Chem. J. Chinese Universities ›› 2015, Vol. 36 ›› Issue (11): 2271.doi: 10.7503/cjcu20150651
• Physical Chemistry • Previous Articles Next Articles
WANG Mei1,2, WANG Jun1, BU Yuxiang1,*()
Received:
2015-08-14
Online:
2015-11-10
Published:
2015-10-21
Contact:
BU Yuxiang
E-mail:byx@sdu.edu.cn
CLC Number:
TrendMD:
WANG Mei, WANG Jun, BU Yuxiang. Metastable Hydrogen-bonds Featuring Negative Dissociation Energies in Protein-bound DNA in Hole Migration[J]. Chem. J. Chinese Universities, 2015, 36(11): 2271.
Fig.2 Optimized geometrical structures of eight complexes ArgH+-G+C-n(n=1—8) in which positive charged arginine residue resides in the major-groove face of DNA base pair
Complex | R(N—H…N) | R(N—H…O) | RE | ΔE | ΔEBSSE | DE | AIP |
---|---|---|---|---|---|---|---|
ArgH+-G+C-1 | 0.2354 | 0.2123 | 11.25 | -118.95 | -120.79 | 5.56 | 911.19 |
ArgH+-G+C-2 | 0.2203 | 0.2290 | 9.75 | -117.45 | -119.04 | 4.81 | 908.51 |
ArgH+-G+C-3 | 0.2150 | 0.2003 | 3.01 | -110.67 | -113.22 | 5.98 | 919.22 |
ArgH+-G+C-4 | 0.2101 | 0.2017 | 0.38 | -108.07 | -110.46 | 6.07 | 918.05 |
ArgH+-G+C-5 | 0.2153 | 0.2429 | 9.87 | -117.53 | -119.12 | 4.56 | 920.73 |
ArgH+-G+C-6 | 0.2101 | 0.2050 | 0 | -111.21 | -113.72 | 6.40 | 937.09 |
ArgH+-G+C-7 | 0.2104 | 0.2011 | 3.51 | -107.70 | -110.08 | 5.94 | 934.50 |
ArgH+-G+C-8 | 0.2117 | 0.2687 | 11.21 | -118.87 | -120.67 | 4.48 | 922.99 |
Table 1 Lengths(nm) of two hydrogen bonds(N—H…N7 H-bond and N—H…O6 H-bond) and dissociation energies(ΔE) of eight complexes ArgH+-G+C-n(n=1—8)*
Complex | R(N—H…N) | R(N—H…O) | RE | ΔE | ΔEBSSE | DE | AIP |
---|---|---|---|---|---|---|---|
ArgH+-G+C-1 | 0.2354 | 0.2123 | 11.25 | -118.95 | -120.79 | 5.56 | 911.19 |
ArgH+-G+C-2 | 0.2203 | 0.2290 | 9.75 | -117.45 | -119.04 | 4.81 | 908.51 |
ArgH+-G+C-3 | 0.2150 | 0.2003 | 3.01 | -110.67 | -113.22 | 5.98 | 919.22 |
ArgH+-G+C-4 | 0.2101 | 0.2017 | 0.38 | -108.07 | -110.46 | 6.07 | 918.05 |
ArgH+-G+C-5 | 0.2153 | 0.2429 | 9.87 | -117.53 | -119.12 | 4.56 | 920.73 |
ArgH+-G+C-6 | 0.2101 | 0.2050 | 0 | -111.21 | -113.72 | 6.40 | 937.09 |
ArgH+-G+C-7 | 0.2104 | 0.2011 | 3.51 | -107.70 | -110.08 | 5.94 | 934.50 |
ArgH+-G+C-8 | 0.2117 | 0.2687 | 11.21 | -118.87 | -120.67 | 4.48 | 922.99 |
Fig.3 Schematic profiles of PES along WC and Hoogsteen H-bond dissociation coordinates of trimer complex units in their initial(ArgH+-GC) and oxidized(ArgH+-G+C) The corresponding dissociation are also shown. All the energies are expressed in kJ/mol.
Fig.7 Effects of R(ArgH+…O6)(the distance between ArgH+ and O6 atom) on attraction interaction between ArgH+ and GC in ArgH+-GC, and added electrostatic repulsion upon one-electron oxidation The data for this figure are given in Table S4(see the Electronic Supporting Information of this paper).
Fig.8 Potential energy surfaces of complexes XGC, X+GC(A) and their one-electron oxidized derivatives(XGC)+ and (X+GC)+(B) when the monomer X(or X+) is separated from GC and G+C, respectively En is the corresponding energy; the corresponding IPs are also shown.
Fig.10 Schematic representation of potential energy landscapes through duplex DNA oligomers The DNA sequence is shown in Fig.S1. The “G”, “GG” and “GGG” denote an “isolated” guanine and two or three adjacent guanines, respectively. The “T” or “A” or “C” separates G or GG steps. The X-axis(“G-index”) indicates the position of guanines, GG steps, and GGG triplet along the oligomer and the energy barriers may be one base pair or some base pairs. The numbers in black and red indicate the band intensity relative to that of G24 in the protein-bound DNA duplex in the absence and presence of BamHI.
