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Journal of Molecular Graphics and Modelling

Volumn 29, Issue 7, 2011, Pages 928-934

Theoretical design of a specific DNA-Zinc-finger protein interaction with semi-empirical quantum chemical methods

(4) Nagy, Gábor a Gyurcsik, Béla a Hoffmann, Eufrozina A a Körtvélyesi, Tamás a

a UNIVERSITY OF SZEGED (Hungary)

Author keywords

DNA; Docking; PM6 DH2; Semi empirical quantum chemical methods; Zinc finger protein

Indexed keywords

BASE PAIRS; BINDING ENTHALPIES; COMPLEX STRUCTURE; DNA BINDING; DNA COMPLEX; DNA DUPLEXES; DNA MOLECULES; DOCKING CALCULATIONS; GASPHASE; INTERACTION ENTHALPIES; NON-SPECIFIC INTERACTIONS; OPTIMIZED STRUCTURES; PM6-DH2; PROTEIN INTERACTION; QUANTUM-CHEMICAL METHODS; SEMI-EMPIRICAL; SPECIFIC RECOGNITION; STACKING INTERACTION; THEORETICAL DESIGN; ZINC-FINGER PROTEIN;

COMPLEXATION; DOCKING; ENTHALPY; PROTEINS; QUANTUM CHEMISTRY; SOLVATION; ZINC;

DNA;

DNA; WATER; ZINC FINGER PROTEIN;

ARTICLE; CALCULATION; DNA BINDING; DNA PROTEIN COMPLEX; DNA STRUCTURE; ENTHALPY; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; QUANTUM CHEMISTRY; SOLVATION;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BINDING SITES; COMPUTER SIMULATION; DATABASES, PROTEIN; DNA; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; QUANTUM THEORY; THERMODYNAMICS; ZINC FINGERS;

EID: 79955792624 PISSN: 10933263 EISSN: None Source Type: Journal
DOI: 10.1016/j.jmgm.2011.03.002 Document Type: Article

Times cited : (12)

References (47)

1
- 1542364377
- D. Jantz, B.T. Amann, G.J. Gatto Jr., J.M. Berg, Chem. Rev. 104 (2004) 789-799.
- (2004) Chem. Rev. , vol.104 , pp. 789-799
- Jantz, D.¹ Amann, B.T.² Gatto Jr., G.J.³ Berg, J.M.⁴

2
- 33747816812
- J.G. Mandell, C.F.III Barbas, Nucleic Acids Res. 34 (2006) W516-W523.
- (2006) Nucleic Acids Res. , vol.34
- Mandell, J.G.¹ Barbas III, C.F.²

3
- 0025773296
- N.P. Pavletich, C.O. Pabo, Science 252 (1991) 809-817.
- (1991) Science , vol.252 , pp. 809-817
- Pavletich, N.P.¹ Pabo, C.O.²

4
- 15444366094
- T. Nakatsukasa, Y. Shiraishi, S. Negi, M. Imanishi, S. Futaki, Y. Sugiura, Biochem. Biophys. Res. Commun. 330 (2005) 247-252.
- (2005) Biochem. Biophys. Res. Commun. , vol.330 , pp. 247-252
- Nakatsukasa, T.¹ Shiraishi, Y.² Negi, S.³ Imanishi, M.⁴ Futaki, S.⁵ Sugiura, Y.⁶

5
- 0030032063
- Y.-G. Kim, J. Cha, S. Chandrasegaran, Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 1156-1160.
- (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 1156-1160
- Kim, Y.-G.¹ Cha, J.² Chandrasegaran, S.³

6
- 33646182222
- K. Beumer, G. Bhattacharya, M. Bibikova, J.K. Trautman, D. Carroll, Genetics 172 (2006) 2391-2403.
- (2006) Genetics , vol.172 , pp. 2391-2403
- Beumer, K.¹ Bhattacharya, G.² Bibikova, M.³ Trautman, J.K.⁴ Carroll, D.⁵

