Małolepsza Edyta, Straub John E
Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.
J Phys Chem B. 2014 Jul 17;118(28):7848-55. doi: 10.1021/jp412827s. Epub 2014 Apr 11.
New sets of parameters (maps) for calculating amide I vibrational spectra for proteins through a vibrational exciton model are proposed. The maps are calculated as a function of electric field and van der Waals forces on the atoms of peptide bonds, taking into account the full interaction between peptide bonds and the surrounding environment. The maps are designed to be employed using data obtained from standard all-atom molecular simulations without any additional constraints on the system. Six proteins representing a wide range of sizes and secondary structure complexity were chosen as a test set. Spectra calculated for these proteins reproduce experimental data both qualitatively and quantitatively. The proposed maps lead to spectra that capture the weak second peak observed in proteins containing β-sheets, allowing for clear distinction between α-helical and β-sheet proteins. While the parametrization is specific to the CHARMM force field, the methodology presented can be readily applied to any empirical force field.
提出了通过振动激子模型计算蛋白质酰胺I振动光谱的新参数集（图谱）。这些图谱是根据肽键原子上的电场和范德华力计算得出的，同时考虑了肽键与周围环境之间的完整相互作用。这些图谱旨在使用从标准全原子分子模拟获得的数据，而无需对系统施加任何额外约束。选择了六种代表不同大小和二级结构复杂性的蛋白质作为测试集。为这些蛋白质计算的光谱在定性和定量上都能重现实验数据。所提出的图谱产生的光谱能够捕捉到含β-折叠的蛋白质中观察到的微弱第二峰，从而能够清晰地区分α-螺旋蛋白和β-折叠蛋白。虽然参数化是特定于CHARMM力场的，但所提出的方法可以很容易地应用于任何经验力场。
