Sequence-specific recognition of cancer drug-DNA adducts by HMGB1a repair protein

Biophysical Journal

Volumn 102, Issue 10, 2012, Pages 2331-2338

  Elder, Robert M ^a   Jayaraman, Arthi ^a  

^a University of Colorado at Boulder   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT; CISPLATIN; DNA; HIGH MOBILITY GROUP B1 PROTEIN; OXALIPLATIN; PLATINUM COMPLEX; THYMINE;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DNA ADDUCT; DNA REPAIR; METABOLISM; NEOPLASM; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; THERMODYNAMICS;

ANTINEOPLASTIC AGENTS; BASE SEQUENCE; CISPLATIN; COMPUTER SIMULATION; DNA ADDUCTS; DNA REPAIR; DNA, NEOPLASM; HMGB1 PROTEIN; NEOPLASMS; NUCLEIC ACID CONFORMATION; ORGANOPLATINUM COMPOUNDS; PROTEIN BINDING; THERMODYNAMICS; THYMINE;

EID: 84861152869     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.04.013     Document Type: Article

References (52)

1. E.R. Jamieson, and S.J. Lippard Structure, recognition, and processing of cisplatin-DNA adducts Chem. Rev. 99 1999 2467 2498
2. D. Wang, and S.J. Lippard Cellular processing of platinum anticancer drugs Nat. Rev. Drug Discov. 4 2005 307 320 (Pubitemid 41130944)
3. J.M. Woynarowski, and S. Faivre P.E. Juniewicz Oxaliplatin-induced damage of cellular DNA Mol. Pharmacol. 58 2000 920 927
4. S.G. Chaney, and S.L. Campbell Y. Wu Recognition and processing of cisplatin- and oxaliplatin-DNA adducts Crit. Rev. Oncol. Hematol. 53 2005 3 11 (Pubitemid 39656106)
5. M. Wei, and S.M. Cohen S.J. Lippard Effects of spectator ligands on the specific recognition of intrastrand platinum-DNA cross-links by high mobility group box and TATA-binding proteins J. Biol. Chem. 276 2001 38774 38780
6. J. Malina, and O. Novakova V. Brabec Conformation of DNA GG intrastrand cross-link of antitumor oxaliplatin and its enantiomeric analog Biophys. J. 93 2007 3950 3962 (Pubitemid 350223811)
7. J.C. Huang, and D.B. Zamble A. Sancar HMG-domain proteins specifically inhibit the repair of the major DNA adduct of the anticancer drug cisplatin by human excision nuclease Proc. Natl. Acad. Sci. USA 91 1994 10394 10398 (Pubitemid 24329003)
8. D.S. Pilch, and S.U. Dunham K.J. Breslauer DNA sequence context modulates the impact of a cisplatin 1,2-d(GpG) intrastrand cross-link on the conformational and thermodynamic properties of duplex DNA J. Mol. Biol. 296 2000 803 812
9. S.U. Dunham, and S.J. Lippard DNA sequence context and protein composition modulate HMG-domain protein recognition of cisplatin-modified DNA Biochemistry 36 1997 11428 11436 (Pubitemid 27408625)
10. S.M. Cohen, and Y. Mikata S.J. Lippard HMG-domain protein recognition of cisplatin 1,2-intrastrand d(GpG) cross-links in purine-rich sequence contexts Biochemistry 39 2000 11771 11776
11. R.M. Elder, and A. Jayaraman Role of structure and dynamics of DNA with cisplatin and oxaliplatin adducts in various sequence contexts on binding of HMGB1a Mol. Simul. 2012 In press
12. S. Sharma, and P. Gong S.G. Chaney Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastrand cross-links reveal differences in their conformational dynamics J. Mol. Biol. 373 2007 1123 1140 (Pubitemid 47539475)
13. S. Ramachandran, and B.R. Temple N.V. Dokholyan Structural basis for the sequence-dependent effects of platinum-DNA adducts Nucleic Acids Res. 37 2009 2434 2448
14. D. Bhattacharyya, and S. Ramachandran S.G. Chaney Flanking bases influence the nature of DNA distortion by platinum 1,2-intrastrand (GG) cross-links PLoS ONE 6 2011 e23582
15. R. Stefl, and H. Wu J. Feigon DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum Proc. Natl. Acad. Sci. USA 101 2004 1177 1182
16. J.A. Parkinson, and Y. Chen P.J. Sadler Sequence-dependent bending of DNA induced by cisplatin: NMR structures of an A.T-rich 14-mer duplex Chemistry 6 2000 3636 3644
17. J. Srinivasan, and T.E. Cheatham III D.A. Case Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices J. Am. Chem. Soc. 120 1998 9401 9409 (Pubitemid 28452628)
18. J. Aaqvist Ion-water interaction potentials derived from free energy perturbation simulations J. Phys. Chem. 94 1990 8021 8024
19. D. Rodriguez-Gomez, E. Darve, and A. Pohorille Assessing the efficiency of free energy calculation methods J. Chem. Phys. 120 2004 3563 3578
20. S. Kumar, and J.M. Rosenberg P.A. Kollman The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 13 1992 1011 1021
21. J. Curuksu, and M. Zacharias K. Zakrzewska Local and global effects of strong DNA bending induced during molecular dynamics simulations Nucleic Acids Res. 37 2009 3766 3773
22. J. Curuksu, K. Zakrzewska, and M. Zacharias Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites Nucleic Acids Res. 36 2008 2268 2283 (Pubitemid 351567000)
23. K. Spiegel, and A. Magistrato M.L. Klein Azole-bridged diplatinum anticancer compounds. Modulating DNA flexibility to escape repair mechanism and avoid cross resistance J. Phys. Chem. B 111 2007 11873 11876 (Pubitemid 350068899)