7
- 0036021389
- M. Bibikova, M. Golic, K.G. Golic, D. Carroll, Genetics 161 (2002) 1169-1175.
- (2002) Genetics , vol.161 , pp. 1169-1175
- Bibikova, M.¹ Golic, M.² Golic, K.G.³ Carroll, D.⁴

8
- 0034749283
- M. Bibikova, D. Carroll, D.J. Segall, J.K. Trautman, J. Smith, Y.-G. Kim, S. Chandrasegaran, Mol. Cell. Biol. 21 (2001) 289-297.
- (2001) Mol. Cell. Biol. , vol.21 , pp. 289-297
- Bibikova, M.¹ Carroll, D.² Segall, D.J.³ Trautman, J.K.⁴ Smith, J.⁵ Kim, Y.-G.⁶ Chandrasegaran, S.⁷

9
- 33750804666
- J. Morton, M.W. Davis, E.M. Jorgensen, D. Carroll, Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 16370-16375.
- (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 16370-16375
- Morton, J.¹ Davis, M.W.² Jorgensen, E.M.³ Carroll, D.⁴

10
- 13844319542
- M.A. Lloyd, C.L. Plaisier, D. Carroll, G.N. Drews, Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 2232-2237.
- (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 2232-2237
- Lloyd, M.A.¹ Plaisier, C.L.² Carroll, D.³ Drews, G.N.⁴

11
- 33644693285
- D.A. Wright, J.A. Townsend, R.J. Winfrey Jr., P.A. Irwin, J. Rajagopal, P.M. Lonosky, B.D. Hall, M.D. Jondle, D.F. Voytas, Plant J. 44 (2005) 693-705.
- (2005) Plant J. , vol.44 , pp. 693-705
- Wright, D.A.¹ Townsend, J.A.² Winfrey Jr., R.J.³ Irwin, P.A.⁴ Rajagopal, J.⁵ Lonosky, P.M.⁶ Hall, B.D.⁷ Jondle, M.D.⁸ Voytas, D.F.⁹

12
- 23744462771
- M. Mani, K. Kandavelou, F.J. Dy, S. Durai, S. Chandrasegaran, Biochem. Biophys. Res. Commun. 335 (2005) 447-457.
- (2005) Biochem. Biophys. Res. Commun. , vol.335 , pp. 447-457
- Mani, M.¹ Kandavelou, K.² Dy, F.J.³ Durai, S.⁴ Chandrasegaran, S.⁵

13
- 34447314165
- A. Pingoud, G.H. Silva, Nat. Biotechnol. 25 (2007) 743-744.
- (2007) Nat. Biotechnol. , vol.25 , pp. 743-744
- Pingoud, A.¹ Silva, G.H.²

14
- 35948946526
- A. Lombardo, P. Genovese, C.M. Beausejour, S. Colleoni, Y.L. Lee, K.A. Kim, D. Ando, F.D. Urnov, C. Galli, P.D. Gregory, M.C. Holmes, L. Naldini, Nat. Biotechnol. 25 (2007) 1298-1306.
- (2007) Nat. Biotechnol. , vol.25 , pp. 1298-1306
- Lombardo, A.¹ Genovese, P.² Beausejour, C.M.³ Colleoni, S.⁴ Lee, Y.L.⁵ Kim, K.A.⁶ Ando, D.⁷ Urnov, F.D.⁸ Galli, C.⁹ Gregory, P.D.¹⁰ Holmes, M.C.¹¹ Naldini, L.¹²

15
- 18944373328
- F.D. Urnov, J.C. Miller, Y.-L. Lee, C.M. Beausejour, J.M. Rock, S. Augustus, A.C. Jamieson, M.H. Porteus, P.D. Gregory, M.C. Holmes, Nature 435 (2005) 646-651.
- (2005) Nature , vol.435 , pp. 646-651
- Urnov, F.D.¹ Miller, J.C.² Lee, Y.-L.³ Beausejour, C.M.⁴ Rock, J.M.⁵ Augustus, S.⁶ Jamieson, A.C.⁷ Porteus, M.H.⁸ Gregory, P.D.⁹ Holmes, M.C.¹⁰

