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-  2016 


DOI: 10.3866/PKU.WHXB201602291

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Abstract:

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。
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

 References

[1]  3 Dill K. A. ; MacCallum J. L. Science 2012, 338, 1042. doi: 10.1126/science.1219021
[2]  4 DeToma A. S. ; Salamekh S. ; Ramamoorthy A. ; Lim M. H. Chem. Soc. Rev. 2012, 41, 608. doi: 10.1039/C1CS15112F
[3]  18 Zheng J. R. Physics 2010, 39, 162. doi: 10.3969/j.issn.0254-6086.2010.02.013
[4]  郑俊荣. 物理, 2010, 39, 162. doi: 10.3969/j.issn.0254-6086.2010.02.013
[5]  19 Carr J. K. ; Zabuga A. V. ; Roy S. ; Rizzo T. R. ; Skinner J. L. J. Chem. Phys. 2014, 140, 224111. doi: 10.1063/1.4882059
[6]  25 Lee H. ; Choi J. H. ; Cho M. J. Chem. Phys. 2012, 137, 114307. doi: 10.1063/1.4751477
[7]  26 Reppert M. ; Tokmakoff A. J. Chem. Phys. 2015, 143, 061102. doi: 10.1063/1.4928637
[8]  28 Shi J. P. ; Zhao J. ; Yang F. ; Wang J. P. Acta Phys. -Chim. Sin. 2013, 29, 695. doi: 10.3866/PKU.WHXB201302213
[9]  29 Cai K. ; Du F. ; Zheng X. ; Liu J. ; Zheng R. ; Zhao J. ; Wang J. J. Phys. Chem. B 2016, 120, 1069. doi: 10.1021/acs.jpcb.5b11643
[10]  30 Jansen T. L. C. ; Knoester J. J. Phys. Chem. B 2006, 110, 22910. doi: 10.1021/jp064795t
[11]  33 Jorgensen W. L. ; Chandrasekhar J. ; Madura J. D. ; Impey R. W. ; Klein M. L. J. Chem. Phys. 1983, 79, 926. doi: 10.1063/1.445869
[12]  34 Jamróz M. H. Vibrational Energy Distribution Analysis VEDA 4 Warsaw: Poland 2004-2010.
[13]  35 Frisch M. J. ; Trucks G.W. ; Schlegel H. B. ; et al Gaussian 09, Revision A.01; Gaussian Inc.:Wallingford, CT 2009.
[14]  36 Schmidt J. R. ; Corcelli S. A. ; Skinner J. L. J. Chem. Phys. 2004, 121, 8887. doi: 10.1063/1.1791632
[15]  37 Papamokos G. V. ; Demetropoulos I. N. J. Phys. Chem. A 2004, 108, 7291. doi: 10.1021/jp049563d
[16]  38 Kim Y. S. ; Hochstrasser R. M. J. Phys. Chem. B 2005, 109, 6884. doi: 10.1021/jp0449511
[17]  43 Han C. ; Wang J. ChemPhysChem 2012, 13, 1522. doi: 10.1002/cphc.v13.6
[18]  5 Krimm S. ; Bandekar J. Adv. Protein Chem. 1986, 38, 181. doi: 10.1016/S0065-3233(08)60528-8
[19]  6 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
[20]  王建平. 科学通报, 2007, 52, 1221. doi: 10.3321/j.issn:0023-074X.2007.11.001
[21]  20 Jansen T. L. C. J. Phys. Chem. B 2014, 118, 8162. doi: 10.1021/jp5012445
[22]  21 Reppert M. ; Tokmakoff A. J. Chem. Phys. 2013, 138, 134116. doi: 10.1063/1.4798938
[23]  22 Lin Y. S. ; Shorb J. M. ; Mukherjee P. ; Zanni M. T. ; Skinner J. L. J. Phys. Chem. B 2009, 113, 592. doi: 10.1021/jp807528q
[24]  23 Wang L. ; Middleton C. T. ; Zanni M. T. ; Skinner J. L. J. Phys. Chem. B 2011, 115, 3713. doi: 10.1021/jp200745r
[25]  24 Dijkstra A. G. ; Jansen T. L. C. ; Knoester J. J. Phys. Chem. B 2011, 115, 5392. doi: 10.1021/jp109431a
