Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
Molecules. 2018 Oct 16;23(10):2652. doi: 10.3390/molecules23102652.
HlyB functions as an adenosine triphosphate (ATP)-binding cassette (ABC) transporter that enables bacteria to secrete toxins at the expense of ATP hydrolysis. Our previous work, based on potential energy profiles from combined quantum mechanical and molecular mechanical (QM/MM) calculations, has suggested that the highly conserved H-loop His residue H662 in the nucleotide binding domain (NBD) of HlyB may catalyze the hydrolysis of ATP through proton relay. To further test this hypothesis when entropic contributions are taken into account, we obtained QM/MM minimum free energy paths (MFEPs) for the HlyB reaction, making use of the string method in collective variables. The free energy profiles along the MFEPs confirm the direct participation of H662 in catalysis. The MFEP simulations of HlyB also reveal an intimate coupling between the chemical steps and a local protein conformational change involving the signature-loop residue S607, which may serve a catalytic role similar to an Arg-finger motif in many ATPases and GTPases in stabilizing the phosphoryl-transfer transition state.
HlyB 作为一种三磷酸腺苷 (ATP) 结合盒 (ABC) 转运蛋白，使细菌能够以水解 ATP 为代价分泌毒素。我们之前的工作基于结合量子力学和分子力学 (QM/MM) 计算的势能曲线，表明 HlyB 的核苷酸结合域 (NBD) 中高度保守的 H 环组氨酸残基 H662 可能通过质子传递来催化 ATP 的水解。为了在考虑熵贡献时进一步验证这一假设，我们利用集体变量中的字符串方法获得了 HlyB 反应的 QM/MM 最小自由能途径 (MFEPs)。沿 MFEPs 的自由能曲线证实了 H662 直接参与催化。HlyB 的 MFEP 模拟还揭示了化学步骤与涉及特征环残基 S607 的局部蛋白质构象变化之间的紧密耦合，该变化可能类似于许多 ATP 酶和 GTP 酶中的 Arg-手指模体，在稳定磷酸转移过渡态方面发挥催化作用。
