Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
Biochemistry. 2023 Jan 17;62(2):451-461. doi: 10.1021/acs.biochem.2c00626. Epub 2022 Dec 27.
The acid-base behavior of amino acids plays critical roles in several biochemical processes. Depending on the interactions with the protein environment, the p values of these amino acids shift from their respective solution values. As the side chains interact with the polypeptide backbone, a pH-induced change in the protonation state of aspartic and glutamic acids might significantly influence the structure and stability of a protein. In this work, we have combined two-dimensional infrared spectroscopy and molecular dynamics simulations to elucidate the pH-induced structural changes in an antimicrobial enzyme, lysozyme, over a wide range of pH. Simultaneous measurements of the carbonyl signals arising from the backbone and the acidic side chains provide detailed information about the pH dependence of the local and global structural features. An excellent agreement between the experimental and the computational results allowed us to obtain a residue-specific molecular understanding. Although lysozyme retains the helical structure for the entire pH range, one distinct loop region (residues 65-75) undergoes local structural deformation at low pH. Interestingly, combining our experiments and simulations, we have identified the aspartic acid residues in lysozyme, which are influenced the most/least by pH modulation.
氨基酸的酸碱行为在许多生化过程中起着关键作用。根据与蛋白质环境的相互作用，这些氨基酸的 p 值会从它们各自的溶液值发生偏移。当侧链与多肽主链相互作用时，天冬氨酸和谷氨酸的质子化状态的 pH 诱导变化可能会显著影响蛋白质的结构和稳定性。在这项工作中，我们结合二维红外光谱和分子动力学模拟，阐明了在广泛的 pH 范围内，一种抗菌酶溶菌酶中 pH 诱导的结构变化。对源于骨架和酸性侧链的羰基信号的同时测量提供了关于局部和全局结构特征的 pH 依赖性的详细信息。实验和计算结果之间的极好一致性使我们能够获得残基特异性的分子理解。尽管溶菌酶在整个 pH 范围内保留了螺旋结构，但一个独特的环区（残基 65-75）在低 pH 下会发生局部结构变形。有趣的是，通过结合我们的实验和模拟，我们已经确定了溶菌酶中受 pH 调节影响最大/最小的天冬氨酸残基。
