| [1] | Henderson ER, Blackburn EH (1989) An overhanging 3′ terminus is a conserved feature of telom-eres. Mol Cell Biol 9: 345–348.
|
| [2] | Griffith JD, Comeau L, Rosenfield S, Stansel RM, Bianchi A, et al. (1999) Mammalian telomeres end in a large duplex loop. Cell 97: 503–514. doi: 10.1016/s0092-8674(00)80760-6
|
| [3] | de Lange T (2004) T-loops and the origin of telomeres. Nat Rev Mol Cell Biol 5: 323–329. doi: 10.1038/nrm1359
|
| [4] | de Lange T (2005) Shelterin: the protein complex that shapes and safeguards human telomeres. Genes Dev 19: 2100–2110. doi: 10.1101/gad.1346005
|
| [5] | Collins K, Mitchell JR (2002) Telomerase in the human organism. Oncogene 21: 564–579. doi: 10.1038/sj.onc.1205083
|
| [6] | Denchi EL, de Lange T (2007) Protection of telomeres through independent control of ATM and ATR by TRF2 and POT1. Nature 448: 1068–1071. doi: 10.1038/nature06065
|
| [7] | Sfeir A, de Lange T (2012) Removal of shelterin reveals the telomere end-protection problem. Science 336: 593–597. doi: 10.1126/science.1218498
|
| [8] | Smogorzewska A, Karlseder J, Holtgreve-Grez H, Jauch A, de Lange T (2002) DNA ligase IV-dependent NHEJ of deprotected mammalian telomeres in G1 and G2. Curr Biol 12: 1635–1644. doi: 10.1016/s0960-9822(02)01179-x
|
| [9] | Karlseder J, Broccoli D, Dai YM, Hardy S, de Lange T (1999) p53- and ATM-dependent apoptosis induced by telomeres lacking TRF2. Science 283: 1321–1325. doi: 10.1126/science.283.5406.1321
|
| [10] | Neidle S, Parkinson G (2002) Telomere maintenance as a target for anticancer drug discovery. Nat Rev Drug Discov 1: 383–393. doi: 10.1038/nrd793
|
| [11] | Herbig U, Ferreira M, Condel L, Carey D, Sedivy JM (2006) Cellular senescence in aging primates. Science 311: 1257. doi: 10.1126/science.1122446
|
| [12] | Zhong Z, Shiue L, Kaplan S, de Lange T (1992) A mammalian factor that binds telomeric TTAGGG repeats in vitro. Mol Cell Biol 12: 4834–4843.
|
| [13] | Broccoli D, Smogorzewska A, Chong L, de Lange T (1997) Human telomeres contain two distinct Myb-related proteins, TRF1 and TRF2. Nat Genet 17: 231–235. doi: 10.1038/ng1097-231
|
| [14] | Karlseder J (2003) Telomere repeat binding factors: keeping the ends in check. Cancer Lett 194: 189–197. doi: 10.1016/s0304-3835(02)00706-1
|
| [15] | van Steensel B, de Lange T (1997) Control of telomere length by the human telomeric protein TRF1. Nature 385: 740–743. doi: 10.1038/385740a0
|
| [16] | Muftuoglu M, Wong HK, Imam SZ, Wilson DM, Bohr VA, et al. (2006) Telomere repeat bind-ing factor 2 interacts with base excision repair proteins and stimulates DNA synthesis by DNA polymerase beta. Cancer Res 66: 113–124. doi: 10.1158/0008-5472.can-05-2742
|
| [17] | Nishikawa T, Okamura H, Nagadoi A, Knig P, Rhodes D, et al. (2001) Solution structure of a telomeric DNA complex of human TRF1. Structure 9: 1237–1251. doi: 10.1016/s0969-2126(01)00688-8
|
| [18] | Hanaoka S, Nagadoi A, Nishimura Y (2005) Comparison between TRF2 and TRF1 of their telom-eric DNA-bound structures and DNA-binding activities. Protein Sci 14: 119–130. doi: 10.1110/ps.04983705
|
| [19] | Court R, Chapman L, Fairall L, Rhodes D (2005) How the human telomeric proteins TRF1 and TRF2 recognize telomeric DNA: a view from high-resolution crystal structures. EMBO Rep 6: 39–45. doi: 10.1038/sj.embor.7400314
|
| [20] | Lemke K, Wojciechowski M, Laine W, Bailly C, Colson P, et al. (2005) Induction of unique struc-tural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase ii inhibitor with antitumor activities. Nucleic Acids Res 33: 6034–6047. doi: 10.1093/nar/gki904
|
| [21] | Bidzinska J, Olewniak J, Skladanowski A (2009) Conference poster: Compound C-1305 binds to telomeric DNA and prevents its interactions with TRF1/2 proteins. Acta Bioch Pol 56, Supp. 3: p. 27.