16
- 33847682924
- E.A. Moehle, J.M. Rock, Y.-L. Lee, Y. Jouvenot, R.C. DeKelver, P.D. Gregory, F.D. Urnov, M.C. Holmes, Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 3055-3060.
- (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 3055-3060
- Moehle, E.A.¹ Rock, J.M.² Lee, Y.-L.³ Jouvenot, Y.⁴ DeKelver, R.C.⁵ Gregory, P.D.⁶ Urnov, F.D.⁷ Holmes, M.C.⁸

17
- 4644370973
- G. Cossu, M. Sampaolesi, TRENDS Mol. Med. 10 (2004) 516-520.
- (2004) TRENDS Mol. Med. , vol.10 , pp. 516-520
- Cossu, G.¹ Sampaolesi, M.²

18
- 33845261384
- J.S. Chamberlain, Nature 444 (2006) 552-553.
- (2006) Nature , vol.444 , pp. 552-553
- Chamberlain, J.S.¹

19
- 16644402070
- K.J. Nowak, K.E. Davies, EMBO Rep. 5 (2004) 872-876.
- (2004) EMBO Rep. , vol.5 , pp. 872-876
- Nowak, K.J.¹ Davies, K.E.²

20
- 34250834236
- W. Nomura, Y. Sugiura, Methods Mol. Biol. 352 (2007) 83-93.
- (2007) Methods Mol. Biol. , vol.352 , pp. 83-93
- Nomura, W.¹ Sugiura, Y.²

21
- 33344464022
- M. Dhanasekaran, Sh. Negi, Y. Sugiura, Acc. Chem. Res. 39 (2006) 45-52.
- (2006) Acc. Chem. Res. , vol.39 , pp. 45-52
- Dhanasekaran, M.¹ Negi, Sh.² Sugiura, Y.³

22
- 0035712253
- D.J. Segall, C.F. Barbas III, Curr. Opin. Biotechnol. 12 (2001) 632-637.
- (2001) Curr. Opin. Biotechnol. , vol.12 , pp. 632-637
- Segall, D.J.¹ Barbas III, C.F.²

23
- 34347265280
- D. Carroll, J.J. Morton, K.J. Beumer, D.J. Segal, Nat. Protocols 1 (2006) 1329-1341.
- (2006) Nat. Protocols , vol.1 , pp. 1329-1341
- Carroll, D.¹ Morton, J.J.² Beumer, K.J.³ Segal, D.J.⁴

24
- 47349097567
- M.L. Maeder, S. Thibodeau-Beganny, A. Osiak, D.A. Wright, R.M. Anthony, M. Eic htinger, T. Jiang, J.E. Foley, R.J. Winfrey, J.A. Townsend, E. Unger-Wallace, J.D. Sander, F. Müller-Lerch, F. Fu, J. Pearlberg, C. Göbel1, J.P. Dassie, S.M. Pruett-Miller, M.H. Porteus, D.C. Sgroi, A.J. Iafrate, D. Dobbs, P.B. McCray Jr., T. Cathomen, D.F. Voytas, J.K. Joung, Mol. Cell 31 (2008) 294-301.
- (2008) Mol. Cell , vol.31 , pp. 294-301
- Maeder, M.L.¹ Thibodeau-Beganny, S.² Osiak, A.³ Wright, D.A.⁴ Anthony, R.M.⁵ Eic Htinger, M.⁶ Jiang, T.⁷ Foley, J.E.⁸ Winfrey, R.J.⁹ Townsend, J.A.¹⁰ Unger-Wallace, E.¹¹ Sander, J.D.¹² Müller-Lerch, F.¹³ Fu, F.¹⁴ Pearlberg, J.¹⁵ Göbel, C.¹⁶ Dassie, J.P.¹⁷ Pruett-Miller, S.M.¹⁸ Porteus, M.H.¹⁹ Sgroi, D.C.²⁰ more..

