疏水蛋白在云母表面的吸附

doi:10.7503/cjcu20140808

高等学校化学学报 ›› 2015, Vol. 36 ›› Issue (1): 110.doi: 10.7503/cjcu20140808

疏水蛋白在云母表面的吸附

何佳¹, 冯喜增^2,³, 邵学广^1,², 蔡文生¹()

1. 天津化学化工协同创新中心, 南开大学化学学院分析科学研究中心
2. 药物化学生物学国家重点实验室, 3. 生命科学学院, 天津 300071

收稿日期:2014-09-05 修回日期:2014-12-15 出版日期:2015-01-10 发布日期:2014-12-15
作者简介:联系人简介: 蔡文生, 女, 博士, 教授, 博士生导师, 主要从事分子模拟和化学信息学研究. E-mail: wscai@nankai.edu.cn
基金资助:
国家自然科学基金(批准号: 21373117)资助

Adsorption Behavior of Hydrophobin Proteins on Surface of Mica^†

HE Jia¹, FENG Xizeng^2,³, SHAO Xueguang^1,², CAI Wensheng^1,^*()

1. Collaborative Innovation Center of Chemical Science and Engineering(Tianjin), Research Center for Analytical Sciences, College of Chemistry
2. State Key Laboratory of Medicinal Chemical Biology,3. College of Life Science, Nankai University, Tianjin 300071, China

Received:2014-09-05 Revised:2014-12-15 Online:2015-01-10 Published:2014-12-15
Contact: CAI Wensheng E-mail:wscai@nankai.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China(No21373117)

摘要/Abstract

摘要：

采用分子动力学模拟方法研究了疏水蛋白(HFBI)在亲水云母表面的吸附过程. 通过6组平行的分子动力学模拟得到了2种不同的稳定吸附结构, 即通过N端和通过亲水的α螺旋与表面吸附, 得到了5种吸附残基. 进一步用自适应偏置力方法计算了所有吸附残基与表面的结合自由能. 结果表明, 残基Lys是吸附过程的关键残基, 即当HFBI通过含有Lys残基的α螺旋与云母表面作用时, 其吸附构象最稳定. 静电作用是吸附过程的主要驱动力. 在该吸附结构中, HFBI的疏水面暴露在溶液中, 有效降低了云母表面的润湿性.

关键词: 疏水蛋白, 云母, 分子动力学模拟, 自由能计算, 吸附构象, 自适应偏置力方法

Abstract:

Atomistic molecular dynamics(MD) simulations were conducted to elucidate the adsorption beha-vior of hydrophobin protein(HFBI) on the hydrophilic mica surface. Six independent simulations starting from three representative initial orientations of HFBI toward the surface were performed. The adsorbed patches are clustered into two classes, namely the α-helix and the N-terminal part. The main secon-dary structures of protein were preserved in the entire course of adsorption due to four disulfide bonds. Furthermore, binding free energies of five different adsorbed residues were calculated employing the adaptive biasing force method. The results showed that Lys was the key residue for the adsorption. It can be deduced that the adsorption of HFBI via the α-helix part consisting of Gln36, Asn37, Lys50, and Thr51 is most energetically favored. Electrostatic interactions constitute the main driving forces responsible for the adsorption of HFBI on the mica surface. In the most stable adsorbed structure, the hydrophobic patch was exposed in the aqueous media, leading to the reduction of the wettability of mica.

Key words: Hydrophobin protein, Mica, Molecular dynamics simulation, Free-energy calculation, Adsorbed structure, Adaptive biasing force method

中图分类号:

O641

TrendMD:

何佳, 冯喜增, 邵学广, 蔡文生. 疏水蛋白在云母表面的吸附. 高等学校化学学报, 2015, 36(1): 110.

HE Jia, FENG Xizeng, SHAO Xueguang, CAI Wensheng. Adsorption Behavior of Hydrophobin Proteins on Surface of Mica^†. Chem. J. Chinese Universities, 2015, 36(1): 110.

图/表 9

Fig.1 Initial structures of HFBI(A) and mica(B)HFBI is represented by new cartoon style.

Fig.2 Initial conformations of the molecular systems with three orientations of HFBI towards the surface of mica Three possible orientations are denoted as O1(A), O2(B) and O3(C), indicating the helix of HFBI back to, face to and vertical to the Mica surface. The drawing and coloring style is the same as Fig.1. The water and the ions are omitted for clarity.

Fig.3 Center of mass distance between HFBI and micas as a function of simulation time(A) and time evolution of interaction energy between HFBI and mica(B)

Fig.4 Final conformations of HFBI after the adsorption on Mica The adsorbed patches are clustered into two classes, namely the α-helix(O1-1, O1-2, O3-1) and N-terminus(O2-1, O2-2, O3-2). The adsorbed residues are highlighted in licorice and the rest of drawing and coloring style is the same as Fig.1. The water molecules are omitted for clarity.

