Dynamic structures in DNA damage responses & cancer

Progress in Biophysics and Molecular Biology

Volumn 117, Issue 2-3, 2015, Pages 129-133

  Tainer, John A ^a,b  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

CHEMISTRY; CONFORMATION; DNA DAMAGE; DNA REPAIR; GENETICS; HUMAN; NEOPLASM; ULTRASTRUCTURE;

DNA DAMAGE; DNA REPAIR; DNA, NEOPLASM; HUMANS; NEOPLASMS; NUCLEIC ACID CONFORMATION;

EID: 84938893100     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbiomolbio.2015.04.003     Document Type: Editorial

References (62)

1. Al-Ahmadie H., Iyer G., Hohl M., Asthana S., Inagaki A., Schultz N., Hanrahan A.J., Scott S.N., Brannon A.R., McDermott G.C., Pirun M., Ostrovnaya I., Kim P., Socci N.D., Viale A., Schwartz G.K., Reuter V., Bochner B.H., Rosenberg J.E., Bajorin D.F., Berger M.F., Petrini J.H.J., Solit D.B., Taylor B.S. Synthetic lethality in ATM-deficient RAD50-mutant tumors underlies outlier response to cancer therapy. Cancer Discov. 2014, 4:1014-1021. http://dx.doi.org/10.1158/2159-8290.CD-14-0380.
2. Bianco P.R. I came to a fork in the DNA and there was RecG. Prog. Biophys. Mol. Biol. 2015, 117(2-3):166-173.
3. Cohen A.E., et al. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc. Nat. Ac. Sci. U. S. A. 2014, 111. 10.1073/pnas.1418733111.
4. Crick F. The double helix: a personal view. Nature 1974, 248:766-769.
5. Dalhus B., Alseth I., Bjørås M. Structural basis for incision at deaminated adenines in DNA and RNA by endonuclease V. Prog. Biophys. Mol. Biol. 2015, 117(2-3):134-142. 10.1016/j.pbiomolbio.2015.03.005.
6. Deshpande R.A., Williams G.J., Limbo O., Williams R.S., Kuhnlein J., Lee J.H., Classen S., Guenther G., Russell P., Tainer J.A., Paull T.T. ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling. EMBO J. 2014, 33:482-500.
7. Fan L., Du Prez K.T. XPB: an unconventional SF2 DNA helicase. Prog. Biophys. Mol. Biol. 2015, 117(2-3):174-181.
8. Fan L., Fuss J.O., Cheng Q.J., Arvai A.S., Hammel M., Roberts V.A., Cooper P.K., Tainer J.A. XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations. Cell 2008, 133:789-800.
9. Fuss J.O., Tainer J.A. XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase. DNA Repair 2011, 10:697-713.
10. Garcin E.D., Arvai A.S., Rosenfeld R.J., et al. Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase. Nat. Chem. Biol. 2008, 4:700-707.
11. Getzoff E.D., Tainer J.A., Weiner P.K., Kollman P.A., Richardson J.S., Richardson D.C. Electrostatic recognition between superoxide and copper, zinc superoxide dismutase. Nature 1983, 306:287-290.
12. Guarné A., Charbonnier J.B. Insights from a decade of biophysical studies on MutL: roles in strand discrimination and removal. Prog. Biophys. Mol. Biol. 2015, 117(2-3):149-156.
13. Hegde M.L., Tsutakawa S.E., Hegde P.M., Holthauzen L.M., Li J., Oezguen N., Hilser V.J., Tainer J.A., Mitra S. The disordered C-terminal domain of human DNA glycosylase NEIL1 contributes to its stability via intramolecular interactions. J. Mol. Biol. 2013 Jul 10, 425(13):2359-2371.
14. Helleday Thomas, Petermann Eva, Lundin Cecilia, et al. DNA repair pathways as targets for cancer therapy. Nat. Rev. Cancer 2008, 8:193-204.
15. Hitomi K., Iwai S., Tainer J.A. The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair. DNA Repair 2007, 6:410-428.
16. Holton J.M., Classen S., Frankel K.A., Tainer J.A. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. FEBS J. 2014, 281:4046-4060.
17. Hopfner K.P., Parikh S.S., Tainer J.A. Envisioning the fourth dimension of the genetic code: the structural biology of macromolecular recognition and conformational switching in DNA repair. Cold Spring Harb. Symp. Quant. Biol. 2000, 65:113-126.
18. Hopfner K.P., Karcher A., Craig L., Woo T.T., Carney J.P., Tainer J.A. Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase. Cell 2001, 105:473-485.
19. Huffman J.L., Sundheim O., Tainer J.A. DNA base damage recognition and removal: new twists and grooves. Mutat. Res. 2005, 577:55-76.