25
- 0031053362
- H.A. Greisman, C.O. Pabo, Science J.C.A.M.D. 275 (1997) 657-661.
- (1997) Science J.C.A.M.D. , vol.275 , pp. 657-661
- Greisman, H.A.¹ Pabo, C.O.²

26
- 0029822407
- A.C. Jamieson, H. Wang, S.-H. Kim, Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 12389-12834.
- (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 12389-12834
- Jamieson, A.C.¹ Wang, H.² Kim, S.-H.³

27
- 0029942895
- E.J. Rebar, H.A. Greisman, C.O. Pabo, Methods Enzymol. 267 (1996) 129-149.
- (1996) Methods Enzymol. , vol.267 , pp. 129-149
- Rebar, E.J.¹ Greisman, H.A.² Pabo, C.O.³

28
- 33646844421
- H. Ihara, M. Mie, H. Funabashi, F. Takahashi, T. Sawasaki, Y. Endo, E. Kobatake, Biochem. Biophys. Res. Commun. 345 (2006) 1149-1154.
- (2006) Biochem. Biophys. Res. Commun. , vol.345 , pp. 1149-1154
- Ihara, H.¹ Mie, M.² Funabashi, H.³ Takahashi, F.⁴ Sawasaki, T.⁵ Endo, Y.⁶ Kobatake, E.⁷

29
- 0037945507
- N. Gresh, P. Derreumaux, J. Phys. Chem. B 107 (2003) 4862-4870.
- (2003) J. Phys. Chem. B , vol.107 , pp. 4862-4870
- Gresh, N.¹ Derreumaux, P.²

30
- 35348991050
- T. Dudev, C. Lim, J. Am. Chem. Soc. 129 (2007) 12497-12504.
- (2007) J. Am. Chem. Soc. , vol.129 , pp. 12497-12504
- Dudev, T.¹ Lim, C.²

31
- 0034976978
- I.A. Topol, C. McGrath, E. Chertova, C. Dasenbrock, W.R. Lacourse, M.A. Eissenstat, S.K. Burt, L.E. Henderson, J.R. Casas-Finet, Prot. Sci. 10 (2008) 1434-1445.
- (2008) Prot. Sci. , vol.10 , pp. 1434-1445
- Topol, I.A.¹ McGrath, C.² Chertova, E.³ Dasenbrock, C.⁴ Lacourse, W.R.⁵ Eissenstat, M.A.⁶ Burt, S.K.⁷ Henderson, L.E.⁸ Casas-Finet, J.R.⁹

32
- 0025238867
- M.D. Carr, A. Pastore, H. Gausepohl, R. Franck, P. Roesch, J. Eur. Biochem. 188 (1990) 455-461.
- (1990) J. Eur. Biochem. , vol.188 , pp. 455-461
- Carr, M.D.¹ Pastore, A.² Gausepohl, H.³ Franck, R.⁴ Roesch, P.⁵

33
- 0029662017
- C.A. Kim, J.M. Berg, Nat. Struct. Biol. (1996) 940-945.
- (1996) Nat. Struct. Biol. , pp. 940-945
- Kim, C.A.¹ Berg, J.M.²

34
- 85135599642
- A. Pedretti, L. Villa, G. Vistoli, 18 (2004) 167-173
- A. Pedretti, L. Villa, G. Vistoli, 18 (2004) 167-173.

35
- 0035850731
- W.K. Olson, M. Bansal, S.K. Burley, R.E. Dickerson, M. Gerstein, S.C. Harvey, U. Heinemann, X.-J. Lu, S. Neidle, Z. Shakked, H. Sklenar, M. Suzuki, C.-S. Tung, E. Westhof, C. Wolberger, H.M. Berman, J. Mol. Biol. 313 (2001) 229-237.
- (2001) J. Mol. Biol. , vol.313 , pp. 229-237
- Olson, W.K.¹ Bansal, M.² Burley, S.K.³ Dickerson, R.E.⁴ Gerstein, M.⁵ Harvey, S.C.⁶ Heinemann, U.⁷ Lu, X.-J.⁸ Neidle, S.⁹ Shakked, Z.¹⁰ Sklenar, H.¹¹ Suzuki, M.¹² Tung, C.-S.¹³ Westhof, E.¹⁴ Wolberger, C.¹⁵ Berman, H.M.¹⁶

36
- 79955827016
- http://www.loria.fr/~ritchied/hex.

