact of 30 mutations on the activity and stability of PTDH. Molecular docking results suggest that E266Q, K76A, K76M, K76R, K76C, and R237K can act on the NAD⁺ binding site through relatively weak bond development due to their high free binding energy. Moreover, Mulliken population analysis and potential energy barrier indicate that T101A, E175A, E175A/A176R, A176R, and E266Q act on phosphite oxidation. The mutants M53N, M53A, K76R, D79N, D79A, T101A, W134A, W134F Y139F, A146S, E175A, F198I, F198M, E266Q, H292K, S295A, R301K, and R301A were found to act on the structural dynamic of PTDH. The remaining mutants cause the loss of the nitrogen atom of R237 and H292, respectively, inactivating the enzyme. This study provides specific explanations of how mutations affect weak interactions of PTDH. The results should allow researchers to conduct experimental studies to improve PTDH activity and stability.Communicated by Ramaswamy H. Sarma.

Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme

Flavin coenzymes are universally found in biological redox reactions. DNA photolyases, with their flavin chromophore (FAD), utilize blue light for DNA repair and photoreduction. The latter process involves two single-electron transfers to FAD with an intermittent protonation step to prime the enzyme active for DNA repair. Here we use time-resolved serial femtosecond X-ray crystallography to describe how light-driven electron transfers trigger subsequent nanosecond-to-microsecond entanglement between FAD and its Asn/Arg-Asp redox sensor triad. We found that this key feature within the photolyase-cryptochrome family regulates FAD re-hybridization and protonation. After first electron transfer, the FAD^•- isoalloxazine ring twists strongly when the arginine closes in to stabilize the negative charge. Subsequent breakage of the arginine-aspartate salt bridge allows proton transfer from arginine to FAD^•-. Our molecular videos demonstrate how the protein environment of redox cofactors organizes multiple electron/proton transfer events in an ordered fashion, which could be applicable to other redox systems such as photosynthesis.