Fig.5 RMSF of backbone carbon atoms of HFBI averaged by the whole trajectory

Table 1 Summary of the simulated systems with averaged HFBI properties by the last 10 ns simulations

System	RMSD/nm	R_g/nm	Eccentricity	System	RMSD/nm	R_g/nm	Eccentricity
O1-1	0.19±0.01	1.08±0.01	0.10±0.01	O2-2	0.19±0.01	1.09±0.01	0.08±0.03
O1-2	0.16±0.01	1.08±0.01	0.11±0.02	O3-1	0.30±0.02	1.12±0.01	0.14±0.02
O2-1	0.34±0.07	1.14±0.01	0.10±0.02	O3-2	0.18±0.01	1.09±0.01	0.07±0.02

Fig.6 Free-energy profiles for the adsorption of Lys(A), Ser(B), Asn(C), Gln(D) and Thr(E) on the mica surface Inset: Number of samples(N) vs. distance.

Fig.7 Snapshots of the adsorption structures of Lys(A) and Ser(B) near the global minima of the PMFs The residues are highlighted in licorice. Water and ion molecules are omitted for clarity.

Fig.8 Decomposition of the total free energy into Lys-Mica(A) and Ser-Mica(B) a. van der Waals interaction; b. electrostatic interaction.

参考文献 26

[1]	Linder M. B., Curr. Opin. Colloid In., 2009, 14(5), 356—363
[2]	Liu Y. Z., Wu M., Feng X. Z., Shao X. G., Cai W. S., J. Phys. Chem. B, 2012, 116(40), 12227—12234
[3]	Liu Y. Z., Cai W. S., Shao X. G., Chem. J. Chinese Universities, 2012, 33(9), 2013—2018
	(刘英哲, 蔡文生, 邵学广. 高等学校化学学报, 2012, 33(9), 2013—2018 )
[4]	Wang L. K., Feng X. Z., Hou S., Chan Q. L., Qin M., Surf. Interface. Anal., 2006, 38, 44—50
[5]	Qin M., Wang L. K., Feng X. Z., Yang Y. L., Wang R., Wang C., Yu L., Shao B., Qiao M. Q., Langmuir , 2007, 23, 4465—4471
[6]	He J., Wu M., Feng X. Z., Shao X. G., Cai W. S., RSC Advances, 2014, 4(26), 13304—13312
[7]	Brancolini G., Kokh D. B., Calzolai L., Wade R. C., Corni S., ACS Nano, 2012, 6, 9863—9878
[8]	Schlegel M. L., Nagy K. L., Fenter P., Cheng L., Sturchio N. C., Jacobsen S. D., Geochim. Cosmochim. Ac., 2006, 70, 3549—3565
[9]	Cheng T., Sun H., J. Phys. Chem. C, 2012, 116, 16436—16446
[10]	Phillips J. C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R. D., Kale L., Schulten K., J. Comput. Chem., 2005, 26(16), 1781—1802
[11]	MacKerell A. D., Bashford D., Bellott M., Dunbrack 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., 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(18), 3586—3616
[12]	Mackerell A. D., Feig M., Brooks C. L., J. Comput. Chem., 2004, 25(11), 1400—1415
[13]	Jorgensen W. L., Chandrasekhar J., Madura J. D., Impey R. W., Klein M. L., J. Chem. Phys., 1983, 79(2), 926—935
[14]	Heinz H., Koerner H., Anderson K. L., Vaia R. A., Farmer B. L., Chem. Mater., 2005, 17, 5658—5669
[15]	Feller S. E., Zhang Y., Pastor R. W., Brooks B. R., J. Chem. Phys., 1995, 103, 4613—4621
[16]	Tuckerman M., Berne B. J., Martyna G. J., J. Chem. Phys., 1992, 97(3), 1990—2001
[17]	Ryckaert J. P., Ciccotti G., Berendsen H. J. C., J. Comput. Phys., 1977, 23(3), 327—341
[18]	Andersen H. C., J. Comput. Phys., 1983, 52(1), 24—34
[19]	Miyamoto S., Kollman P. A., J. Comput. Chem., 1992, 13(8), 952—962
[20]	Darden T., York D., Pedersen L., J. Chem. Phys., 1993, 98(12), 10089—10092
[21]	Humphrey W., Dalke A., Schulten K., J. Mol. Graphics, 1996, 14(1), 33—38
[22]	Hoefling M., Iori F., Corni S., Gottschalk K. E., Langmuir , 2010, 26(11), 8347—8351
[23]	Darve E., Pohorille A., J. Chem. Phys., 2001, 115, 9169—9183
[24]	Hénin J., Chipot C., J. Chem. Phys., 2004, 121, 2904—2914
[25]	Hénin J., Fiorin G., Chipot C., Klein M. L., J. Chem. Theory Comput., 2010, 6, 35—47
[26]	Fiorin G., Klein M. L., Hénin J., Mol. Phys., 2013, 111, 22—23

疏水蛋白在云母表面的吸附

Adsorption Behavior of Hydrophobin Proteins on Surface of Mica^†

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疏水蛋白在云母表面的吸附

Adsorption Behavior of Hydrophobin Proteins on Surface of Mica†

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Adsorption Behavior of Hydrophobin Proteins on Surface of Mica^†