蛋白质构象由不同的构型异构体组成。配体结合和催化过程本身能显著改变蛋白质构象状态和分布。深入理解蛋白质构象转换机理，对揭示酶生化功能发挥重要作用。在蛋白质特定位置置入振动探针分子，获取蛋白质局部静电场的详细信息，能帮助表征、识别蛋白质的构象异构态。本项目拟发展理论计算方法，精确模拟含探针基团的生物酶或多肽在水溶液中的一、二维振动光谱。目的是了解酶催化反应路径中的动态构象变化和底物-蛋白复合物中的构象异构态。为了实现上述目标，我们通过分子动力学取样，应用QM/MM方法确定探针与溶剂分子间的相互作用势能和偶极矩，应用微扰理论有效确定含时动力学轨迹中的瞬时跃迁频率和跃迁偶极矩，模拟体系在时域或频域的一、二维振动光谱。 该项目汇集两位在生物、光谱领域内各具特色的专家组成团队，形成了良好交叉和融合，在生物光谱学领域找到了新的生长点。发展的新方法将不仅适用于该项目特定体系，还可广泛应用于化学生物体系。

Protein exists as an ensemble of conformers; however, its biological function is often carried out through higher energy states. Ligand binding and the catalytic process itself can significantly shift the relative populations of protein conformation states. An understanding of the mechanism of protein conformational inter-conversion is important to elucidating the biological functions of enzymes. Vibrational spectroscopy of probe molecules, strategically placed inside a protein, can provide detailed information on the local electrostatic field, and can help characterize protein conformational heterogeneity. The aim of this proposal is to develop theoretical and computational techniques to accurately determine one and two dimensional vibrational spectra of functional groups inside enzymes and small peptides in solution. The primary goal is to understand the dynamic conformational changes along the reaction pathway of enzymatic catalysis in ketosteroid isomerase and dihydrofolate reductase, and the protein conformational heterogeneity in the substrate-protein complex of lactate dehydrogenase. To achieve these goals, we propose to employ combined quantum mechanical and molecular mechanical (QM/MM) methods to represent the potential energy surface of the probe molecule and to model intermolecular interactions through molecular dynamics simulations. Furthermore, we plan on determining one and two dimensional vibrational spectra based on the time evolution of molecular dipole moment and transition moment of the probe molecules from QM/MM simulations. We also propose to use a perturbative approach to efficiently determine the instantaneous vibrational frequencies of probe molecules along the dynamic trajectories. The proposed research brings together the expertise of two leading research groups in their fields, and the method developed in this work can be applied to other chemical and biochemical systems. The understanding of protein conformational states will likely to be generally applicable to other enzymes.