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Volumn 111, Issue 15, 2014, Pages

From a structural average to the conformational ensemble of a DNA bulge

Author keywords

Helix junction helix; SAXS

Indexed keywords

ADENOSINE; DNA; DOUBLE STRANDED DNA; THYMINE;

EID: 84898787427     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1317032111     Document Type: Article
Times cited : (26)

References (53)
  • 1
    • 79960562804 scopus 로고    scopus 로고
    • Discovery of selective bioactive small molecules by targeting an rna dynamic ensemble
    • Stelzer AC, et al. (2011) Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. Nat Chem Biol 7(8):553-559.
    • (2011) Nat Chem Biol , vol.7 , Issue.8 , pp. 553-559
    • Stelzer, A.C.1
  • 2
    • 64849113665 scopus 로고    scopus 로고
    • Trapping moving targets with small molecules
    • Lee GM, Craik CS (2009) Trapping moving targets with small molecules. Science 324(5924):213-215.
    • (2009) Science , vol.324 , Issue.5924 , pp. 213-215
    • Lee, G.M.1    Craik, C.S.2
  • 4
    • 84856751089 scopus 로고    scopus 로고
    • Rna dynamics: Perspectives from spin labels
    • Nguyen P, Qin PZ (2012) RNA dynamics: Perspectives from spin labels. Wiley Interdiscip Rev RNA 3(1):62-72.
    • (2012) Wiley Interdiscip Rev Rna , vol.3 , Issue.1 , pp. 62-72
    • Nguyen, P.1    Qin, P.Z.2
  • 5
    • 79251586250 scopus 로고    scopus 로고
    • Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic nmr relaxation
    • Clore GM (2011) Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation. Protein Sci 20(2):229-246.
    • (2011) Protein Sci , vol.20 , Issue.2 , pp. 229-246
    • Clore, G.M.1
  • 6
    • 44449134820 scopus 로고    scopus 로고
    • A practical guide to single-molecule fret
    • Roy R, Hohng S, Ha T (2008) A practical guide to single-molecule FRET. Nat Methods 5(6):507-516.
    • (2008) Nat Methods , vol.5 , Issue.6 , pp. 507-516
    • Roy, R.1    Hohng, S.2    Ha, T.3
  • 7
    • 79958037883 scopus 로고    scopus 로고
    • Constructing ensembles for intrinsically disordered proteins
    • Fisher CK, Stultz CM (2011) Constructing ensembles for intrinsically disordered proteins. Curr Opin Struct Biol 21(3):426-431.
    • (2011) Curr Opin Struct Biol , vol.21 , Issue.3 , pp. 426-431
    • Fisher, C.K.1    Stultz, C.M.2
  • 9
    • 0034884233 scopus 로고    scopus 로고
    • A novel interactive tool for rigidbody modeling of multi-domain macromolecules using residual dipolar couplings
    • Dosset P, Hus JC, Marion D, Blackledge M (2001) A novel interactive tool for rigidbody modeling of multi-domain macromolecules using residual dipolar couplings. J Biomol NMR 20(3):223-231.
    • (2001) J Biomol NMR , vol.20 , Issue.3 , pp. 223-231
    • Dosset, P.1    Hus, J.C.2    Marion, D.3    Blackledge, M.4
  • 10
    • 77953627413 scopus 로고    scopus 로고
    • Nmr characterization of long-range order in intrinsically disordered proteins
    • Salmon L, et al. (2010) NMR characterization of long-range order in intrinsically disordered proteins. J Am Chem Soc 132(24):8407-8418.
    • (2010) J Am Chem Soc , vol.132 , Issue.24 , pp. 8407-8418
    • Salmon, L.1
  • 11
    • 33846839463 scopus 로고    scopus 로고
    • A physical picture of atomic motions within the dickerson dna dodecamer in solution derived from joint ensemble refinement against nmr and large-Angle x-ray scattering data
    • Schwieters CD, Clore GM (2007) A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-Angle X-ray scattering data. Biochemistry 46(5):1152-1166.
