Effect of Electronic Polarization to Human <em>α</em>-Thrombin

doi:10.1088/0256-307X/31/4/048701

Chin. Phys. Lett.

2014, Vol. 31

Issue (04): 048701 DOI: 10.1088/0256-307X/31/4/048701

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY

Effect of Electronic Polarization to Human α-Thrombin

DUAN Li-Li^1**, LI Zong-Chao¹, HE Xiang², ZHANG Qing-Gang¹

¹College of Physics and Electronics, Shandong Normal University, Jinan 250014
²Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008

Cite this article:

DUAN Li-Li, LI Zong-Chao, HE Xiang et al 2014 Chin. Phys. Lett. 31 048701

Download: PDF(1237KB)
Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks

Abstract The polarized protein-specific charges (PPC) of human α-thrombin (thrombin) and its inhibitor (L86) are made possible by employing the recently developed molecular fractionation with conjugate caps approach incorporated the Poisson–Boltzmann model. Molecular dynamics (MD) simulations of thrombin have been carried out to investigate the dynamics and stability of the thrombin-inhibitor using PPC and AMBER charges respectively. Detailed analysis and comparison of MD results show that the PPC can correctly describe the polarized state of the thrombin and L86. Especially, the root-mean-square deviation of backbone atoms and the hydrogen bonds using PPC are more stable than the AMBER charge. The present results indicate that protein polarization plays critical roles in maintaining the compact structure of thrombin.

Received: 25 December 2013 Published: 25 March 2014

PACS:	87.15.-v	(Biomolecules: structure and physical properties)
	82.30.Rs	(Hydrogen bonding, hydrophilic effects)

TRENDMD:

URL:

https://cpl.iphy.ac.cn/10.1088/0256-307X/31/4/048701 OR https://cpl.iphy.ac.cn/Y2014/V31/I04/048701

Service
	E-mail this article
	E-mail Alert
	RSS
Articles by authors
	DUAN Li-Li
	LI Zong-Chao
	HE Xiang
	ZHANG Qing-Gang

[1] Petrey D and Honig B 2000 Protein Sci. 9 2181
[2] Xu Z Y and Gao J 2009 Chin. Phys. B 18 370
[3] Ran S Y 2012 Acta Phys. Sin. 61 170503 (in Chinese)
[4] Cornell W D et al 1995 J. Am. Chem. Soc. 117 5179
[5] Qi W P and Lei X L 2011 Chin. Phys. Lett. 28 048702
[6] MacKerell A D et al 1998 J. Phys. Chem. B 102 3586
[7] Sheng Y B et al 2005 Chin. Phys. B 14 2365
[8] Kaminski G A et al 2001 J. Phys. Chem. B 105 6474
[9] Ma B et al 2000 J. Comput. Chem. 21 813
[10] Lu Y P et al 2006 J. Am. Chem. Soc. 128 11830
[11] Kamath P et al 2010 J. Biol. Chem. 285 28651
[12] Davie E W et al 1991 Biochemistry 30 10363
[13] Pierce A C and Jorgensen W L 2001 J. Med. Chem. 44 1043
[14] Fenton J W et al 1991 Blood Coagul. Fibrin. 2 69
[15] Wu E L et al 2007 Biophys. J. 92 4244
[16] Duan L L et al 2007 J. Chem. Phys. 127 145101
[17] Mei Y et al 2005 Proteins: Struct. Funct. Bioinf. 59 489
[18] Mei Y et al 2006 Int. J. Quantum Chem. 106 1267
[19] Mei Y et al 2005 J. Phys. Chem. A 109 2
[20] Zhang D W and Zhang J Z H 2003 J. Chem. Phys. 119 3599
[21] Ji C G et al 2008 Biophys. J. 95 1080
[22] Ji C G and Zhang J Z H 2008 J. Am. Chem. Soc. 130 17129
[23] Duan L L et al 2009 J. Chem. Phys. 130 115102
[24] Duan L L et al 2010 J. Am. Chem. Soc. 132 11159
[25] Ji C G and Zhang J Z H 2011 J. Am. Chem. Soc. 133 17727
[26] Mei Y et al 2011 Sci. Chin. B 54 1974
[27] Duan L L et al 2012 J. Phys. Chem. B 116 3430
[28] Li Y et al 2012 J. Phys. Chem. B 116 13368
[29] Wei C et al 2011 J. Chem. Phys. 134 171101
[30] Ferrara P et al 2004 J. Med. Chem. 47 3032
[31] Jorgensen W L et al 1983 J. Chem. Phys. 79 926
[32] Essmann U et al 1995 J. Chem. Phys. 103 8577
[33] Ryckaert J P et al 1977 J. Comput. Chem. 23 327
[34] Comell W D et al 1993 J. Am. Chem. Soc. 115 9620
[35] Li Y F et al 1993 Chin. Phys. B 2 128
[36] Duan Y et al 2003 J. Comput. Chem. 24 1999
[37] Simonson T et al 2004 J. Am. Chem. Soc. 126 4167
[38] Mirsky A E and Pauling L 1936 Proc. Natl. Acad. Sci. USA 22 439

