丙氨酸二肽分子二级结构与振动光谱特性

doi:10.3866/PKU.WHXB201205021

物理化学学报 >> 2012, Vol. 28 >> Issue (08): 1837-1842.doi: 10.3866/PKU.WHXB201205021

丙氨酸二肽分子二级结构与振动光谱特性

蔡开聪, 留珊红, 刘的文, 林深

福建师范大学化学与化工学院, 福州 350007

收稿日期:2012-03-12 修回日期:2012-05-02 发布日期:2012-07-10
通讯作者: 蔡开聪, 林深 E-mail:ckc1117@iccas.ac.cn; shenlin@fjnu.edu.cn
基金资助:
国家自然科学基金(21103021), 福建省自然科学基金(2011J05022)和福建师范大学优秀青年骨干教师培养基金(fjsdjk2012066)资助项目

Secondary Structure and Vibrational Spectral Feature of Alanine Dipeptide

CAI Kai-Cong, LIU Shan-Hong, LIU Di-Wen, LIN Shen

College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, P. R. China

Received:2012-03-12 Revised:2012-05-02 Published:2012-07-10
Contact: CAI Kai-Cong, LIN Shen E-mail:ckc1117@iccas.ac.cn; shenlin@fjnu.edu.cn
Supported by:
The project was supported by the National Natural Science Foundation of China (21103021), Natural Science Foundation of Fujian Province, China (2011J05022), and Outstanding Young Teachers Research Foundation of Fujian Normal University, China (fjsdjk2012066).

摘要/Abstract

摘要：

利用从头算方法探索蛋白质模型分子——丙氨酸二肽的二级结构布居特性以及体系势能变化. 引入对分子结构敏感的振动探针(酰胺振动吸收带), 借助其光谱表象, 寻求振动光谱参数与分子结构之间的联系. 研究结果表明: 丙氨酸二肽分子处于C_7eq构型(Φ/Ψ=-80°/80°)时具有最低能量值, 且分子易形成β折叠、PP_II、C₅及C₇等能量较低的稳定构型. 通过简正模式分析, 得到分子3N-6 个振动模式的吸收光谱, 并通过势能分布分析方法对分子骨架上酰胺振动吸收带的特征振动模式进行了指认. 重点考察分子骨架上酰胺-I带振动光谱参数与分子构型变化之间的相关性, 建立振动光谱参数与蛋白质二级结构之间的联系, 为在化学键水平上研究蛋白质的结构及其发挥作用的机制提供科学依据.

关键词: 从头算, 丙氨酸二肽, 振动光谱, 酰胺-I带, 简正模式分析, 势能分布

Abstract:

Ab initio calculation was performed on the model peptide compound alanine dipeptide. The population of the secondary structures and the corresponding potential energies of alanine dipeptide were investigated. Normal mode analysis was performed on the amide vibrational modes, which are known to be quite sensitive to the molecular structure, and the correlation between the vibrational feature and the molecular structure was then revealed. The results show that alanine dipeptide has a minimum potential energy when the backbone dihedral is positioned at Φ/Ψ =-80°/80° , which can be denoted as a C_7eq conformation. It is also possible to form the secondary structures with β sheet, PP_II, C₅, and C₇ conformations for their low potential energies. The vibrational parameters of the 3N-6 vibrational motions were obtained through normal mode analysis. The amide vibrational modes were then assigned by the potential energy distribution analysis. The amide-I mode, mostly consisting of backbone C＝O stretching, was introduced for the prediction of the secondary structure of alanine dipeptide. The correlation between the amide-I vibrational parameters and the molecular structures is then demonstrated. Thus is a new way for the prediction of structural features of peptide and protein systems at the chemical bond level.