    • (2007) Biochemistry , vol.46 , Issue.5 , pp. 1152-1166
    • Schwieters, C.D.1    Clore, G.M.2
  • 12
    • 67649891135 scopus 로고    scopus 로고
    • Constructing rna dynamical ensembles by combining md and motionally decoupled nmr rdcs: New insights into rna dynamics and adaptive ligand recognition
    • Frank AT, Stelzer AC, Al-Hashimi HM, Andricioaei I (2009) Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: New insights into RNA dynamics and adaptive ligand recognition. Nucleic Acids Res 37(11): 3670-3679.
    • (2009) Nucleic Acids Res , vol.37 , Issue.11 , pp. 3670-3679
    • Frank, A.T.1    Stelzer, A.C.2    Al-Hashimi, H.M.3    Andricioaei, I.4
  • 13
    • 37549017736 scopus 로고    scopus 로고
    • Visualizing spatially correlated dynamics that directs rna conformational transitions
    • Zhang Q, Stelzer AC, Fisher CK, Al-Hashimi HM (2007) Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature 450(7173):1263-1267.
    • (2007) Nature , vol.450 , Issue.7173 , pp. 1263-1267
    • Zhang, Q.1    Stelzer, A.C.2    Fisher, C.K.3    Al-Hashimi, H.M.4
  • 14
    • 84876030925 scopus 로고    scopus 로고
    • A general method for constructing atomic-resolution rna ensembles using nmr residual dipolar couplings: The basis for interhelical motions revealed
    • Salmon L, Bascom G, Andricioaei I, Al-Hashimi HM (2013) A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: The basis for interhelical motions revealed. J Am Chem Soc 135(14):5457-5466.
    • (2013) J Am Chem Soc , vol.135 , Issue.14 , pp. 5457-5466
    • Salmon, L.1    Bascom, G.2    Andricioaei, I.3    Al-Hashimi, H.M.4
  • 15
    • 34250728646 scopus 로고    scopus 로고
    • Characterizing the relative orientation and dynamics of rna a-form helices using nmr residual dipolar couplings
    • Bailor MH, et al. (2007) Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings. Nat Protoc 2(6):1536-1546.
    • (2007) Nat Protoc , vol.2 , Issue.6 , pp. 1536-1546
    • Bailor, M.H.1
  • 16
    • 72949113618 scopus 로고    scopus 로고
    • Conformational averaging in structural biology: Issues, challenges and computational solutions
    • Kruschel D, Zagrovic B (2009) Conformational averaging in structural biology: Issues, challenges and computational solutions. Mol Biosyst 5(12):1606-1616.
    • (2009) Mol Biosyst , vol.5 , Issue.12 , pp. 1606-1616
    • Kruschel, D.1    Zagrovic, B.2
  • 17
    • 54249088052 scopus 로고    scopus 로고
    • Remeasuring the double helix
    • Mathew-Fenn RS, Das R, Harbury PA (2008) Remeasuring the double helix. Science 322(5900):446-449.
    • (2008) Science , vol.322 , Issue.5900 , pp. 446-449
    • Mathew-Fenn, R.S.1    Das, R.2    Harbury, P.A.3
  • 18
    • 84876229136 scopus 로고    scopus 로고
    • Structural ensemble and microscopic elasticity of freely diffusing dna by direct measurement of fluctuations
    • Shi X, Herschlag D, Harbury PA (2013) Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations. Proc Natl Acad Sci USA 110(16):E1444-E1451.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.16
    • Shi, X.1    Herschlag, D.2    Harbury, P.A.3
  • 19
    • 0019127860 scopus 로고
    • Determination of the distance between heavy-Atom markers in haemoglobin and histidine decarboxylase in solution by small-Angle x-ray scattering
    • Vainshtein BK, et al. (1980) Determination of the distance between heavy-Atom markers in haemoglobin and histidine decarboxylase in solution by small-Angle x-ray scattering. FEBS Lett 116(1):107-110.
    • (1980) FEBS Lett , vol.116 , Issue.1 , pp. 107-110
    • Vainshtein, B.K.1
  • 20
    • 0024278336 scopus 로고
    • Positions of s2, s13, s16, s17, s19 and s21 in the 30 s ribosomal subunit of escherichia coli
    • Capel MS, Kjeldgaard M, Engelman DM, Moore PB (1988) Positions of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit of Escherichia coli. J Mol Biol 200(1): 65-87.