37
- 50549092426
- D.W. Ritchie, D. Kozakov, S. Vajda, Bioinformatics 24 (2008) 1865-1873.
- (2008) Bioinformatics , vol.24 , pp. 1865-1873
- Ritchie, D.W.¹ Kozakov, D.² Vajda, S.³

38
- 35448937584
- J.J.P. Stewart, J. Mol. Mod. 13 (2007) 1173-1213.
- (2007) J. Mol. Mod. , vol.13 , pp. 1173-1213
- Stewart, J.J.P.¹

39
- 73349120806
- J.J.P. Stewart, Mopac2009, http://www.openmopac.net/MOPAC2009.html.
- Mopac2009
- Stewart, J.J.P.¹

40
- 84961980743
- A. Klamt, G. Schüümann, J. Chem. Soc. Perkin Trans. 2 (1993) 799-805.
- (1993) J. Chem. Soc. Perkin Trans. , vol.2 , pp. 799-805
- Klamt, A.¹ Schüümann, G.²

41
- 77950139248
- M. Korth, M. Pitonák, J. Rezác, P. Hobza, J. Chem. Theory Comp. 6 (2010) 344-352.
- (2010) J. Chem. Theory Comp. , vol.6 , pp. 344-352
- Korth, M.¹ Pitonák, M.² Rezác, J.³ Hobza, P.⁴

42
- 67849101722
- J. Rezác, J. Fanfrlik, D. Salahub, P. Hobza, J. Chem. Theory Comp. 5 (2009) 1749-1760.
- (2009) J. Chem. Theory Comp. , vol.5 , pp. 1749-1760
- Rezác, J.¹ Fanfrlik, J.² Salahub, D.³ Hobza, P.⁴

43
- 84892303534
- keywords EPS and Mozyme
- MOPAC2009 Manual, www.openmopac.net (keywords EPS and Mozyme).
- MOPAC2009 Manual

44
- 0344839044
- D.J. Segal, R.R. Beerli, P. Blancafort, B. Dreier, K. Effertz, A. Huber, B. Koksch, C.V. Lund, L. Magnenat, D. Valente, Biochemistry 42 (2003) 2137-2148.
- (2003) Biochemistry , vol.42 , pp. 2137-2148
- Segal, D.J.¹ Beerli, R.R.² Blancafort, P.³ Dreier, B.⁴ Effertz, K.⁵ Huber, A.⁶ Koksch, B.⁷ Lund, C.V.⁸ Magnenat, L.⁹ Valente, D.¹⁰

45
- 0348110653
- P. Jurecka, P. Hobza, J. Am. Chem. Soc. 125 (2003) 15608-15613.
- (2003) J. Am. Chem. Soc. , vol.125 , pp. 15608-15613
- Jurecka, P.¹ Hobza, P.²

46
- 1542779956
- M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, G. Seifert, Phys. Rev. B 58 (1998) 7260-7268.
- (1998) Phys. Rev. B , vol.58 , pp. 7260-7268
- Elstner, M.¹ Porezag, D.² Jungnickel, G.³ Elsner, J.⁴ Haugk, M.⁵ Frauenheim, T.⁶ Suhai, S.⁷ Seifert, G.⁸

47
- 79955793799
- prepared for publication
- T. Körtvélyesi, E.A. Hoffmann, I. Pálinkó, G. Nagy, B. Gyurcsik, B. Penke, prepared for publication.
- Körtvélyesi, T.¹ Hoffmann, E.A.² Pálinkó, I.³ Nagy, G.⁴ Gyurcsik, B.⁵ Penke, B.⁶

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