Key words: Ab initio calculation, Alanine dipeptide, Vibrational spectroscopy, Amide-I mode, Normal mode analysis, Potential energy distribution

蔡开聪, 留珊红, 刘的文, 林深. 丙氨酸二肽分子二级结构与振动光谱特性[J]. 物理化学学报, 2012, 28(08), 1837-1842. doi: 10.3866/PKU.WHXB201205021

CAI Kai-Cong, LIU Shan-Hong, LIU Di-Wen, LIN Shen. Secondary Structure and Vibrational Spectral Feature of Alanine Dipeptide[J]. Acta Phys. -Chim. Sin. 2012, 28(08), 1837-1842. doi: 10.3866/PKU.WHXB201205021

链接本文: https://www.whxb.pku.edu.cn/CN/10.3866/PKU.WHXB201205021

https://www.whxb.pku.edu.cn/CN/Y2012/V28/I08/1837

参考文献

(1) Krimm, S.; Bandekar, J. Adv. Protein Chem. 1986, 38, 181. doi: 10.1016/S0065-3233(08)60528-8
(2) Wang, J. P. Chinese Science Bulletin 2007, 52, 1221. [王建平.科学通报, 2007, 52, 1221.]
(3) Cho, M. Chem. Rev. 2008, 108, 1331. doi: 10.1021/cr078377b
(4) Zheng, J. R. Physics 2010, 39, 162. [郑俊荣. 物理, 2010, 39,162.]
(5) Kim, Y. S.; Hochstrasser, R. M. J. Phys. Chem. B 2009, 113,8231. doi: 10.1021/jp8113978
(6) Wang, J. P. Chin. J. Chem. Phys. 2007, 20, 509. [王建平. 化学物理学报, 2007, 20, 509.] doi: 10.1088/1674-0068/20/05/509-517
(7) Zhuang,W.; Hayashi, T.; Mukamel, S. Angew. Chem. Int. Edit.2009, 48, 3750. doi: 10.1002/anie.200802644
(8) Cai, K. C.;Wang, J. P. Acta Phys. -Chim. Sin. 2009, 25, 677.[蔡开聪, 王建平. 物理化学学报, 2009, 25, 677.] doi: 10.3866/PKU.WHXB200904021
(9) Zhuang,W.; Sgourakis, N. G.; Li, Z. Y.; Garcia, A. E.;Mukamel, S. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 15687.doi: 10.1073/pnas.1002131107
(10) Bian, H.;Wen, X.; Li, J.; Chen, H.; Han, S.; Sun, X.; Song, J.;Zhuang,W.; Zheng, J. Proc. Natl. Acad. Sci. U. S. A. 2011, 108,4737. doi: 10.1073/pnas.1019565108
(11) Cai, K.;Wang, J. J. Phys. Chem. B 2009, 113, 1681. doi: 10.1021/jp8070025
(12) Barber-Armstrong,W.; Donaldson, T.;Wijesooriya, H.; Silva,R. A. G. D.; Decatur, S. M. J. Am. Chem. Soc. 2004, 126, 2339.doi: 10.1021/ja037863n
(13) Huang, C. Y.; Getahun, Z.; Zhu, Y.; Klemke, J.W.; DeGrado,W.F.; Gai, F. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 2788. doi: 10.1073/pnas.052700099
(14) Du, D.; Zhu, Y.; Huang, C. Y.; Gai, F. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 15915. doi: 10.1073/pnas.0405904101
(15) Lin, Y. S.; Shorb, J. M.; Mukherjee, P.; Zanni, M. T.; Skinner, J.L. J. Phys. Chem. B 2009, 113, 592.
(16) Roy, S.; Lessing, J.; Meisl, G.; Ganim, Z.; Tokmakoff, A.;Knoester, J.; Jansen, T. L. C. J. Chem. Phys. 2011, 135, 234507.
(17) Wang, J. Phys. Chem. Chem. Phys. 2009, 11, 5310.
(18) Cai, K. C.; Han, C.;Wang, J. P. Phys. Chem. Chem. Phys. 2009,11, 9149.
(19) Wang, J. J. Phys. Chem. B 2008, 112, 4790. doi: 10.1021/jp710641x
(20) Wang, J.; Hochstrasser, R. M. J. Phys. Chem. B 2006, 110, 3798.doi: 10.1021/jp0530092
(21) Han, C.;Wang, J. Chin. J. Chem. Phys. 2011, 24, 529.[韩晨, 王建平. 化学物理学报, 2011, 24, 529.] doi: 10.1088/1674-0068/24/05/529-537
(22) Wang, L.; Middleton, C. T.; Zanni, M. T.; Skinner, J. L. J. Phys. Chem. B 2011, 115, 3713.
(23) Hermans, J. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 3095. doi: 10.1073/pnas.1019470108
(24) Jamróz, M. H. Vibrational Energy Distribution Analysis VEDA 4,Warsaw, 2004-2010.
(25) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al . Gaussian 09, Revision A.01; Gaussian Inc.:Wallingford, CT, 2009.
(26) Wang, Z. X.; Duan, Y. J. Comput. Chem. 2004, 25, 1699. doi: 10.1002/jcc.20092
(27) Kim, Y. S.;Wang, J.; Hochstrasser, R. M. J. Phys. Chem. B2005, 109, 7511. doi: 10.1021/jp044989d
(28) Vargas, R.; Garza, J.; Hay, B. P.; Dixon, D. A. J. Phys. Chem. A2002, 106, 3213. doi: 10.1021/jp013952f
(29) Kim, Y. S.; Hochstrasser, R. M. J. Phys. Chem. B 2005, 109,6884. doi: 10.1021/jp0449511
(30) Badger, R. M. J. Chem. Phys. 1934, 2, 128. doi: 10.1063/1.1749433
(31) Badger, R. M. J. Chem. Phys. 1935, 3, 710. doi: 10.1063/1.1749581

