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- W2912884093 abstract "Molecular diffusion plays a fundamental role in a vast array of biological processes. Brownian dynamics is a computational simulation technique used to model the diffusional encounter of two molecules in solution. It can be used to estimate second-order rate constants, calculate reaction probabilities, and report reaction trajectories. Here, we applied such methods to explore two time-consuming diffusional processes: substrate binding to a protein and intermediate channeling among enzymes. The objective of the former study is to understand the details of molecular encounter that may play a role in the efficient operation of the 3′-5′-cyclic adenosine monophosphate (cAMP) signaling apparatus which is terminated by phosphodiesterases (PDEs). The latter study focuses on the mechanistic basis of oxaloacetate (OAA) channeling within possible malate dehydrogenase-citrate synthase (MDH-CS) metabolons that have different structural orientations in their complexes. We reported that the electrostatic potential of the active site from PDE and an electrostatic channel formed in the enzyme metabolons guide the oppositely-charged substrate molecules toward the target spots. This electrostatic steering promotes the capture of diffusing substrates and is of significance in sequestering intermediates released from a nearby binding site or in attracting more freely diffusing molecules to enhance the binding and transfer efficiency." @default.
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- W2912884093 date "2019-02-01" @default.
- W2912884093 modified "2023-10-16" @default.
- W2912884093 title "Brownian Dynamics Study of Camp Degradation in Phosphodiesterase and Enzyme Metabolon in the TCA Cycle" @default.
- W2912884093 doi "https://doi.org/10.1016/j.bpj.2018.11.1646" @default.
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