    • (1988) J Mol Biol , vol.200 , Issue.1 , pp. 65-87
    • Capel, M.S.1    Kjeldgaard, M.2    Engelman, D.M.3    Moore, P.B.4
  • 21
    • 0020729934 scopus 로고
    • Anomalous x-ray scattering from terbium-labeled parvalbumin in solution
    • Miake-Lye RC, Doniach S, Hodgson KO (1983) Anomalous x-ray scattering from terbium-labeled parvalbumin in solution. Biophys J 41(3):287-292.
    • (1983) Biophys J , vol.41 , Issue.3 , pp. 287-292
    • Miake-Lye, R.C.1    Doniach, S.2    Hodgson, K.O.3
  • 22
    • 84886437286 scopus 로고    scopus 로고
    • Dna conformations in mismatch repair probed in solution by x-ray scattering from gold nanocrystals
    • Hura GL, et al. (2013) DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals. Proc Natl Acad Sci USA 110(43):17308-17313.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.43 , pp. 17308-17313
    • Hura, G.L.1
  • 24
    • 70349602563 scopus 로고    scopus 로고
    • Probing the conformational distributions of subpersistence length dna
    • Mastroianni AJ, Sivak DA, Geissler PL, Alivisatos AP (2009) Probing the conformational distributions of subpersistence length DNA. Biophys J 97(5):1408-1417.
    • (2009) Biophys J , vol.97 , Issue.5 , pp. 1408-1417
    • Mastroianni, A.J.1    Sivak, D.A.2    Geissler, P.L.3    Alivisatos, A.P.4
  • 25
    • 34249894142 scopus 로고    scopus 로고
    • Small-Angle x-ray scattering from rna, proteins, and protein complexes
    • Lipfert J, Doniach S (2007) Small-Angle X-ray scattering from RNA, proteins, and protein complexes. Annu Rev Biophys Biomol Struct 36:307-327.
    • (2007) Annu Rev Biophys Biomol Struct , vol.36 , pp. 307-327
    • Lipfert, J.1    Doniach, S.2
  • 27
    • 0026727214 scopus 로고
    • Distance distribution in a dye-linked oligonucleotide determined by time-resolved fluorescence energy transfer
    • Hochstrasser RA, Chen SM, Millar DP (1992) Distance distribution in a dye-linked oligonucleotide determined by time-resolved fluorescence energy transfer. Biophys Chem 45(2):133-141.
    • (1992) Biophys Chem , vol.45 , Issue.2 , pp. 133-141
    • Hochstrasser, R.A.1    Chen, S.M.2    Millar, D.P.3
  • 28
    • 84859888767 scopus 로고    scopus 로고
    • Deer distance measurements on proteins
    • Jeschke G (2012) DEER distance measurements on proteins. Annu Rev Phys Chem 63:419-446.
    • (2012) Annu Rev Phys Chem , vol.63 , pp. 419-446
    • Jeschke, G.1
  • 29
    • 0029111762 scopus 로고
    • Kinking of dna and rna by base bulges
    • Lilley DMJ (1995) Kinking of DNA and RNA by base bulges. Proc Natl Acad Sci USA 92(16):7140-7142.
    • (1995) Proc Natl Acad Sci USA , vol.92 , Issue.16 , pp. 7140-7142
    • Lilley, D.M.J.1
  • 30
    • 0028072693 scopus 로고
    • Kinking of dna and rna helices by bulged nucleotides observed by fluorescence resonance energy transfer
    • Gohlke C, Murchie AIH, Lilley DMJ, Clegg RM (1994) Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer. Proc Natl Acad Sci USA 91(24):11660-11664.
    • (1994) Proc Natl Acad Sci USA , vol.91 , Issue.24 , pp. 11660-11664
    • Gohlke, C.1    Murchie, A.I.H.2    Lilley, D.M.J.3    Clegg, R.M.4
  • 32
    • 0003437218 scopus 로고    scopus 로고
    • (Addison Wesley, San Francisco) 3rd Ed
    • Goldstein H (2002) Classical Mechanics (Addison Wesley, San Francisco) 3rd Ed.
