Adsorption Behavior of Hydrophobin Proteins on Surface of Mica†

doi:10.7503/cjcu20140808

Abstract

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

CLC Number:

O641

TrendMD:

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

Figures/Tables 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.

References 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