丝素氨基酸寡肽链生长过程中的尺寸效应

羊梦诗; 李鑫; 叶志鹏; 陈亮; 徐灿; 储修祥

doi:10.7498/aps.62.236101

摘要

运用密度泛函理论，对甘氨酸丙氨酸依次交替组成的13 条丝素寡肽链进行结构优化，并计算了平均结合能、偶极矩，绘出寡肽链的振动红外光谱. 计算结果发现，随着寡肽链的生长，平均结合能单调变化，典型官能团的红外特征峰均发生频移. 但官能团的伸缩振动和弯曲振动表现出相反的红移和蓝移趋势. 揭示出丝素氨基肽链的物理化学性质在生长过程存在尺寸效应及各向异性. 该现象源于同类官能团之间的耦合效应，以及分子内氢键作用对伸缩振动和弯曲振动具有不同的影响.

关键词:

Abstract

A theoretical study on 13 oligopeptides of glycine and alanine by density function theory (DFT) is given in this paper. Geometric structures, vibration frequency, average binding energies, dipole moment are studied, and IR spectra of the oligopeptides are examined. Results show that with increasing number of residues the average binding energies tend to a regular pattern, IR frequencies of typical functional groups start to shift, but stretching and bending vibrations of the groups show the opposite trend of red shift and blue shift. It is revealed that the physical and chemical properties of the silk fibroin peptide chain show size effect and anisotropic in the growth process. This phenomenon may come from the coupling effect of the similar groups, and the different effects of intramolecular hydrogen bond on the stretching and bending vibration.

Keywords:

作者及机构信息

1.
浙江农林大学工程学院, 临安 311300;

2.
浙江农林大学理学院, 临安 311300;

3.
兰州大学磁学与磁性材料教育部重点实验室, 兰州 730000

基金项目: 国家杰出青年科学基金（批准号：50925103）和浙江农林大学理学院大学生创新训练基地项目资助的课题.

Authors and contacts

1.
School of Engineering, Zhejiang A&F University, Zhejiang Province, Linan 311300, China;

2.
School of Science, Zhejiang A&F University, Zhejiang Province, Linan 311300, China;

3.
Key Lab for Magnetism and Magnetic Materials of Ministry of Education Lanzhou University, Lanzhou 730000, China

Funds: Supported by the National Science Fund for Distinguished Young Scholars (Grant No. 50925103), and the Students Innovation Training Base of Science College, Zhejiang AF University.