20. Hura G.L., Budworth H., Dyer K.N., Rambo R.P., Hammel M., McMurray C.T., Tainer J.A. Comprehensive macromolecular conformations mapped by quantitative SAXS analyses. Nat. Methods 2013, 10:453-454.
21. Hura G.L., Tsai C.L., Claridge S.A., Mendillo M.L., Smith J.M., Williams G.J., Mastroianni A.J., Alivisatos A.P., Putnam C.D., Kolodner R.D., Tainer J.A. DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:17308-17313.
22. Jette N., Lees-Miller Susan P. The DNA-dependent protein kinase: a multifunctional protein kinase with roles in DNA double strand break repair and mitosis. Prog. Biophys. Mol. Biol. 2015, 117(2-3):194-205. 10.1016/j.pbiomolbio.2014.12.003.
23. Jin Y.H., Clark A.B., Slebos R.J.C., Al-Refai H., Taylor J.A., Kunkel T.A., Resnick M.A., Gordenin D.A. Cadmium is a mutagen that acts by inhibiting mismatch repair. Nat. Genet. 2003, 34:326-329.
24. Kola I., Landis J. Can the pharmaceutical industry reduce attrition rates?. Nat. Rev. Drug Discov. August 2004, 3:711-716. 10.1038/nrd1470.
25. Kuper J., Wolski S.C., Michels G., Kisker C. Functional and structural studies of the nucleotide excision repair helicase XPD suggest a polarity for DNA translocation. EMBO J. 2012, 31:494-502.
26. Lafrance-Vanasse J., Williams Gareth J., Tainer J.A. Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles in DNA replication and repair. Prog. Biophys. Mol. Biol. 2015, 117(2-3):182-193. http://dx.doi.org/10.1016/j.pbiomolbio.2014.12.004.
27. Lees-Miller S.P., Anderson C.W. The human double-stranded DNA-activated protein kinase phosphorylates the 90-kDa heat-shock protein, hsp90 alpha at two NH2-terminal threonine residues. J. Biol. Chem. 1989 Oct 15, 264(29):17275-17280.
28. Liu H., Rudolf J., Johnson K.A., McMahon S.A., Oke M., Carter L., McRobbie A.M., Brown S.E., Naismith J.H., White M.F. Structure of the DNA repair helicase XPD. Cell 2008, 133(5):801-812.
29. McMurray C.T., Tainer J.A. Cancer, cadmium and genome integrity. Nat. Genet. 2003, 34:239-241.
30. Mer G., Bochkarev A., Gupta R., et al. Structural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor RPA. Cell 2000, 103:449-456.
31. Mol C.D., Izumi T., Mitra S., Tainer J.A. DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination. Nature 2000, 403:451-456.
32. Orans J., McSweeney E.A., Iyer R.R., Hast M.A., Hellinga H.W., Modrich P., Beese L.S. Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family. Cell 2011, 145:212-223.
33. Pascal J.M., Tsodikov O.V., Hura G.L., Song W., Cotner E.A., Classen S., Tomkinson A.E., Tainer J.A., Ellenberger T. A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol. Cell 2006, 24:279-291.
34. Pearl L.H., Schierz A.C., Ward S.E., Al-Lazikani B., Pearl F.M. Therapeutic opportunities within the DNA damage response. Nat. Rev. Cancer 2015, 15:166-180.
35. Perry J.J., Asaithamby A., Barnebey A., Kiamanesch F., Chen D.J., Han S., Tainer J.A., Yannone S.M. Identification of a coiled coil in Werner syndrome protein that facilitates multimerization and promotes exonuclease processivity. J. Biol. Chem. 2010, 285:25699-25707.
36. Putnam C.D., Hammel M., Hura G.L., Tainer J.A. X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q. Rev. Biophys. 2007, 40:191-285.
37. Putnam C.D., Shroyer M.J., Lundquist Mol C.D., Arvai A.S., Mosbaugh D.W., Tainer J.A. Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase. J. Mol. Biol. 1999, 287:331-346.
38. Putnam C.D., Tainer J.A. Protein mimicry of DNA and pathway regulation. DNA Repair 2005, 4:1410-1420.
39. Rambo R.P., Tainer J.A. Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers 2011, 95:559-571.
40. Rambo R.P., Tainer J.A. Accurate assessment of mass, models and resolution by small-angle scattering. Nature 2013, 496:477-481.
41. Roberts V.A., Freeman H.C., Olson A.J., Tainer J.A., Getzoff E.D. Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c. J. Biol. Chem. 1991, 266:13431-13441.
