Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071 Moscow, Russia.
Department of Chemistry, Interdisciplinary Scientific and Educational School of Moscow University «Brain, Cognitive Systems, Artificial Intelligence», Lomonosov Moscow State University, 119991 Moscow, Russia.
Molecules. 2022 Oct 18;27(20):7031. doi: 10.3390/molecules27207031.
The influence of the active site flexibility on the efficiency of catalytic reaction is studied by taking two members of metallo-β-lactamases, L1 and NDM-1, with the same substrate, imipenem. Active sites of these proteins are covered by L10 loops, and differences in their amino acid compositions affect their rigidity. A more flexible loop in the NDM-1 brings additional flexibility to the active site in the ES complex. This is pronounced in wider distributions of key interatomic distances, such as the distance of the nucleophilic attack, coordination bond lengths, and covalent bond lengths in the substrate. Substrate activation, quantified by Fukui electrophilicity index of the carbonyl carbon atom of the substrate, is also sensitive to the active site flexibility. In the tighter and more rigid L1 enzyme-substrate complex, the substrate is activated more efficiently. In the NDM-1 containing system, only one third of the states are activated to the same extent. Other fractions demonstrate lower substrate activation. Efficiency of the substrate activation and rigidity of the ES complex influence the following chemical reaction. In the more rigid L1-containing system, the reaction barrier of the first step of the reaction is lower, and the first intermediate is more stabilized compared to the NDM-1 containing system.
通过对具有相同底物亚胺培南的两种金属β-内酰胺酶 L1 和 NDM-1 的研究，考察了活性部位柔性对催化反应效率的影响。这些蛋白质的活性部位被 L10 环覆盖，其氨基酸组成的差异影响其刚性。NDM-1 中更灵活的环为 ES 复合物中的活性部位带来了额外的灵活性。这在关键原子间距离的分布更广泛时表现得更为明显，例如亲核进攻的距离、配体键长度和底物中的共价键长度。通过底物羰基碳原子的 Fukui 亲电指数来量化的底物激活对活性部位的柔性也很敏感。在更紧密和刚性的 L1 酶-底物复合物中，底物的激活效率更高。在含有 NDM-1 的体系中，只有三分之一的状态被激活到相同程度。其他分数表现出较低的底物激活。底物激活的效率和 ES 复合物的刚性影响后续的化学反应。在更刚性的含有 L1 的体系中，反应的第一步的反应势垒较低，与含有 NDM-1 的体系相比，第一个中间体更稳定。
