甘氨酸二肽分子酰胺-Ⅰ带光谱与结构相关性

doi:10.3866/PKU.WHXB201602291

物理化学学报 >> 2016, Vol. 32 >> Issue (5): 1289-1296.doi: 10.3866/PKU.WHXB201602291

研究论文上一篇

甘氨酸二肽分子酰胺-Ⅰ带光谱与结构相关性

蔡开聪^1,^2,*(),郑轩^1,²,刘亚男^1,²,留珊红^1,²,杜芬芬^1,²

¹ 福建师范大学化学与化工学院,福州350007
² 福建省理论与计算化学重点实验室,福建厦门361005

收稿日期:2015-12-24 发布日期:2016-05-07
通讯作者: 蔡开聪 E-mail:ckc1117@fjnu.edu.cn
基金资助:
国家自然科学基金(21103021);福建省高校杰出青年科学人才培育计划(JA13063)

Correlation between Amide-Ⅰ Spectra and Structural Features of Glycine Dipeptide

Kai-Cong CAI^1,^2,*(),Xuan ZHENG^1,²,Ya-Nan LIU^1,²,Shan-Hong LIU^1,²,Fen-Fen DU^1,²

¹ College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, P. R. China
² Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, Fujian Province, P. R. China

Received:2015-12-24 Published:2016-05-07
Contact: Kai-Cong CAI E-mail:ckc1117@fjnu.edu.cn
Supported by:
the National Natural Science Foundation of China(21103021);Education Department of Fujian Province of China(JA13063)

摘要/Abstract

摘要：

系统探索了蛋白质二肽模型分子——甘氨酸二肽(GLYD)在气相与水溶液中的结构与光谱特性。从分子动力学轨迹中提取具有代表性结构的GLYD-D₂O聚集体的瞬态结构开展简正模式分析,获取了对蛋白质二级结构敏感的酰胺-Ⅰ带的振动光谱参数,建立起振动光谱与特征基团结构间的相关性。将溶剂作用以静电势场的形式投影至二肽分子骨架中,与酰胺-Ⅰ带在气/液相中的频率差相关联,并引入酰胺-Ⅰ带简正模式随二级结构变化的规律,将各个构象态可能存在的振动耦合包含在内,构建具有二级结构敏感性的静电频率转换图,实现溶液相中多肽骨架酰胺-Ⅰ带的快速准确预测。

关键词: 甘氨酸二肽, 酰胺-Ⅰ带, 振动光谱, 静电频率图

Abstract:

Structural and spectroscopic features of a model dipeptide, glycine dipeptide (GLYD), were systematically investigated in the gas phase and in aqueous solution. Normal mode analysis was performed on the representative GLYD-D₂O clusters selected from molecular dynamics (MD) trajectory for the vibrational parameters of amide-Ⅰ mode, which is known to be sensitive to the secondary structure of proteins. On this basis, the correlation between the vibrational spectrum and the structural features of specific groups in the polypeptide was constructed. The electrostatic potential from the solvent molecules was calculated and projected onto the backbone of GLYD, and related to the amide-Ⅰ frequency difference for GLYD in gas phase and solution phase. The secondary structure-dependent normal mode amide-Ⅰ frequency database was also introduced for the consideration of the possible vibrational coupling that is intrinsically included in GLYD conformers. An electrostatic frequency map with secondary structural sensitivity was then built for the fast and accurate vibrational frequency prediction of the amide-Ⅰ vibrational band for polypeptides in solution.

Key words: Glycine dipeptide, Amide-Ⅰ band, Vibrational spectrum, Electrostatic frequency map

蔡开聪,郑轩,刘亚男,留珊红,杜芬芬. 甘氨酸二肽分子酰胺-Ⅰ带光谱与结构相关性[J]. 物理化学学报, 2016, 32(5), 1289-1296. doi: 10.3866/PKU.WHXB201602291

Kai-Cong CAI,Xuan ZHENG,Ya-Nan LIU,Shan-Hong LIU,Fen-Fen DU. Correlation between Amide-Ⅰ Spectra and Structural Features of Glycine Dipeptide[J]. Acta Phys. -Chim. Sin. 2016, 32(5), 1289-1296. doi: 10.3866/PKU.WHXB201602291

链接本文: https://www.whxb.pku.edu.cn/CN/10.3866/PKU.WHXB201602291

https://www.whxb.pku.edu.cn/CN/Y2016/V32/I5/1289

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甘氨酸二肽分子酰胺-Ⅰ带光谱与结构相关性

Correlation between Amide-Ⅰ Spectra and Structural Features of Glycine Dipeptide

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