42. Rojowska A., Lammens K., Seifert F.U., Direnberger C., Feldmann H., Hopfner K.P. Structure of the Rad50 DNA double-strand break repair protein in complex with DNA. EMBO J. 2014, 33:2847-2859.
43. Schellenberg M.J., Tumbale P.P., Williams R.S. Molecular underpinnings of Aprataxin RNA/DNA deadenylase function and dysfunction in neurological disease. Prog. Biophys. Mol. Biol. 2015, 117(2-3):157-165.
44. Schlacher K., Christ N., Siaud N., Egashira A., Wu H., Jasin M. Double-strand break repair-independent role for BRCA2 in blocking stalled replication fork degradation by MRE11. Cell 2011, 145:529-542.
45. Schlacher K., Wu H., Jasin M. A distinct replication fork protection pathway connects Fanconi anemia tumor suppressors to RAD51-BRCA1/2. Cancer Cell 2012, 22:106-116.
46. Shibata A., Moiani D., Arvai A.S., Perry J., Harding S.M., Genois M.M., Maity R., van Rossum-Fikkert S., Kertokalio A., Romoli F., Ismail A., Ismalaj E., Petricci E., Neale M.J., Bristow R.G., Masson J.Y., Wyman C., Jeggo P.A., Tainer J.A. DNA double-strand break repair pathway choice is directed by distinct MRE11 nuclease activities. Mol. Cell 2014, 53:7-18.
47. Sibanda B.L., Chirgadze D.Y., Blundell T.L. Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats. Nature 2010, 463(7277):118-121.
48. Slupphaug G., Mol C.D., Kavli B., Arvai A.S., Krokan H.E., Tainer J.A. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature 1996, 384:87-92.
49. Sugitani N., Chazin W.J. Characteristics and concepts of dynamic hub proteins in DNA processing machinery from studies of RPA. Prog. Biophys. Mol. Biol. 2015, 117(2-3):206-211. 10.1016/j.pbiomolbio.2014.12.001.
50. Tainer J.A., Getzoff E.D., Alexander H., Houghten R.A., Olson A.J., Lerner R.A., Hendrickson W.A. The reactivity of anti-peptide antibodies is a function of the atomic mobility of sites in a protein. Nature 1984, 312:127-134.
51. Tomkinson A.E., Howes T.R., Wiest N.E. DNA ligases as therapeutic targets. Transl. Cancer Res. 2013, 2(3):1219.
52. Tsutakawa S.E., Classen S., Chapados B.R., Arvai A.S., Finger L.D., Guenther G., Tomlinson C.G., Thompson P., Sarker A.H., Shen B., Cooper P.K., Grasby J.A., Tainer J.A. Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily. Cell 2011, 145:198-211.
53. Tsutakawa S.E., Lafrance-Vanasse J., Tainer J.A. The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once. DNA Repair (Amst.) 2014 Jul, 19:95-107. 10.1016/j.dnarep.2014.03.022.
54. Walker J.R., Corpina R.A., Goldberg J. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature 2001, 412(6847):607-614.
55. Watson J.D., Crick F.H.C. A structure for deoxyribose nucleic acid. Nature 1953, 171:737-738.
56. Williams R.S., Moncalian G., Williams J.S., Yamada Y., Limbo O., Shin D.S., Groocock L.M., Cahill D., Hitomi C., Guenther G., Moiani D., Carney J.P., Russell P., Tainer J.A. Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair. Cell 2008, 135:97-109.
57. Williams R.S., Dodson G.E., Limbo O., et al. Nbs1 flexibly tethers Ctp1 and Mre11-Rad50 to coordinate DNA double-strand break processing and repair. Cell 2009, 139:87-99.
58. Williams G.J., Lees-Miller S.P., Tainer J.A. Mre11-Rad50-Nbs1 conformations and the control of sensing, signaling, and effector responses at DNA double-strand breaks. DNA Repair 2010, 9:1299-1306.
59. Williams G.J., Hammel M., Radhakrishnan S.K., Ramsden D., Lees-Miller S.P., Tainer J.A. Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time. DNA Repair (Amst.) 2014 May, 17:110-120.
60. Winter A., Higueruelo A.P., Marsh M., Sigurdardottir A., Pitt W.R., Blundell T.L. Biophysical and computational fragment-based approaches to targeting protein-protein interactions: applications in structure-guided drug discovery. Q. Rev. Biophys. 2012 Nov, 45(4):383-426.
61. Wu L., Hickson I.D. The Bloom's syndrome helicase suppresses crossing over during homologous recombination. Nature 2003, 426:870-874.
62. Wu Q., Jubb H., Blundell T.L. Phosphopeptide interactions with BRCA1 BRCT domains: more than just a motif. Prog. Biophys. Mol. Biol. 2015, 117(2-3):143-148.