College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, PR China; Fujian Provincial Key Laboratory of Featured Biochemical and Chemical Materials, Ningde Normal University, Ningde 352100, PR China.
College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, PR China.
Spectrochim Acta A Mol Biomol Spectrosc. 2022 Mar 5;268:120675. doi: 10.1016/j.saa.2021.120675. Epub 2021 Nov 30.
Infrared spectroscopy is a powerful tool for the understanding of molecular structure and function of polypeptides. Theoretical interpretation of IR spectra relies on ab initio calculations may be very costly in computational resources. Herein, we developed a neural network (NN) modeling protocol to evaluate a model dipeptide's backbone amide-I spectra. DFT calculations were performed for the amide-I vibrational motions and structural parameters of alanine dipeptide (ALAD) conformers in different micro-environments ranging from polar to non-polar ones. The obtained backbone dihedrals, C = O bond lengths and amide-I frequencies of ALAD were gather together for NN architecture. The applications of built NN protocols for the prediction of amide-I frequencies of ALAD in other solvation conditions are quite satisfactory with much less computational cost comparing with electronic structure calculations. The results show that this cost-effective way enables us to decipher the polypeptide's dynamic secondary structures and biological functions with their backbone vibrational probes.
红外光谱是理解多肽分子结构和功能的有力工具。理论上对红外光谱的解释依赖于从头算计算，这可能需要大量的计算资源。在此，我们开发了一种神经网络（NN）建模方案，以评估模型二肽的酰胺-I 光谱。对丙氨酸二肽（ALAD）在不同的微环境中的酰胺-I 振动运动和构象参数进行了从头算计算，这些微环境的极性范围从极性到非极性。获得的 ALAD 的骨架二面角、C=O 键长和酰胺-I 频率被收集在一起，用于 NN 架构。与电子结构计算相比，所建立的 NN 协议在其他溶剂化条件下预测 ALAD 的酰胺-I 频率的应用具有令人满意的效果，计算成本要低得多。结果表明，这种具有成本效益的方法使我们能够通过其骨架振动探针来破译多肽的动态二级结构和生物功能。
