Chem. J. Chinese Universities ›› 2016, Vol. 37 ›› Issue (10): 1809.doi: 10.7503/cjcu20160375
• Physical Chemistry • Previous Articles Next Articles
SHEN Wen1, SHAO Xueguang1,2, CAI Wensheng1,*()
Received:
2016-05-25
Online:
2016-10-10
Published:
2016-09-23
Contact:
CAI Wensheng
E-mail:wscai@nankai.edu.cn
Supported by:
CLC Number:
TrendMD:
SHEN Wen, SHAO Xueguang, CAI Wensheng. Inclusion Mechanism of Cyclodextrins with Glutathione†[J]. Chem. J. Chinese Universities, 2016, 37(10): 1809.
Fig.2 Initial spacial arrangements of molecular systems with two orientations of GSH towards the CDs(A) Orien(Ⅰ); (B) Orien(Ⅱ). ξ: Projection onto the Z axis of the distance between the center of mass of Glu and that of CD.
System | Method | Number of atoms | Time/ns |
---|---|---|---|
GSH: α-CD[Gly(Ⅰ)]a | MD | 7243 | 10 |
GSH: α-CD[Gly(Ⅱ)]b | MD | 7147 | 10 |
GSH: α-CD[Glu(Ⅰ)]c | MD + ABF | 7243 | 10+100 |
GSH: α-CD[Glu(Ⅱ)]d | MD + ABF | 7579 | 10+100 |
GSH: α-CD[Cys(Ⅰ)]e | MD | 7099 | 10 |
GSH: α-CD[Cys(Ⅱ)]f | MD | 7228 | 10 |
GSH: β-CD[Gly(Ⅰ)]a | MD | 7546 | 10 |
GSH: β-CD[Gly(Ⅱ)]b | MD | 7753 | 10 |
GSH: β-CD[Glu(Ⅰ)]c | MD + ABF | 7270 | 10+100 |
GSH: β-CD[Glu(Ⅱ)]d | MD + ABF | 7777 | 10+100 |
GSH: β-CD[Cys(Ⅰ)]e | MD | 7168 | 10 |
GSH: β-CD[Cys(Ⅱ)]f | MD | 7753 | 10 |
GSH: γ-CD[Gly(Ⅰ)]a | MD | 7450 | 10 |
GSH: γ-CD[Gly(Ⅱ)]b | MD | 8008 | 10 |
GSH: γ-CD[Glu(Ⅰ)]c | MD + ABF | 7450 | 10+100 |
GSH: γ-CD[Glu(Ⅱ)]d | MD + ABF | 8008 | 10+100 |
GSH: γ-CD[Cys(Ⅰ)]e | MD | 7783 | 10 |
GSH: γ-CD[Cys(Ⅱ)]f | MD | 7666 | 10 |
Table 1 Summary of simulation systems with GSH and CDs
System | Method | Number of atoms | Time/ns |
---|---|---|---|
GSH: α-CD[Gly(Ⅰ)]a | MD | 7243 | 10 |
GSH: α-CD[Gly(Ⅱ)]b | MD | 7147 | 10 |
GSH: α-CD[Glu(Ⅰ)]c | MD + ABF | 7243 | 10+100 |
GSH: α-CD[Glu(Ⅱ)]d | MD + ABF | 7579 | 10+100 |
GSH: α-CD[Cys(Ⅰ)]e | MD | 7099 | 10 |
GSH: α-CD[Cys(Ⅱ)]f | MD | 7228 | 10 |
GSH: β-CD[Gly(Ⅰ)]a | MD | 7546 | 10 |
GSH: β-CD[Gly(Ⅱ)]b | MD | 7753 | 10 |
GSH: β-CD[Glu(Ⅰ)]c | MD + ABF | 7270 | 10+100 |
GSH: β-CD[Glu(Ⅱ)]d | MD + ABF | 7777 | 10+100 |
GSH: β-CD[Cys(Ⅰ)]e | MD | 7168 | 10 |
GSH: β-CD[Cys(Ⅱ)]f | MD | 7753 | 10 |
GSH: γ-CD[Gly(Ⅰ)]a | MD | 7450 | 10 |
GSH: γ-CD[Gly(Ⅱ)]b | MD | 8008 | 10 |
GSH: γ-CD[Glu(Ⅰ)]c | MD + ABF | 7450 | 10+100 |
GSH: γ-CD[Glu(Ⅱ)]d | MD + ABF | 8008 | 10+100 |
GSH: γ-CD[Cys(Ⅰ)]e | MD | 7783 | 10 |
GSH: γ-CD[Cys(Ⅱ)]f | MD | 7666 | 10 |
Fig.4 Free-energy profiles for the inclusion of the Glu of GSH into CDs in two orientations(A) GSH:α-CD; (B) GSH:β-CD; (C) GSH:γ-CD. a. Orien(Ⅰ); b. Orien(Ⅱ).
