engleski

Computational study of the substrate specificity of monoamine oxidase B

Histamine plays an important role in the human body and is involved in more than twenty different physiological processes. Due to histamine potent physiological activity, its degradation has to be carefully regulated to avoid adverse reactions. The major routes of histamine inactivation in mammals include monoamine oxidase B (MAO B) and diamine oxidase (DAO) enzymes. The fact that MAO B metabolizes only N-methylhistamine while DAO prefers histamine pinpoints their remarkable selectivity towards two compounds that differ only in one methyl group. The mechanism of enzyme catalysis and s pecificity are usually elucidated from the differences in mechanistic aspects of enzymatic reactions for each possible substrate, which provide unambiguous quantitative information about the thermodynamics and the kinetics of reaction pathways. Unfortunately, mechanistic studies are not always experimentally approachable. Therefore, we utilized a combination of molecular dynamics (MD) simulations, MM-PBSA binding free energy analysis, quantum mechanical cluster approach and empirical valence bond QM/MM calculations to address the substrate specificity and mechanism of MAO B catalysis. We have identified favourable hydrophobic interactions between methyl group of the N-methylhistamine substrate and the hydrophobic side chains of the enzyme binding site that keep substrate anchored and properly oriented for the enzymatic reaction. Since histamine is deprived of a methyl group, it cannot be properly anchored and rotates within the active site, which results in non-productive orientation for the reaction. Quantum-chemical mechanistic analysis revealed higher activation parameters for histamine relative to its N-methyl counterpart, thus aiding in rationalizing the mentioned selectivity. Inspection of the calculated free-energy profiles convincingly shows that MAO B selectivity for the N-methylhistamine over histamine is a result of two synergistic effects: lower activation barrier and more favourable reaction thermodynamics. Moreover, reaction pathway obtained from QM calculations is consistent with recently propose d hydride mechanism of MAO B mechanism of catalysis. EVB simulations of the rate-limiting hydride transfer step, including full enzyme structure and extensive thermal sampling, gave barriers of 16.2 and 17.9 kcal/mol for N-methylhistamine and histamine, respectively, thus putting our results in a firm agreement with experiments.

N-methylhistamine, histamine, MAO B, EVB

nije evidentirano