Mechanisms of Electron Transfer Rate Modulations in Cytochrome P450 BM3

Instantaneous Marcus theory for photoinduced charge transfer dynamics in multistate harmonic model systems

Modeling the dynamics of photoinduced charge transfer (CT) in condensed phases presents challenges due to complicated many-body interactions and the quantum nature of electronic transitions. While traditional Marcus theory is a robust method for calculating CT rate constants between electronic states, it cannot account for the nonequilibrium effects arising from the initial nuclear state preparation. In this study, we employ the instantaneous Marcus theory (IMT) to simulate photoinduced CT dynamics. IMT incorporates nonequilibrium structural relaxation following a vertical photoexcitation from the equilibrated ground state, yielding a time-dependent rate coefficient. The multistate harmonic (MSH) model Hamiltonian characterizes an organic photovoltaic carotenoid-porphyrin-fullerene triad dissolved in explicit tetrahydrofuran solvent, constructed by mapping all-atom inputs from molecular dynamics simulations. Our calculations reveal that the electronic population dynamics of the MSH models obtained with IMT agree with the more accurate quantum-mechanical nonequilibrium Fermi's golden rule. This alignment suggests that IMT provides a practical approach to understanding nonadiabatic CT dynamics in condensed-phase systems.

Molecular recognition of ITIM/ITSM domains with SHP2 and their allosteric effect

Src homology 2-domain-containing tyrosine phosphatase 2 (SHP2) is a non-receptor protein tyrosine phosphatase that is widely expressed in a variety of cells and regulates the immune response of T cells through the PD-1 pathway. However, the activation mechanism and allosteric effects of SHP2 remain unclear, hindering the development of small molecule inhibitors. For the first time, in this study, the complex structure formed by the intact PD-1 tail and SHP2 was modeled. The molecular recognition and conformational changes of inactive/active SHP2 versus ITIM/ITSM were compared based on prolonged MD simulations. The relative flexibility of the two SH2 domains during MD simulations contributes to the recruitment of ITIM/ITSM and supports the subsequent conformational change of SHP2. The binding free energy calculation shows that inactive SHP2 has a higher affinity for ITIM/ITSM than active SHP2, mainly because the former's N-SH2 refers to the α-state. In addition, a significant decrease in the contribution to the binding energy of certain residues (e.g., R32, S34, K35, T42, and K55) of conformationally transformed SHP2 contributes to the above result. These detailed changes during conformational transition will provide theoretical guidance for the molecular design of subsequent novel anticancer drugs.