Related articles from Frontiers Journals

[1]	Xiu-Lian Xu, Jin-Xuan Shi . Characterization of the Topological Features of Catalytic Sites in Protein Coevolution Networks[J]. Chin. Phys. Lett., 2020, 37(6): 048701
[2]	Xiu-Lian Xu, Jin-Xuan Shi . Characterization of the Topological Features of Catalytic Sites in Protein Coevolution Networks *[J]. Chin. Phys. Lett., 0, (): 048701
[3]	GAO Guang-Yu, LI Yu, WANG Wei, ZHONG Dong-Ping, WANG Shu-Feng, GONG Qi-Huang. Spectroscopic Characterization of Staphylococcal Nuclease Mutants with Tryptophan at Internal Sites[J]. Chin. Phys. Lett., 2015, 32(4): 048701
[4]	XI Wen-Hui, LI Wen-Fei, and WANG Wei. Modulation of Amyloid-β Conformation by Charge State of N-Terminal Disordered Region[J]. Chin. Phys. Lett., 2012, 29(8): 048701
[5]	TIE Zuo-Xiu, QIN Meng, ZOU Da-Wei, CAO Yi, WANG Wei . Photo-Crosslinking Induced Geometric Restriction Controls the Self-Assembly of Diphenylalanine Based Peptides[J]. Chin. Phys. Lett., 2011, 28(2): 048701
[6]	PAN Bing-Yi, ZHANG Ling-Yun, DOU Shuo-Xing, WANG Peng-Ye. Effect of Laser Field and Mechanical Force on Deoxyribonucleic Acid Melting[J]. Chin. Phys. Lett., 2010, 27(7): 048701
[7]	M. D. Ganji, H. Yazdani. Interaction between B-Doped C₆₀ Fullerene and Glycine Amino Acid from First-Principles Simulation[J]. Chin. Phys. Lett., 2010, 27(4): 048701
[8]	ZHANG Ping, WANG Hai-Jun,. Monte Carlo Simulation on Growth of Antibody-Antigen Complexes: the Role of Unequal Reactivity[J]. Chin. Phys. Lett., 2010, 27(3): 048701
[9]	WU Zheng-Yi, FENG Jin-Fu, WU Xiao-Shan. Thermal Vibration and Twist Induced Semiconducting Behaviour in Short DNA Wires[J]. Chin. Phys. Lett., 2009, 26(2): 048701
[10]	HU Dong-Sheng, ZHU Chen-Ping, ZHANG Long-Qiang, HE Da-Ren, WANG Bing-Hong. Gap Caused by Strong Pairing in the Ladder Model of DNA Molecules[J]. Chin. Phys. Lett., 2008, 25(5): 048701
[11]	ZHAO Wei-Jia, WENG Yu-Quan, FU Jing-Li,. Lie Symmetries and Conserved Quantities for Super-Long Elastic Slender Rod[J]. Chin. Phys. Lett., 2007, 24(10): 048701
[12]	ZHANG Hong-Yan, LIANG Ru-Qiang, JIN Kui-Juan, Lü Hui-Bin, ZHU Xiang-Dong, ZHOU Yue-Liang, RUAN Kang-Cheng, YANG Guo-Zhen. Applications of Oblique-Incidence Reflectivity Difference Method in Primary Study of Protein Biomolecules[J]. Chin. Phys. Lett., 2006, 23(4): 048701
[13]	SONG Fan, MOYNE Christian, BAI Yi-Long. Electrostatic Interactions Between Glycosaminoglycan Molecules[J]. Chin. Phys. Lett., 2005, 22(2): 048701
[14]	WANG Ao-Jin, HU Kun-Sheng. Calibration of Membrane Viscosity of the Reconstituted Vesicles by Measurement of Rotational Diffusion of Bacteriorhodopsin[J]. Chin. Phys. Lett., 2002, 19(11): 048701
[15]	ZHANG Yi, HU Jun, WU Shi-Ying, AI Xiao-Bai, LI Min-Qian. Experiments and Models of DNA Nano-Catenary Patterns Manipulated by Liquid Flow[J]. Chin. Phys. Lett., 2002, 19(3): 048701

Viewed

Full text

Abstract