Adhikari Puja, Podgornik Rudolf, Jawad Bahaa, Ching Wai-Yim
Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
School of Physical Sciences, Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China.
Materials (Basel). 2021 Oct 2;14(19):5774. doi: 10.3390/ma14195774.
The dielectric spectra of complex biomolecules reflect the molecular heterogeneity of the proteins and are particularly important for the calculations of electrostatic (Coulomb) and electrodynamic (van der Waals) interactions in protein physics. The dielectric response of the proteins can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. We present a new robust simulation method anchored in rigorous ab initio quantum mechanical calculations of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the dielectric spectra of small proteins under different conditions. We implement this methodology to a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the spike protein of SARS-COV-2. Two peaks at 5.2-5.7 eV and 14.4-15.2 eV in the dielectric absorption spectra are observed for 1FUV and SD1 in vacuum as well as in their solvated and salted models.
复杂生物分子的介电谱反映了蛋白质的分子异质性，对于蛋白质物理学中静电（库仑）和电动力学（范德华）相互作用的计算尤为重要。一般来说，蛋白质的介电响应可根据蛋白质的大小、结构、组成、局部性和环境分解为不同的成分。我们提出了一种新的稳健模拟方法，该方法基于对显式原子模型进行严格的从头算量子力学计算，无需任何不确定参数即可计算并深入了解不同条件下小蛋白质的介电谱。我们将此方法应用于不同环境中的多肽RGD - 4C（1FUV）以及严重急性呼吸综合征冠状病毒2（SARS - COV - 2）刺突蛋白中的SD1结构域。在真空以及它们的溶剂化和加盐模型中，观察到1FUV和SD1的介电吸收光谱在5.2 - 5.7 eV和14.4 - 15.2 eV处有两个峰。
