AQM /MM simulation study of transamination reaction at the active site of aspartate aminotransferase: Free energy landscape and proton transfer pathways
| Autor: | Amalendu Chandra, Arindam Bankura, Sindrila Dutta Banik |
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| Rok vydání: | 2020 |
| Předmět: |
Models
Molecular Conformational change Protein Conformation Stereochemistry Transamination Imine 010402 general chemistry 01 natural sciences Catalysis QM/MM Residue (chemistry) chemistry.chemical_compound Catalytic Domain 0103 physical sciences Amino Acid Sequence Aspartate Aminotransferases Schiff Bases chemistry.chemical_classification Aspartic Acid Schiff base 010304 chemical physics biology Active site General Chemistry Rate-determining step 0104 chemical sciences Computational Mathematics chemistry Pyridoxal Phosphate biology.protein Thermodynamics Imines Protons |
| Zdroj: | Journal of Computational Chemistry. 41:2684-2694 |
| ISSN: | 1096-987X 0192-8651 |
| DOI: | 10.1002/jcc.26422 |
| Popis: | Transaminase is a key enzyme for amino acid metabolism, which reversibly catalyzes the transamination reaction with the help of PLP (pyridoxal 5' -phosphate) as its cofactor. Here we have investigated the mechanism and free energy landscape of the transamination reaction involving the aspartate transaminase (AspTase) enzyme and aspartate-PLP (Asp-PLP) complex using QM/MM simulation and metadynamics methods. The reaction is found to follow a stepwise mechanism where the active site residue Lys258 acts as a base to shuttle a proton from α-carbon (CA) to imine carbon (C4A) of the PLP-Asp Schiff base. In the first step, the Lys258 abstracts the CA proton of the substrate leading to the formation of a carbanionic intermediate which is followed by the reprotonation of the Asp-PLP Schiff base at C4A atom by Lys258. It is found that the free energy barrier for the proton abstraction by Lys258 and that for the reprotonation are 17.85 and 3.57 kcal/mol, respectively. The carbanionic intermediate is 7.14 kcal/mol higher in energy than the reactant. Hence, the first step acts as the rate limiting step. The present calculations also show that the Lys258 residue undergoes a conformational change after the first step of transamination reaction and becomes proximal to C4A atom of the Asp-PLP Schiff base to favor the second step. The active site residues Tyr70* and Gly38 anchor the Lys258 in proper position and orientation during the first step of the reaction and stabilize the positive charge over Lys258 generated at the intermediate step. |
| Databáze: | OpenAIRE |
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