    • (2002) Classical Mechanics
    • Goldstein, H.1
  • 34
    • 74249115345 scopus 로고    scopus 로고
    • Topology links rna secondary structure with global conformation, dynamics, and adaptation
    • Bailor MH, Sun X, Al-Hashimi HM (2010) Topology links RNA secondary structure with global conformation, dynamics, and adaptation. Science 327(5962):202-206.
    • (2010) Science , vol.327 , Issue.5962 , pp. 202-206
    • Bailor, M.H.1    Sun, X.2    Al-Hashimi, H.M.3
  • 35
    • 84855902184 scopus 로고    scopus 로고
    • New insights into the fundamental role of topological constraints as a determinant of twoway junction conformation
    • Mustoe AM, Bailor MH, Teixeira RM, Brooks CL, 3rd, Al-Hashimi HM (2012) New insights into the fundamental role of topological constraints as a determinant of twoway junction conformation. Nucleic Acids Res 40(2):892-904.
    • (2012) Nucleic Acids Res , vol.40 , Issue.2 , pp. 892-904
    • Mustoe, A.M.1    Bailor, M.H.2    Teixeira, R.M.3    Brooks III, C.L.4    Al-Hashimi, H.M.5
  • 37
    • 77958510026 scopus 로고    scopus 로고
    • Modeling intrinsically disordered proteins with bayesian statistics
    • Fisher CK, Huang A, Stultz CM (2010) Modeling intrinsically disordered proteins with bayesian statistics. J Am Chem Soc 132(42):14919-14927.
    • (2010) J Am Chem Soc , vol.132 , Issue.42 , pp. 14919-14927
    • Fisher, C.K.1    Huang, A.2    Stultz, C.M.3
  • 38
    • 84882940564 scopus 로고    scopus 로고
    • Accurate saxs profile computation and its assessment by contrast variation experiments
    • Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A (2013) Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J 105(4): 962-974.
    • (2013) Biophys J , vol.105 , Issue.4 , pp. 962-974
    • Schneidman-Duhovny, D.1    Hammel, M.2    Tainer, J.A.3    Sali, A.4
  • 39
    • 84858228831 scopus 로고    scopus 로고
    • Electrostatics of nucleic acid folding under conformational constraint
    • Anthony PC, et al. (2012) Electrostatics of nucleic acid folding under conformational constraint. J Am Chem Soc 134(10):4607-4614.
    • (2012) J Am Chem Soc , vol.134 , Issue.10 , pp. 4607-4614
    • Anthony, P.C.1
  • 40
    • 36848999901 scopus 로고    scopus 로고
    • Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids
    • Bai Y, et al. (2007) Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. J Am Chem Soc 129(48):14981-14988.
    • (2007) J Am Chem Soc , vol.129 , Issue.48 , pp. 14981-14988
    • Bai, Y.1
  • 41
    • 0001301693 scopus 로고    scopus 로고
    • Screening of a macroion by multivalent ions: Correlation-induced inversion of charge
    • Shklovskii BI (1999) Screening of a macroion by multivalent ions: Correlation-induced inversion of charge. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 60(5 Pt B):5802-5811.
    • (1999) Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics , vol.60 , Issue.5 PART B , pp. 5802-5811
    • Shklovskii, B.I.1
  • 42
    • 0028969693 scopus 로고
    • Bulge-induced bends in rna: Quantification by transient electric birefringence
    • Zacharias M, Hagerman PJ (1995) Bulge-induced bends in RNA: Quantification by transient electric birefringence. J Mol Biol 247(3):486-500.
    • (1995) J Mol Biol , vol.247 , Issue.3 , pp. 486-500
    • Zacharias, M.1    Hagerman, P.J.2
  • 43
    • 0036798069 scopus 로고    scopus 로고
    • The bulge region of hiv-1 tar rna binds metal ions in solution
    • Olejniczak M, et al. (2002) The bulge region of HIV-1 TAR RNA binds metal ions in solution. Nucleic Acids Res 30(19):4241-4249.