参考文献

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施引文献

[1]	Liu H T, Xu W L, Zhao S P, Yang H J, Huang J J, Wang Y L, Ouyang C X 2010 J. Appl. Polym. Sci. 117 235
[2]	Zhou W, Chen X, Shao Z Z 2006 Prog. Chem. 18 1514 (in Chinese) [周文, 陈新, 邵正中 2006 化学进展 18 1514]
[3]	Chen G L, Zheng X, L"u G H, Zhang Z X, Massey S, Smith W, Tatoulian M, Yang S Z 2012 Chin. Phys. B 21 105201
[4]	Liu H T, Xu W L, Huang J J, Zuo D Y, Ke G Z 2009 Polym. Bull. 6 48 (in Chinese) [刘洪涛, 徐卫林, 黄菁菁, 左丹英, 柯贵珍 2009 高分子通报 6 48]
[5]	Smeenk J M, Ayres L, Stunnenberg H G, Hest J C M 2005 Macrom. Symp 225 1
[6]	Jin H J, Park J, Valluzzi R, Cebe P, Kaplan D L 2004 Biomacromolecules 5 711
[7]	Hu A, Zuo B, Zhang F, Zhang H, Lan Q 2013 Oto Neurotol. 34 311
[8]	Yu W B, Liang L, Lin Z J, Ling S L, Haranczyk M, Gutowski M 2009 J. Comput. Chem. 30 589
[9]	Yu W B, Wu Z Q, Chen H B, Liu X, MacKerell A D, Jr, Lin Z J 2012 J. Phys. Chem. B 116 2269
[10]	Yu W B, Xu X, Li H B, Pang R, Fang K, Lin Z J 2009 J. Comput. Chem. 30 2105
[11]	Chen Y, Wang J, Wang W 2007 Chin. Phys. 16 868
[12]	Zhu P, Xu Z Y, Tang X Q 2009 Chin. Phys. B 18 363
[13]	Li W F, Qin M, Tie Z X, Wang W 2011 Phys. Rev. E 84 041933
[14]	Xu C, Cao J, Zhu L F, Gao C Y 2006 Acta Phys. Chim. Sin. 22 445 (in Chinese) [徐灿, 曹娟, 朱莉芳, 高晨阳 2006 物理化学学报 22 445]
[15]	Xu C, Zhang X F, Chen L, Zhu L F, Zhang R J 2007 Acta Phys. Chim. Sin. 23 1733 (in Chinese) [徐灿, 张小芳, 陈亮, 张荣君 2007 物理化学学报 23 1733]
[16]	Zhou G R, Teng X Y, Wang Y, Geng H R, Hur B Y 2012 Acta Phys. Sin. 61 066101 (in Chinese) [周国荣, 滕新营, 王艳, 耿浩然, 徐甫宁 2012 61 066101]
[17]	Wei J, Chen Y J, Xu Z 2012 Acta Phys. Sin. 61 057502 (in Chinese) [魏杰, 陈彦均, 徐卓 2012 61 057502]
[18]	Li C, Hou Q Y, Zhang Z D, Zhang B 2012 Acta Phys. Sin. 61 077102 (in Chinese) [李聪, 侯清玉, 张振铎, 张冰 2012 61 077102]
[19]	Hou G H, Wang H Y, Liu T, Yuan Z, Fang J, Li D H, Qiu Q, Guo S D 2005 Chem. J. Chinese U 26 1277 (in Chinese) [侯光辉, 王慧彦, 刘涛, 袁直, 房杰, 李冬华, 邱奇, 郭世铎 2005 高等学校化学学报 26 1277]
[20]	Li Y, Zhang H J, Liao M X, Liu T 2011 Chem. J. Chinese U 32 1100 (in Chinese) [李晔, 张恒建, 廖明霞, 刘涛 2011 高等学校化学学报 32 1100 ]
[21]	Stewart J J P 1989 J. Comput. Chem. 10 209
[22]	Becke A D 1988 Phys. Rev. A 38 3098
[23]	Lee C, Yang W, Parr R G 1988 Phys. Rev. B 37 785
[24]	Frisch M J, Trucks G W, Schlegel H B 2010 Gaussian 09, Revision C. 01, Wallingford CT: Gaussian, Inc.
[25]	Puente E de la, Aguado A, Ayucla A, Lopez J M 1997 Phys Rev B 56 7607
[26]	Roberts C, Johnston R L 2001 Phys. Chem. Phys. 3 5024
[27]	Santosh K, Amareshwar K R, Singh V B, Rai S B 2005 Spectrochim. Acta A 61 2741
[28]	Malgorzata B, Julien B, Ivan C, Pawel P, Vincenzo B 2012 J. Mol. Struct. 1009 74
[29]	Wolpert M, Hellwig P 2006 Spectrochim. Acta A 64 987
[30]	Barth A 2000 Prog. Biophy. Mol. Bio. 74 141
[31]	Balaj O P, Kapota C, Lemaire J, Ohanessian G 2008 Int. J Mass. Spectrom. 269 196
[32]	Barth A 2007 Biochim. Biophys. Acta 1767 1073
[33]	Rosado M T, Duarte M L T S, Fausto R 1998 Vib. Spectrosc 16 35
[34]	Zhou R M, Shen Y J 1997 J. East China Univ. Sci. Technol. 23 422 (in Chinese) [周瑞明, 沈永嘉 1997 华东理工大学学报 23 422]
[35]	Cao J, Xu C, Zhu L F, Wang X M 2007 Spectrosc. Spect. Anal. 27 1715 (in Chinese) [曹娟, 徐灿, 朱莉芳, 王喜民 2007 光谱学与光谱分析 27 1715]
[36]	Wang C S, Qi X J, Ma Y G, Yang Z Z 2004 Chem. J. Chinese U 25 1111 (in Chinese) [王长生, 齐学洁, 马英格, 杨忠志 2004 高等学校化学学报 25 1111]
[37]	Zhang Y, Wang C S 2007 J. At. Mol. Phys. 24 1166 (in Chinese) [张艳, 王长生 2007 原子与分子 24 1166]
[38]	Yang Y, Zhang W J, Pei S X, Shao J, Huang W, Gao X M 2006 Sci. China Ser. B. 36 218 (in Chinese) [杨颙, 张为俊, 裴世鑫, 邵杰, 黄伟, 高晓明 2006 中国科学 B 辑-化学 36 218]
[39]	Yu W B, Lin Z J, Huang Z J 2006 Chem. Phys. Chem. 7 828
[40]	Clark S A C, Bawagan A O, Brion C E 1989 Chem. Phys. 137 407
[41]	Linder R, Seefeld K, Vavra A, Kleinermanns K 2008 Chem Phys. Lett. 453

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