[1] | Burrows C. J., Muller J. G., Chem. Rev., 1998, 98, 1109—1152 |
[2] | LePage F., Guy A., Cadet J., Sarasin A., Gentil A., Nucleic Acids Res., 1998, 26, 1276—1281 |
[3] | Burrows C. J., Muller J. G., Chem. Rev., 1998, 98, 1109—1152 |
[4] | Hirakawa K., Ota K., Hirayama J., Oikawa S., Kawanishi S., Chem. Res. Toxicol., 2014, 27(4), 649—655 |
[5] | Melvin T., Botchway S., Parker A. W., O’Neill P. J., Chem. Soc. Chem. Commun., 1995, 5, 653—654 |
[6] | Steenken S., Jovanovic S. V., J. Am. Chem. Soc., 1997, 119, 617—618 |
[7] | Jortner J., Bixon M., Langenbacher T., Michael-Beyerle M. E., Proc. Natl. Acad. Sci., 1998, 95, 12759—12765 |
[8] | Berlin Y. A., Burin A. L., Ratner M. A., J. Am. Chem. Soc. ,2000, 122, 10903—10909 |
[9] | Schuster G. B., Acc. Chem. Res. 2000, 33, 253—260 |
[10] | Lewis F. D., Letsinger R. L., Wasielewski M. R., Acc. Chem. Res., 2001, 34, 159—170 |
[11] | Wang J., Sun L.X., Bu Y. X., J. Phys. Chem. B, 2010, 114, 1144—1147 |
[12] | Echols H., Science, 1986, 233, 1050—1056 |
[13] | Kathuria P., Sharma P., Abendong M. N., Wetmore S. D., Biochemistry, 2015, 54(15), 2414—2428 |
[14] | Qin P. H., Lü W. C., Qin W., Zhang W., Xie H., Chem. Res. Chinese Universities, 2014, 30(1), 125—129 |
[15] | Corbella M., Voityuk A. A., Curutchet.C., J. Phys. Chem. Lett., 2015, 6(18), 3749—3753 |
[16] | Paillard G., Lavery R., Structure, 2004, 12, 113—122 |
[17] | Peters M., Rozas I., Alkorta I., Elguero J., J. Phys. Chem. B, 2003, 107, 323—330 |
[18] | Wintjens R., Lievin J., Rooman M., Buisine E., J. Mol. Biol., 2000, 302(2), 395—410 |
[19] | Warner D. R., Weinstein L. S., Proc. Natl. Acad. Sci., 1999, 96, 4268—4272 |
[20] | Bond P. J., Guy A. T., Heron A. J., Bayley H., Khalid S., Biochemistry, 2011, 50(18), 3777—3783 |
[21] | Jantz D., Berg J. M., J. Am. Chem. Soc., 2003, 125, 4960—4961 |
[22] | Cheng A. C., Chen W. W., Fuhrmann C. N., Frankel A. D., J. Mol. Biol., 2003, 327, 781—796 |
[23] | Allers J., Shamoo Y., J. Mol. Biol., 2001, 311, 75—86 |
[24] | Davey C. A., Sargent D. F., Luger K., Maeder A. W., Richmond T. J., J. Mol. Biol., 2002, 319, 1097—1113 |
[25] | Widom J., Annu. Rev. Biophys. Biomol. Struct., 1998, 27, 285—327 |
[26] | Harp J. M., Hanson B. L., Tim D. E., Bunick G. J., Biol. Crystallogr., 2000, 56, 1513—1534 |
[27] | Newman M., Strzelecka T., Dorner L. F., Schildkraut I., Aggarwal A. K., Science, 1995, 269, 656—663 |
[28] | Rajski S. R., Barton J. K., Biochemistry, 2001, 40, 5556—5564 |
[29] | Nunez M. E., Noyes K. T., Barton J. K., Chem. Biol., 2002, 9, 403—406 |
[30] | Voityuk A. A., Davis W. B., J. Phys. Chem. B, 2007, 111, 2976—2985 |
[31] | Bjorklund C. C., Davis W. B., Nucleic Acids Res., 2006, 34, 1836—1847 |
[32] | Nakatani K., Dohno C., Saito I., J. Am. Chem. Soc., 2002, 124(24), 6802—6803 |
[33] | Becke A. D., J. Chem. Phys., 1993, 98, 1372—1377 |
[34] | Lee C., Yang W., Parr R. G., Phys. Rev. B, 1988, 37, 785—789 |
[35] | Frisch M.J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Zakrzewski V. G., Montgomery J. A., Stratmann Jr., R.E., Burant J. C., Dapprich S., Millam J. M., Daniels A. D., Kudin K. N., Strain M. C., Farkas O., Tomasi J., Barone V., Cossi M., Cammi R., Mennucci B., Pomelli C., Adamo C., Clifford S., Ochterski J., Petersson G. A., Ayala P. Y., Cui Q., Morokuma K., Rega N., Salvador P., Dannenberg J. J., Malick D. K., Rabuck A. D., Raghavachari K., Foresman J. B., Cioslowski J., Ortiz J.V., Baboul A. G., Stefanov B. B., Liu G., Liashenko A., Piskorz P., Komaromi I., Gomperts R., Martin R. L., Fox D. J., Keith T., Al-Laham M. A., Peng C. Y., Nanayakkara A., Challacombe M., Gill P. M. W., Johnson B., Chen W., Wong M. W., Andres J. L., Gonzalez C., Head-Gordon M., Replogle E.S., Pople J. A., Gaussian 03, Gaussian Inc., Pittsburgh, PA, 2003 |
[36] | Boys S. F., Bernardi F., Mol. Phys., 1970, 19, 553—566 |
[37] | Cioslowski J., Nanayakkara A., Challacombe M., Chem. Phys. Lett., 1993, 203, 137—142 |
[38] | Cioslowski J., Surjan P. R., J. Mol. Struct.: Theochem., 1992, 255, 9—33 |
[39] | Bader R. F. W., Encyclopedia of Computational Chemistry, 1998, 1, 64—86 |
[40] | Bader R. F. W., Chem. Rev., 1991, 91, 893—928 |
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