Xu Rosalind J, Blasiak Bartosz, Cho Minhaeng, Layfield Joshua P, Londergan Casey H
Department of Chemistry , Haverford College , Haverford , Pennsylvania , United States.
Department of Physical and Quantum Chemistry, Faculty of Chemistry , Wrocław University of Science and Technology , Wybrzeże Wyspiańskiego 27 , 50-370 Wrocław , Poland.
J Phys Chem Lett. 2018 May 17;9(10):2560-2567. doi: 10.1021/acs.jpclett.8b00969. Epub 2018 May 2.
A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.
探针标记体系的分子动力学模拟与振动光谱之间的定量联系，将使实验数据能够直接转化为结构和动力学信息。为建立这种联系，对钙调蛋白-靶肽复合物中的两个硫氰酸根（SCN）探针位点（溶剂暴露位点和埋藏位点）进行了全原子分子动力学（MD）模拟。采用了两种具有大量非静电成分的频率计算方法，一种基于量子力学/分子力学（QM/MM）的技术和一种溶剂化显色片段势（SolEFP）方法，来模拟红外探针的线形。虽然QM/MM的结果与实验结果不一致，但SolEFP的结果与实验频率和线形相匹配，并揭示了所观察到的光谱行为的物理和动力学基础。CN探针频率的主要决定因素是探针与其局部结构邻域之间的交换排斥作用，并且对于在“埋藏”探针位点观察到的相对较宽的探针线形有一个清晰的动力学解释。这种方法应该广泛适用于许多环境中的振动探针。