|
| [22] | Bouvier B, Lavery R (2009) A free energy pathway for the interaction of the SRY protein with its binding site on DNA from atomistic simulations. J Am Chem Soc 131: 9864–9865. doi: 10.1021/ja901761a
|
| [23] | Potoyan DA, Papoian GA (2012) Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation. Proc Natl Acad Sci U S A 109: 17857–17862. doi: 10.1073/pnas.1201805109
|
| [24] | Reddy CK, Das A, Jayaram B (2001) Do water molecules mediate protein-DNA recognition? J Mol Biol 314: 619–632. doi: 10.1006/jmbi.2001.5154
|
| [25] | VonHippel PH (1994) Protein-DNA recognition: new perspective and underlying themes. Science 263: 769–770. doi: 10.1126/science.8303292
|
| [26] | Coulocheri SA, Pigis DG, Papavassiliou KA, Papavassiliou AG (2007) Hydrogen bonds in protein-DNA complexes: where geometry meets plasticity. Biochimie 89: 1291–1303. doi: 10.1016/j.biochi.2007.07.020
|
| [27] | Konig P, Fairall L, Rhodes D (1998) Sequence-specific dna recognition by the myb-like domain of the human telomere binding protein trf1: a model for the protein-dna complex. Nucleic Acids Res 26: 1731–1740. doi: 10.1093/nar/26.7.1731
|
| [28] | Saikumar P, Murali R, Reddy EP (1990) Role of tryptophan repeats and anking amino acids in Myb-DNA interactions. Proc Natl Acad Sci U S A 87: 8452–8456. doi: 10.1073/pnas.87.21.8452
|
| [29] | McKerlie M, Zhu XD (2011) Cyclin b-dependent kinase 1 regulates human trf1 to modulate the resolution of sister telomeres. Nat Commun 2: 371. doi: 10.1038/ncomms1372
|
| [30] | Blainey PC, Luo G, Kou S, Mangel WF, Verdine GL, et al. (2009) Nonspecifically bound proteins spin while diffusing along DNA. Nat Struct Mol Biol 16: 1224–1229. doi: 10.1038/nsmb.1716
|
| [31] | Halford SE, Marko JF (2004) How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res 32: 3040–3052. doi: 10.1093/nar/gkh624
|
| [32] | Li H, Robertson AD, Jensen JH (2005) Very fast empirical prediction and rationalization of protein pKa values. Proteins 61: 704–721. doi: 10.1002/prot.20660
|
| [33] | Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS: A message-passing parallel molecular dynamics implementation. Comput Phys Commun 91: 43–56. doi: 10.1016/0010-4655(95)00042-e
|
| [34] | Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, et al. (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins 65: 712–725. doi: 10.1002/prot.21123
|
| [35] | Perez A, Marchan I, Svozil D, Sponer J, Cheatham TE, et al. (2007) Refinenement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophys J 92: 3817–3829. doi: 10.1529/biophysj.106.097782
|
| [36] | Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N*log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089–10092. doi: 10.1063/1.464397
|
| [37] | Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81: 3684–3690. doi: 10.1063/1.448118
|
| [38] | Miyamoto S, Kollman PA (1992) Settle – an analytical version of the shake and rattle algorithm for rigid water models. J Comput Chem 13: 952–962. doi: 10.1002/jcc.540130805
|
| [39] | Hess B (2008) P-lincs: A parallel linear constraint solver for molecular simulation. Journal of Chemical Theory and Computation 4: 116–122. doi: 10.1021/ct700200b
|
| [40] | Torrie GM, Valleau JP (1977) Nonphysical sampling distributions in Monte Carlo free-energy estimations: umbrella sampling. J Comput Phys 23: 187–199. doi: 10.1016/0021-9991(77)90121-8
|
| [41] | Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM (1992) The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules.1. The Method. J Comput Chem 13: 1011–1021. doi: 10.1002/jcc.540130812
|
| [42] | Mi H, Muruganujan A, Casagrande JT, Thomas PD (2013) Large-scale gene function analysis with the PANTHER classification system. Nat Protoc 8: 1551–1566. doi: 10.1038/nprot.2013.092
|
| [43] | Consortium U (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38: D142–D148. doi: 10.1093/nar/gkp846
|
| [44] | Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539. doi: 10.1038/msb.2011.75
|
| [45] | Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690. doi: 10.1093/bioinformatics/btl446
|