[1]	陈文琼, 关永吉, 张姣, 裴俊捷, 张晓萍, 邓友全. 外电场作用下离子液体振动光谱变化的分子动力学模拟研究[J]. 物理化学学报, 2021, 37(10): 2001004 - .
[2]	傅碧娜, 陈俊, 刘天辉, 邵科杰, 张东辉. 多原子反应体系的高精度拟合势能面[J]. 物理化学学报, 2019, 35(2): 145 -157 .
[3]	陈海龙,边红涛,郑俊荣. 基于超快多维振动光谱技术解析分子体系的三维空间构型[J]. 物理化学学报, 2017, 33(1): 40 -62 .
[4]	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 .
[5]	吴沛颖,曾圣渊,蔡青妘,曾文碧. 2, 5-二氟苯酚分子之旋转异构物的质量分辨阈值电离光谱[J]. 物理化学学报, 2016, 32(4): 893 -900 .
[6]	叶传香,马会利,梁万珍. 几个荧光蛋白发色团双光子吸收性质的理论研究[J]. 物理化学学报, 2016, 32(1): 301 -312 .
[7]	孙中发, 高治, 吴向坤, 唐国强, 周晓国, 刘世林. N₂O⁺离子B²П态的光谱与光解离动力学[J]. 物理化学学报, 2015, 31(5): 829 -835 .
[8]	秦晨, 曾圣渊, 张冰, 曾文碧. 间甲基苯甲醚分子旋转异构体的质量分辨阈值电离光谱[J]. 物理化学学报, 2014, 30(8): 1416 -1425 .
[9]	卢晓林, 周杰, 李柏霖. 不同受限状态下链硫醇的非线性光学响应[J]. 物理化学学报, 2014, 30(12): 2342 -2348 .
[10]	李丹, 薛佳丹, 郑旭明. 4-硝基咪唑A-带激发态结构动力学[J]. 物理化学学报, 2014, 30(12): 2216 -2223 .
[11]	刘帅, 李书实, 刘冬佳, 王长生. 碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点[J]. 物理化学学报, 2013, 29(12): 2551 -2557 .
[12]	李明娟, 刘明霞, 郑旭明. 1-甲基胸腺嘧啶A-带结构动力学[J]. 物理化学学报, 2013, 29(05): 903 -910 .
[13]	马丽娟, 王剑锋, 贾建峰, 武海顺. B₁₂Sc₄和B₁₂Ti₄团簇的储氢性质[J]. 物理化学学报, 2012, 28(08): 1854 -1860 .
[14]	马驰骋, 蒲敏, 卫敏, 李军男, 李志宏. L-缬氨酸旋光异构的两种光反应可能途径[J]. 物理化学学报, 2012, 28(08): 1830 -1836 .
[15]	郭晓楠, 杜蕊, 赵彦英, 裴克梅, 王惠刚, 郑旭明. 2-硫代嘧啶酮和2-硫代吡啶酮在B-吸收带中的动态结构[J]. 物理化学学报, 2012, 28(07): 1570 -1578 .

丙氨酸二肽分子二级结构与振动光谱特性

Secondary Structure and Vibrational Spectral Feature of Alanine Dipeptide

PDF

赞

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

Metrics

推荐阅读 0