Unraveling the Molecular Determinants of Catalytic Efficiency and Substrate Specificity in l-Amino Acid Decarboxylases

l-Tryptophan decarboxylase (TDC) and l-3,4-dihydroxyphenylalanine decarboxylase (DDC) catalyze the decarboxylation of l-tryptophan, 5-hydroxytryptophan, and l-3,4-dihydroxyphenylalanine. In this study, we analyzed the amino acid compositions of the substrate-binding pockets of TDC from Catharanthus roseus (CrTDC) and DDC from Sus scrofa (SsDDC), explored the specificity of key amino acids within these pockets, and elucidated mechanisms influencing substrate selectivity and catalytic activity in both enzymes, using whole-cell catalysis to screen mutants and determine enzymatic kinetic parameters. The results demonstrated that residues Ala-103 and Val-122 in CrTDC, along with their corresponding sites Thr-82 and Ile-101 in SsDDC, significantly influence substrate selectivity and catalytic efficiency. Molecular dynamics simulations revealed that substrate selectivity and catalytic efficiency depends on the nucleophilic attack distance between the substrate's amino group and the C4' of pyridoxal 5'-phosphate. This study elucidates the catalytic mechanisms and structural bases of TDC and DDC, guiding enhancements in the related aromatic monoamine biosynthesis.

Molecular dynamics simulation of the interaction between monofluoronitrobenzene and Ti electrode

In the process of degradation of aqueous fluoro-nitrobenzene (FNB) solution by titanium (Ti) electrode, the interaction between aqueous FNB solution and Ti electrode has an important impact on the performance and catalytic performance of electrode materials. The interaction involves complex physical, chemical and physical chemical processes, however, the mechanism of action is still unclear. In this study, Materials Studio software was used to design and construct molecular models of the interactions between aqueous FNB (p-, m-, o-FNB) solutions and Ti electrode, and molecular dynamics (MD) simulation was carried out in the absence of applied electric field and external electric field of 0.02 V/Å, respectively. Density functional theory (DFT) method was used to calculate the frontier molecular orbitals of three FNB molecules. Based on the calculation and analysis of the interaction energy (ΔE), diffusion coefficient (D) and radial distribution function (RDF), the interaction mechanism was discussed. It provides a theoretical basis for further research and development of Ti electrode degradation of fluorine compounds. The results showed that the order of ΔE between the three different aqueous FNB solutions and Ti surface is m-FNB > p-FNB > o-FNB when there is no external electric field. Under electric field of 0.02 V/Å, the order is p-FNB > m-FNB > o-FNB. The substitution position of F has an important effect on the HOMO of the nitro group and the LUMO of C-H in the three FNB molecules, and also affects the chemical reaction activity. In the model system, the diffusivity of different FNB solutions with electric field is less than that without electric field. The presence of an external electric field makes the diffusion of water and FNB molecules more orderly. The analysis results of RDF show that the bonding interactions between different FNB molecules and Ti surface is not much different before 3.5 Å, and all of them are weak. At about 8 Å, FNB molecule forms a non-bond with Ti electrode. ΔE, D and RDF of the model system can be changed by applying a certain external electric field, and the results are in better agreement with the experimental results.