24. M. Zacharias Minor groove deformability of DNA: a molecular dynamics free energy simulation study Biophys. J. 91 2006 882 891 (Pubitemid 44161920)
25. J.C. Phillips, and R. Braun K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802 (Pubitemid 43078511)
26. G.M. Torrie, and J.P. Valleau Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling J. Comput. Phys. 23 1977 187 199
27. Grossfield, A. WHAM: the weighted histogram analysis method, version 2.0.4. http://membrane.urmc.rochester.edu/content/wham.
28. B. Roux The calculation of the potential of mean force using computer simulations Comput. Phys. Commun. 91 1995 275 282
29. A.K. Mazur Evaluation of elastic properties of atomistic DNA models Biophys. J. 91 2006 4507 4518 (Pubitemid 44904235)
30. A. Pérez, F.J. Luque, and M. Orozco Frontiers in molecular dynamics simulations of DNA Acc. Chem. Res. 45 2012 196 205
31. Z. Liu, B. Ensing, and P.B. Moore Quantitative assessment of force fields on both low-energy conformational basins and transition-state regions of the (-ψ) space J. Chem. Theory Comput. 7 2010 402 419
32. E. Vanden-Eijnden, and M. Venturoli Revisiting the finite temperature string method for the calculation of reaction tubes and free energies J. Chem. Phys. 130 2009 194103 194117
33. E. Weinan, W. Ren, and E. Vanden-Eijnden String method for the study of rare events Phys. Rev. B 66 2002 052301
34. E. Weinan, W. Ren, and E. Vanden-Eijnden Simplified and improved string method for computing the minimum energy paths in barrier-crossing events J. Chem. Phys. 126 2007 164103 164108
35. P.A. Wiggins, and T. van der Heijden P.C. Nelson High flexibility of DNA on short length scales probed by atomic force microscopy Nat. Nanotechnol. 1 2006 137 141
36. J. Malina, and M. Vojtiskova T.W. Hambley DNA adducts of the enantiomers of the Pt(II) complexes of the ahaz ligand (ahaz=3-aminohexahydroazepine) and recognition of these adducts by HMG domain proteins Biochem. Biophys. Res. Commun. 332 2005 1034 1041 (Pubitemid 40798190)
37. Z.S. Juo, and T.K. Chiu R.E. Dickerson How proteins recognize the TATA box J. Mol. Biol. 261 1996 239 254 (Pubitemid 26275806)
38. L. Czapla, and J.P. Peters L.J. Maher 3rd Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins J. Mol. Biol. 409 2011 278 289
39. R. Rohs, and X. Jin R.S. Mann Origins of specificity in protein-DNA recognition Annu. Rev. Biochem. 79 2010 233 269
40. N. Margiotta, and G. Natile M. Coluccia Sterically hindered complexes of platinum(II) with planar heterocyclic nitrogen donors. A novel complex with 1-methyl-cytosine has a spectrum of activity different from cisplatin and is able of overcoming acquired cisplatin resistance J. Inorg. Biochem. 100 2006 1849 1857 (Pubitemid 44537415)
41. J. Kasparkova, and T. Suchankova V. Brabec Cytotoxicity, cellular uptake, glutathione and DNA interactions of an antitumor large-ring Pt II chelate complex incorporating the cis-1,4-diaminocyclohexane carrier ligand Biochem. Pharmacol. 79 2010 552 564
42. K.S. Lovejoy, and S.J. Lippard Non-traditional platinum compounds for improved accumulation, oral bioavailability, and tumor targeting Dalton Trans. 48 2009 10651 10659
43. T.J. Macke, and D.A. Case Modeling unusual nucleic acid structures N.B. Leontis, J. Santa Lucia Jr. Molecular Modeling of Nucleic Acids 1997 American Chemical Society Washington, DC 379 393
44. E.D. Scheeff, J.M. Briggs, and S.B. Howell Molecular modeling of the intrastrand guanine-guanine DNA adducts produced by cisplatin and oxaliplatin Mol. Pharmacol. 56 1999 633 643 (Pubitemid 29406890)
45. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38 27-28 (Pubitemid 26152973)
46. S. Yao, and J.P. Plastaras A molecular mechanics AMBER-type force field for modeling platinum complexes of guanine derivatives Inorg. Chem. 33 1994 6061 6077
47. I. Brukner, and M. Dlakic D. Suck Evidence for opposite groove-directed curvature of GGGCCC and AAAAA sequence elements Nucleic Acids Res. 21 1993 1025 1029 (Pubitemid 23153014)
48. A. Pérez, and I. Marchán M. Orozco Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers Biophys. J. 92 2007 3817 3829 (Pubitemid 46910569)
49. V. Hornak, and R. Abel C. Simmerling Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins 65 2006 712 725 (Pubitemid 44583220)
50. T.W. Hambley van der Waals radii of Pt(II) and Pd(II) in molecular mechanics models and an analysis of their relevance to the description of axial M.H(-C), M.H(-N), M.S, and M.M (M = Pd(II) or Pt(II)) Interactions Inorg. Chem. 37 1998 3767 3774 (Pubitemid 128492869)
51. W.D. Cornell, and P. Cieplak P.A. Kollman A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules J. Am. Chem. Soc. 117 1995 5179 5197
52. A. Bondi van der Waals volumes + radii J. Phys. Chem. 68 1964 441