    • (2002) Nucleic Acids Res , vol.30 , Issue.19 , pp. 4241-4249
    • Olejniczak, M.1
  • 44
    • 0032543957 scopus 로고    scopus 로고
    • A 1.3-A resolution crystal structure of the hiv-1 transactivation response region rna stem reveals a metal ion-dependent bulge conformation
    • Ippolito JA, Steitz TA (1998) A 1.3-A resolution crystal structure of the HIV-1 transactivation response region RNA stem reveals a metal ion-dependent bulge conformation. Proc Natl Acad Sci USA 95(17):9819-9824.
    • (1998) Proc Natl Acad Sci USA , vol.95 , Issue.17 , pp. 9819-9824
    • Ippolito, J.A.1    Steitz, T.A.2
  • 45
    • 31944446215 scopus 로고    scopus 로고
    • Resolving the motional modes that code for rna adaptation
    • Zhang Q, Sun X, Watt ED, Al-Hashimi HM (2006) Resolving the motional modes that code for RNA adaptation. Science 311(5761):653-656.
    • (2006) Science , vol.311 , Issue.5761 , pp. 653-656
    • Zhang, Q.1    Sun, X.2    Watt, E.D.3    Al-Hashimi, H.M.4
  • 46
    • 84863338065 scopus 로고    scopus 로고
    • Rna-puzzles: A casp-like evaluation of rna three-dimensional structure prediction
    • Cruz JA, et al. (2012) RNA-puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA 18(4):610-625.
    • (2012) RNA , vol.18 , Issue.4 , pp. 610-625
    • Cruz, J.A.1
  • 47
    • 25844506708 scopus 로고    scopus 로고
    • Weak alignment nmr: A hawk-eyed view of biomolecular structure
    • Bax A, Grishaev A (2005) Weak alignment NMR: A hawk-eyed view of biomolecular structure. Curr Opin Struct Biol 15(5):563-570.
    • (2005) Curr Opin Struct Biol , vol.15 , Issue.5 , pp. 563-570
    • Bax, A.1    Grishaev, A.2
  • 48
    • 80052401629 scopus 로고    scopus 로고
    • Solution structure of a minor and transiently formed state of a t4 lysozyme mutant
    • Bouvignies G, et al. (2011) Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature 477(7362):111-114.
    • (2011) Nature , vol.477 , Issue.7362 , pp. 111-114
    • Bouvignies, G.1
  • 49
    • 35548943472 scopus 로고    scopus 로고
    • Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement
    • Clore GM, Tang C, Iwahara J (2007) Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement. Curr Opin Struct Biol 17(5):603-616.
    • (2007) Curr Opin Struct Biol , vol.17 , Issue.5 , pp. 603-616
    • Clore, G.M.1    Tang, C.2    Iwahara, J.3
  • 50
    • 0029746061 scopus 로고    scopus 로고
    • Detection of rare partially folded molecules in equilibrium with the native conformation of rnaseh
    • Chamberlain AK, Handel TM, Marqusee S (1996) Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. Nat Struct Biol 3(9):782-787.
    • (1996) Nat Struct Biol , vol.3 , Issue.9 , pp. 782-787
    • Chamberlain, A.K.1    Handel, T.M.2    Marqusee, S.3
  • 51
    • 84865546608 scopus 로고    scopus 로고
    • Extreme bendability of dna less than 100 base pairs long revealed by single-molecule cyclization
    • Vafabakhsh R, Ha T (2012) Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 337(6098):1097-1101.
    • (2012) Science , vol.337 , Issue.6098 , pp. 1097-1101
    • Vafabakhsh, R.1    Ha, T.2
  • 52
    • 84875592758 scopus 로고    scopus 로고
    • Gromacs 4.5: A high-throughput and highly parallel open source molecular simulation toolkit
    • Pronk S, et al. (2013) GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29(7):845-854.
    • (2013) Bioinformatics , vol.29 , Issue.7 , pp. 845-854
    • Pronk, S.1
  • 53
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (resp) model perform in calculating conformational energies of organic and biological molecules?
    • Wang JM, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21(12):1049-1074.
    • (2000) J Comput Chem , vol.21 , Issue.12 , pp. 1049-1074
    • Wang, J.M.1    Cieplak, P.2    Kollman, P.A.3


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