[26]  27 Cai K. ; Su T. ; Lin S. ; Zheng R. Spectrochim. Acta A 2014, 117, 548. doi: 10.1016/j.saa.2013.08.058
[27]  31 Phillips J. C. ; Braun R. ; Wang W. ; Gumbart J. ; Tajkhorshid E. ; Villa E. ; Chipot C. ; Skeel R. D. ; Kale L. ; Klaus S. J. Comput. Chem. 2005, 26, 1781. doi: 10.1002/jcc.20289
[28]  32 MacKerell Jr A. D. ; Bashford D. ; Bellott M. ; Dunbrack Jr R. L. ; Evanseck J. D. ; Field M. J. ; Fischer S. ; Gao J. ; Guo H. ; Ha S. ; Joseph-McCarthy D. ; Kuchnir L. ; Kuczera K. ; Lau F. T. K. ; Mattos C. ; Michnick S. ; Ngo T. ; Nguyen D. T. ; Prodhom B. ; Reiher W. E. Ⅲ ; Roux B. ; Schlenkrich M. ; Smith J. C. ; Stote R. ; Straub J. ; Watanabe M. ; Wiorkiewicz-Kuczera J. ; Yin D. ; Karplus M. J. Phys. Chem. B 1998, 102, 3586. doi: 10.1021/jp973084f
[29]  41 Saven J. G. ; Skinner J. L. J. Chem. Phys. 1993, 99, 4391. doi: 10.1063/1.466092
[30]  42 Kubo R. Advances in Chemical Physcis; JohnWiley & Sons, Inc.: New York 2007, p 101.
[31]  石纪培; 赵娟; 杨帆; 王建平. 物理化学学报, 2013, 29, 695. doi: 10.3866/PKU.WHXB201302213
[32]  39 Pohl G. ; Perczel A. ; Vass E. ; Magyarfalvi G. ; Tarczay G. Phys. Chem. Chem. Phys. 2007, 9, 4698. doi: 10.1039/b705098d
[33]  40 Cormanich R. A. ; Rittner R. ; Buhl M. RSC Adv. 2015, 5, 13052. doi: 10.1039/C4RA16472E
[34]  1 Carrell R.W. ; Lomas D. A. Lancet 1997, 350, 134. doi: 10.1016/S0140-6736(97)02073-4
[35]  2 Savelieff M. G. ; DeToma A. S. ; Derrick J. S. ; Lim M. H. Accoutns Chem. Res. 2014, 47, 2475. doi: 10.1021/ar500152x
[36]  7 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
[37]  8 Du D. ; Zhu Y. ; Huang C. Y. ; Gai F. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 15915. doi: 10.1073/pnas.0405904101
[38]  9 Malolepsza E. ; Straub J. E. J. Phys. Chem. B 2014, 118, 7848. doi: 10.1021/jp412827s
[39]  10 Woys A. M. ; Almeida A. M. ; Wang L. ; Chiu C. C. ; McGovern M. ; de Pablo J. J. ; Skinner J. L. ; Gellman S. H. ; Zanni M. T. J. Am. Chem. Soc. 2012, 134, 19118. doi: 10.1021/ja3074962
[40]  11 Kim Y. S. ; Wang J. ; Hochstrasser R. M. J. Phys. Chem. B 2005, 109, 7511. doi: 10.1021/jp044989d
[41]  12 Moran S. D. ; Zanni M. T. J. Phys. Chem. Lett. 2014, 5, 1984. doi: 10.1021/jz500794d
[42]  13 Jones K. C. ; Peng C. S. ; Tokmakoff A. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 2828. doi: 10.1073/pnas.1211968110
[43]  14 Kim H. ; Cho M. Chem. Rev. 2013, 113, 5817. doi: 10.1021/cr3005185
[44]  15 Tucker M. J. ; Abdo M. ; Courter J. R. ; Chen J. ; Brown S. P. ; Smith A. B. ; Hochstrasser R. M. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 17314. doi: 10.1073/pnas.1311876110
[45]  16 Kim Y. S. ; Hochstrasser R. M. J. Phys. Chem. B 2009, 113, 8231. doi: 10.1021/jp8113978
[46]  17 Wang J. P. Chin. Sci. Bull. 2007, 52, 1221. doi: 10.3321/j.issn:0023-074X.2007.11.001

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