Fig.5 Structures of the inclusion complexes of GSH with CD near the global minima of the PMFs in Fig.4(A1) GSH with α-CD, Orien(Ⅰ): ξ=-0.02 nm, d=0.05 nm, θ=14°; (A2) Orien(Ⅱ): ξ=-0.04 nm, d=0.22 nm, θ=12°; (B1) GSH with β-CD, Orien(Ⅰ): ξ=-0.30 nm, d=0.31 nm, θ=28°; (B2) Orien(Ⅱ): ξ=-0.18 nm, d=0.28 nm, θ=22°; (C1) GSH with γ-CD, Orien(Ⅰ): ξ=-0.10 nm, d=0.49 nm, θ=43°; (C2) Orien(Ⅱ): ξ=-0.05 nm, d=0.44 nm, θ=37°. ξ: Reaction coordinate in Fig.4; d: distance between the center of mass of Glu and the principal axis of CD; θ: angle between the side chain of Glu and the principal axis of CD.
Fig.6 Variation of average number of hydrogen bonds formed between GSH and α-CD as a function of the model reaction coordinate(A) and hydrogen bonds formed between GSH and α-CD(near the global minima of the PMF)(B)
Fig.7 Fluctuation of the area of the central plane formed by the six primary side carbon atoms(A) and the six glycosidic oxygen atoms(B) of the α-CD in the course of the threading process
Fig.9 Structure of GSH-(A), free-energy profile for the inclusion of the Glu of GSH- into α-CD in Orien(I)(B) and structure of the inclusion complex of α-CD with GSH- near the global minima of the PMF(C)
[1] | Zetterstrom R., Eijkman C., Hopkins F. G., Acta Paediatr., 2006, 95(11), 1331—1333 |
[2] | Dixon D. P., Skipsey M., Grundy N. M., Plant Physiol., 2005, 138,2233—2244 |
[3] | Garcia-Fuentes M., Trapani A., Alonso M. J., Eur. J. Pharm. Biopharm., 2006, 64(2), 146—153 |
[4] | Song L. X., Guo Z. J., Chinese J. Inorg. Chem., 2001, 17(4), 457—470 |
(宋乐新, 郭子建.无机化学学报, 2001,17(4), 457—470) | |
[5] | You C.C., Liu Y., Chem. J. Chinese Universities, 2000, 21(2), 249—251 |
(尤长城, 刘育.高等学校化学学报, 2000,21(2), 249—251) | |
[6] | You C.C., Zhao Y. L., Liu Y., Chem. J. Chinese Universities, 2001, 22(2), 218—222 |
(尤长城, 赵彦利, 刘育.高等学校化学学报, 2001,22(2), 218—222) | |
[7] | Song L. X.,Wang H. M., Yang Y., Acta Chim. Sinica, 2007, 65(16), 1593—1599 |
(宋乐新, 王海名, 杨燕.化学学报, 2007,65(16), 1593—1599) | |
[8] | He J., Feng X. Z., Shao X. G., Cai W. S., Chem. J. Chinese Universities, 2015, 36(1), 110—115 |
(何佳, 冯喜增, 邵学广, 蔡文生.高等学校化学学报, 2015,36(1), 110—115) | |
[9] | Cai W. S., Sun T. T., Shao X. G., Chipot C., J. Phys. Chem. B, 2009, 113(22), 7836—7843 |
[10] | Harata K., Bull. Chem. Soc. Jpn., 1975, 48(9), 2409—2413 |
[11] | Lindner K., Saenger W., Carbohydr Res., 1982, 99(2), 103—115 |
[12] | Harata K., Bull. Chem. Soc. Jpn., 1987, 60(8), 2763—2767 |
[13] | 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 |
[14] | 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 |
[15] | MacKerell A. D., Feig M., Brooks C. L., J. Comput. Chem., 2004, 25(11), 1400—1415 |
[16] | Jorgensen W. L., Chandrasekhar J., Madura J. D., Impey R. W., Klein M. L., J. Chem. Phys., 1983, 79(2), 926—935 |
[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] | Feller S. E., Zhang Y. H., Pastor R. W., Brooks B. R., J. Chem. Phys., 1995, 103(11), 4613—4621 |
[21] | Humphrey W., Dalke A., Schulten K., J. Mol. Graphics, 1996, 14(1), 33—38 |
[22] | Wang S. S., Liu P., Cai W. S., Shao X. G., Chem. J. Chinese Universities, 2015, 36(11), 2211—2219 |
(汪双双, 刘鹏, 蔡文生, 邵学广.高等学校化学学报, 2015,36(11), 2211—2219) | |
[23] | Darden T., York D., Pedersen L., J. Chem. Phys., 1993, 98(12), 10089—10092 |
[24] | Darve E., Pohorille A., J. Chem. Phys., 2001, 115(20), 9169—9183 |
[25] | Hénin J., Chipot C., J. Chem. Phys., 2004, 121(7), 2904—2914 |
[26] | Rodríguez-Gómez D., Darve E., Pohorille A., J. Chem. Phys., 2004, 120(8), 3563—3578 |
[27] | Chipot C., Hénin J., J. Chem. Phys., 2005, 123(24), 244906 |
[28] | Hénin J., Fiorin G., Chipot C., Klein M. L., J. Chem. Theory Comput., 2010, 6(1), 35—47 |
[29] | Lampela O., Juffer A. H., Rauk A., J. Phys. Chem. A, 2003, 107(43), 9208—9220 |
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