固有无序超嗜热菌FlgM蛋白在两种不同温度下的构象变化特征

doi:10.3866/PKU.WHXB201412161

物理化学学报 >> 2015, Vol. 31 >> Issue (2): 384-392.doi: 10.3866/PKU.WHXB201412161

生物物理化学上一篇

固有无序超嗜热菌FlgM蛋白在两种不同温度下的构象变化特征

朱玉风^1,2,3, 曹赞霞^2,3, 赵立岭^2,3, 王吉华^2,3

1. 山东师范大学物理与电子科学学院, 济南 250014;
2. 山东省功能大分子生物物理重点实验室, 山东德州 253023;
3. 德州学院生物物理研究所, 山东德州 253023

收稿日期:2014-09-15 修回日期:2014-12-16 发布日期:2015-01-26
通讯作者: 王吉华 E-mail:jhw25336@126.com
基金资助:
国家自然科学基金(61271378, 31000324)资助项目

Conformational Change Characteristics in the Intrinsically Disordered FlgM Protein from a Hyperthermophile at Two Different Temperatures

ZHU Yu-Feng^1,2,3, CAO Zan-Xia^2,3, ZHAO Li-Ling^2,3, WANG Ji-Hua^2,3

1. Department of Physics and Electronic Science, Shandong Normal University, Jinan 250014, P. R. China;
2. Shandong Province Key Laboratory of Biophysics for Functional Macromolecules, Dezhou 253023, Shandong Province, P. R. China;
3. Institute of Biophysics, Dezhou University, Dezhou 253023, Shandong Province, P. R. China

Received:2014-09-15 Revised:2014-12-16 Published:2015-01-26
Contact: WANG Ji-Hua E-mail:jhw25336@126.com
Supported by:
The project was supported by the National Natural Science Foundation of China (61271378, 31000324).

摘要/Abstract

摘要：

基于分子动力学模拟方法比较了超嗜热菌FlgM 蛋白在常温(293 K)和生理温度(358 K)下的结构特征.基于GROMACS软件包, 采用OPLS-AA分子力场和TIP3P水模型, 对超嗜热菌FlgM 蛋白在293 和358 K进行了2组独立的长时间分子动力学模拟, 每组体系模拟时间为1500 ns. 主要分析了两种温度下超嗜热菌FlgM蛋白的二级结构特征、整体构象变化及半无序化区域和结构化区域的构象特征. 研究结果表明: 在常温下, N端具有一定程度的螺旋成分, 但在生理温度下, 超嗜热菌FlgM 蛋白的结构变得松散, 螺旋结构减少, 构象稳定性减弱, H1 螺旋散开, FlgM 蛋白构象灵活性增强, 不稳定程度增加. 这些不同温度的结构变化说明: 半无序化区域(N端)在非结合状态下有一定的螺旋结构, 但该段螺旋的稳定性随温度升高而降低. 超嗜热菌FlgM蛋白会通过增加结构的无序程度使结构更加灵活, 以适应高温, 从而使该类固有无序蛋白更好地行使其功能, 如提高同其他成分的结合速率等.

关键词: FlgM蛋白, 固有无序蛋白, 分子动力学模拟, 温度适应性, 结构特征

Abstract:

The aim of this work was to compare the structural characteristics of the FlgM protein from the thermophile aquifex aeolicus at room temperature (293 K) and at the physiological temperature (358 K) using molecular dynamics simulations. Two independent long-time molecular dynamics simulations were performed using the GROMACS software package at 293 and 358 K, respectively. The OPLS-AA force field and the TIP3P water model were used. Each simulation was run for 1500 ns. We mainly analyzed the secondary structural characteristics, the overall conformation variation, the conformational characteristics of a semi-disordered region and the structured region of the FlgM protein at two different temperatures. The results indicate that the helix structure of the N terminal increased at room temperature. The FlgM protein had the following characteristics at the physiological temperature: the structure loosed, the helix structure reduced in size, the conformational stability weakened, the H1 helix spread, the conformational flexibility increased, and the degree of instability increased. In summary, the semi-disordered region (N terminal) formed a helical structure in the unbound state and its stability decreased with an increase in temperature. The FlgM protein adapts to temperature by increasing the degree of disorder, creating a more flexible structure by improving the binding rate.

Key words: FlgM protein, Intrinsically disordered protein, Molecular dynamics simulation, Temperature adapting, Structure characteristic

MSC2000:

O643

朱玉风, 曹赞霞, 赵立岭, 王吉华. 固有无序超嗜热菌FlgM蛋白在两种不同温度下的构象变化特征[J]. 物理化学学报, 2015, 31(2): 384-392.

ZHU Yu-Feng, CAO Zan-Xia, ZHAO Li-Ling, WANG Ji-Hua. Conformational Change Characteristics in the Intrinsically Disordered FlgM Protein from a Hyperthermophile at Two Different Temperatures[J]. Acta Phys. -Chim. Sin., 2015, 31(2): 384-392.

