Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling

Abstract

Malate dehydrogenase (MDH) and citrate synthase (CS) are two pacemaking enzymes involved in the tricarboxylic acid (TCA) cycle. Oxaloacetate (OAA) molecules are the intermediate substrates that are transferred from the MDH to CS to carry out sequential catalysis. It is known that, to achieve a high flux of intermediate transport and reduce the probability of substrate leaking, a MDH-CS metabolon forms to enhance the OAA substrate channeling. In this study, we aim to understand the OAA channeling within possible MDH-CS metabolons that have different structural orientations in their complexes. Three MDH-CS metabolons from native bovine, wild-type porcine, and recombinant sources, published in recent work, were selected to calculate OAA transfer efficiency by Brownian dynamics (BD) simulations and to study, through electrostatic potential calculations, a possible role of charges that drive the substrate channeling. Our results show that an electrostatic channel is formed in the metabolons of native bovine and recombinant porcine enzymes, which guides the oppositely charged OAA molecules passing through the channel and enhances the transfer efficiency. However, the channeling probability in a suggested wild-type porcine metabolon conformation is reduced due to an extended diffusion length between the MDH and CS active sites, implying that the corresponding arrangements of MDH and CS result in the decrease of electrostatic steering between substrates and protein surface and then reduce the substrate transfer efficiency from one active site to another.

Effects of dietary n-3HUFA on juvenile white shrimp, Litopenaeus vannamei: Growth, feed utilization, antioxidant enzymes activities and fatty acid compositions

“…This result suggested that n‐3HUFA at the proper level can promote immunity of juvenile L. vannamei . MDH is the key enzyme of tricarboxylic acid cycle (TCA), which can generate NADPH (Huang, Huber, Wang, Minteer, & McCammon, ; Zhou, Ji, Wang, & Wang, ). NADPH is an important coenzyme of fatty acid synthesis and carbon chain extension in vivo, which would directly affect the synthesis of fat and lipids.…”

Shaping Substrate Selectivity in a Broad-Spectrum Metallo-β-Lactamase

“…MD simulations allowed us to simulate different conformations to later study the accessibility of the substrate by Brownian dynamics (BD) simulations. BD simulations are powerful tools for studying the motion of molecules in solution and have been widely applied to the study of the encounter of an enzyme and its ligand (26). In an attempt to account for the impact of the insertion in the restricted activity profile of the chimera, we calculated the relative probability of association of a substrate (benzylpenicillin) by BD simulations, following the Zn2.…”

Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide pools

“…The thermodynamics and kinetics of molecular signaling in such compartments can differ considerably from analogous processes in bulk solutions or in vitro. Myriad factors contribute to these differences, including smaller compartment volumes that strongly amplify substrate concentration gradients [30, 72], the presence of ‘crowders’ comprising other small molecules, protein or nucleic acid that generally impede diffusion [28, 47, 73, 74], as well as rate enhancements typically exhibited for closely-apposed enzymes [29, 42, 45, 50, 75] or those adopting electrostatic fields complementary to a reacting species [38]. The relative contribution of these factors to coupled NDA activity in a given multi-cellular domain has not been examined previously and could ultimately determine the relative distribution of nucleotides.…”

“…These models provided strong quantitative insights into the efficiency of catalytic processes [46] and limits on efficiency gains for sequentially-coupled enzymes [45], but only implicitly account for geometrical and physiochemical factors. Explicit consideration of those factors for coupled enzyme processes generally utilize partial differential equations or particle-based solutions, which have afforded descriptions of how neighboring reactive enzymes [29, 47, 48], feedback inhibition, [29, 46], protein geometry and electrostatic interactions [19, 21, 49, 50] contribute to enzyme activity. Still, a systematic study of sequential reaction phenomena under physiological variations in solvent ionic strength and intracellular confinement is needed for probing how nucleotide pools are regulated by sequential NDAs in geometrically-constrained intercellular junctions.…”