参考文献

(1) Feller, G. J. Phys.: Condes. Matter 2010, 22 (32), 323101. doi: 10.1088/0953-8984/22/32/323101
(2) Ohnishi, K.; Kutsukake, K.; Suzuki, H.; Iino, T. Mol. Genet. Metab. 1990, 221 (2), 139.
(3) Gillen, K. L.; Hughes, K. T. J. Bacteriol. 1991, 173 (20), 6453.
(4) Ohnishi, K.; Kutsukake, K.; Suzuki, H.; Lino, T. Mol. Microbiol. 1992, 6 (21), 3149. doi: 10.1111/mmi.1992.6.issue-21
(5) Gillen, K. L.; Hughes, K. T. J. Bacteriol. 1993, 175 (21), 7006.
(6) Hughes, K. T.; Gillen, K. L.; Semon, M. J.; Karlinsey, J. E. Science 1993, 262 (5137), 1277. doi: 10.1126/science.8235660
(7) Kutsukake, K. Mol. Genet. Metab. 1994, 243 (6), 605.
(8) Wang, J. H.; Yang, Y. D.; Cao, Z. X.; Li, Z. X.; Zhao, H. L.; Zhou, Y. Q. Biophys. J. 2013, 105 (11), 1.
(9) Dunker, A. K.; Brown, C. J.; Lawson, J. D.; Iakoucheva, L. M.; Obradovic, Z. Biochemistry 2002, 41 (21), 6573. doi: 10.1021/bi012159+
(10) Zhang, T.; Faraggi, E.; Li, Z. X.; Zhou, Y. Q. Cell Biochem. Biophys. 2013, 76 (3), 1193.
(11) Huang, Y. Q.; Liu, Z. R. Acta Phys. -Chim. Sin. 2010, 26, 2061. [黄永棋, 刘志荣. 物理化学学报, 2010, 26, 2061.] doi: 10.3866/PKU.WHXB20100644
(12) Liu, Z. R.; Huang, Y. Q. Protein Sci. 2014, 23 (5), 539. doi: 10.1002/pro.2443
(13) Molloy, R. G.; Ma,W. K.; Allen, A. C.; Greenwood, K.; Bryan, L.; Sacora, R.;Williams, L.; Gage, M. J. Biochim. Biophys. Acta 2010, 1804 (7), 1457. doi: 10.1016/j.bbapap.2010.03.002
(14) Sorenson, M. K.; Ray, S. S.; Darst, S. A. Mol. Cell 2004, 14 (1), 127. doi: 10.1016/S1097-2765(04)00150-9
(15) Xu, Z. Y.; Zhao, L. L.; Cao, Z. X.;Wang, J. H. Acta Phys. -Chim. Sin. 2012, 28, 1665. [许朝莹, 赵立岭, 曹赞霞, 王吉华. 物理化学学报, 2012, 28, 1665.] doi: 10.3866/PKU.WHXB201204182
(16) Luo, F.; Gao, J.; Cheng, Y. H.; Cui,W.; Ji, M. J. Acta Phys. -Chim. Sin. 2012, 28, 2191. [罗芳, 高剑, 成元华, 崔巍, 计明娟. 物理化学学报, 2012, 28, 2191.] doi: 10.3866/PKU.WHXB201207063
(17) Dong, X. Y.; Du,W. J.; Liu, F. F. Acta Phys. -Chim. Sin. 2012, 28, 2735. [董晓燕, 都文婕, 刘夫锋. 物理化学学报, 2012, 28, 2735.] doi: 10.3866/PKU.WHXB201207162
(18) Cao, J.; Cao, Z. X.; Zhao, L. L.;Wang, J. H. Acta Phys. -Chim. Sin. 2012, 28, 479. [曹剑, 曹赞霞, 赵立岭, 王吉华. 物理化学学报, 2012, 28, 479.] doi: 10.3866/PKU.WHXB201111231
(19) Van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. J. Comput. Chem. 2005, 26 (16), 1701.
(20) Jorgensen,W. L.; Tirado-Rives, J. Proc. Natl. Acad. Sci. U. S. A. 2005, 102 (19), 6665. doi: 10.1073/pnas.0408037102
(21) Jorgensen,W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79 (2), 926. doi: 10.1063/1.445869
(22) Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103 (19), 8577. doi: 10.1063/1.470117
(23) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98 (12), 10089. doi: 10.1063/1.464397
(24) Bussi, G.; Donadio, D.; Parrinello, M. J. Chem. Phys. 2007, 126 (1), 014101. doi: 10.1063/1.2408420
(25) Berendsen, H. J.; Postma, J. P. M.; Van Gunsteren,W. F.; DiNola, A.; Haak, J. J. Chem. Phys. 1984, 81 (8), 3684. doi: 10.1063/1.448118
(26) Zhang, T.; Faraggi, E.; Xue, B.; Dunker, A. K.; Uversky, V. N.; Zhou, Y. Q. J. Biomol. Struct. Dyn. 2012, 29 (4), 799. doi: 10.1080/073911012010525022
(27) Faraggi, E.; Yang, Y. D.; Zhang, S. S.; Zhou, Y. Q. Structure 2009, 17 (11), 1515. doi: 10.1016/j.str.2009.09.006
(28) Faraggi, E.; Zhang, T.; Yang, Y. D.; Kurgan, L.; Zhou, Y. Q. J. Comput. Chem. 2012, 33 (3), 259. doi: 10.1002/jcc.v33.3
(29) Frishman, D.; Argos, P. Proteins: Struct. Funct. Bioinf. 1995, 23 (4), 566.
(30) Heinig, M.; Frishman, D. Nucleic Acids Res. 2004, 32 (suppl 2), W500.
(31) Liu, F. F.; Ji, L.; Dong, X. Y.; Sun, Y. J. Phys. Chem. B 2009, 113 (32), 11320. doi: 10.1021/jp905580j
(32) Liu, F. F.; Dong, X. Y.; He, L. Z.; Middelberg, A. P. J.; Sun, Y. J. Phys. Chem. B 2001, 115 (41), 11879.
(33) Tegge, A. N.;Wang, Z.; Eickholt, J.; Cheng, J. L. Nucleic Acids Res. 2009, 37 (suppl 2),W515.

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固有无序超嗜热菌FlgM蛋白在两种不同温度下的构象变化特征

Conformational Change Characteristics in the Intrinsically Disordered FlgM Protein from a Hyperthermophile at Two Different Temperatures

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