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Volumn 202, Issue 1, 2010, Pages 117-121

Variable helix elongation as a tool to modulate RNA alignment and motional couplings

Author keywords

Collective helix motions; HIV; Residual dipolar couplings; Transactivation response element

Indexed keywords

COUPLING LIMITS; HELIX AXIS; HIGHER-DEGREE; INDEPENDENT SET; RESIDUAL DIPOLAR COUPLINGS; RNA STRUCTURES; STATE DYNAMICS; TRANS-ACTIVATION RESPONSE;

EID: 72149096007     PISSN: 10907807     EISSN: 10960856     Source Type: Journal    
DOI: 10.1016/j.jmr.2009.09.022     Document Type: Article
Times cited : (18)

References (43)
  • 1
    • 0029050883 scopus 로고
    • Nuclear magnetic dipole interactions in field-oriented proteins - information for structure determination in solution
    • Tolman J.R., Flanagan J.M., Kennedy M.A., and Prestegard J.H. Nuclear magnetic dipole interactions in field-oriented proteins - information for structure determination in solution. Proc. Natl. Acad. Sci. USA 92 (1995) 9279-9283
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 9279-9283
    • Tolman, J.R.1    Flanagan, J.M.2    Kennedy, M.A.3    Prestegard, J.H.4
  • 2
    • 0030722243 scopus 로고    scopus 로고
    • Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium
    • Tjandra N., and Bax A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278 (1997) 1111-1114
    • (1997) Science , vol.278 , pp. 1111-1114
    • Tjandra, N.1    Bax, A.2
  • 3
    • 33646931175 scopus 로고    scopus 로고
    • NMR residual dipolar couplings as probes of biomolecular dynamics
    • Tolman J.R., and Ruan K. NMR residual dipolar couplings as probes of biomolecular dynamics. Chem. Rev. 106 (2006) 1720-1736
    • (2006) Chem. Rev. , vol.106 , pp. 1720-1736
    • Tolman, J.R.1    Ruan, K.2
  • 4
    • 34748876721 scopus 로고    scopus 로고
    • Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings
    • Bouvignies G., Markwick P.R., and Blackledge M. Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings. Chemphyschem 8 (2007) 1901-1909
    • (2007) Chemphyschem , vol.8 , pp. 1901-1909
    • Bouvignies, G.1    Markwick, P.R.2    Blackledge, M.3
  • 5
    • 34547820982 scopus 로고    scopus 로고
    • NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings
    • Getz M., Sun X., Casiano-Negroni A., Zhang Q., and Al-Hashimi H.M. NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings. Biopolymers 86 (2007) 384-402
    • (2007) Biopolymers , vol.86 , pp. 384-402
    • Getz, M.1    Sun, X.2    Casiano-Negroni, A.3    Zhang, Q.4    Al-Hashimi, H.M.5
  • 6
    • 0000242574 scopus 로고
    • Magnetic field induced alignment of molecules
    • Grant D.M., and Harris R.K. (Eds), Wiley, Chichester
    • Bothner-By A.A. Magnetic field induced alignment of molecules. In: Grant D.M., and Harris R.K. (Eds). Encyclopedia of Nuclear Magnetic Resonance (1995), Wiley, Chichester 2932-2938
    • (1995) Encyclopedia of Nuclear Magnetic Resonance , pp. 2932-2938
    • Bothner-By, A.A.1
  • 7
    • 25844506708 scopus 로고    scopus 로고
    • Weak alignment NMR: a hawk-eyed view of biomolecular structure
    • Bax A., and Grishaev A. Weak alignment NMR: a hawk-eyed view of biomolecular structure. Curr. Opin. Struct. Biol. 15 (2005) 563-570
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 563-570
    • Bax, A.1    Grishaev, A.2
  • 8
    • 0032517327 scopus 로고    scopus 로고
    • Measurement of residual dipolar couplings of macromolecules aligned in the nematic phase of a colloidal suspension of rod-shaped viruses
    • Clore G.M., Starich M.R., and Gronenborn A.M. Measurement of residual dipolar couplings of macromolecules aligned in the nematic phase of a colloidal suspension of rod-shaped viruses. J. Am. Chem. Soc. 120 (1998) 10571-10572
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 10571-10572
    • Clore, G.M.1    Starich, M.R.2    Gronenborn, A.M.3
  • 9
    • 0034130999 scopus 로고    scopus 로고
    • Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions
    • Hansen M.R., Hanson P., and Pardi A. Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions. Methods Enzymol. 317 (2000) 220-240
    • (2000) Methods Enzymol. , vol.317 , pp. 220-240
    • Hansen, M.R.1    Hanson, P.2    Pardi, A.3
  • 10
    • 0037551646 scopus 로고    scopus 로고
    • Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments
    • Ruckert M., and Otting G. Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments. J. Am. Chem. Soc. 122 (2000) 7793-7797
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 7793-7797
    • Ruckert, M.1    Otting, G.2
  • 11
    • 0032500340 scopus 로고    scopus 로고
    • Modulation of the alignment tensor of macromolecules dissolved in a dilute liquid crystalline medium
    • Ramirez B.E., and Bax A. Modulation of the alignment tensor of macromolecules dissolved in a dilute liquid crystalline medium. J. Am. Chem. Soc. 120 (1998) 9106-9107
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9106-9107
    • Ramirez, B.E.1    Bax, A.2
  • 12
    • 44949209342 scopus 로고    scopus 로고
    • De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media
    • Ruan K., Briggman K.B., and Tolman J.R. De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media. J. Biomol. NMR 41 (2008) 61-76
    • (2008) J. Biomol. NMR , vol.41 , pp. 61-76
    • Ruan, K.1    Briggman, K.B.2    Tolman, J.R.3
  • 13
    • 0037157093 scopus 로고    scopus 로고
    • Model-free analysis of protein backbone motion from residual dipolar couplings
    • Peti W., Meiler J., Bruschweiler R., and Griesinger C. Model-free analysis of protein backbone motion from residual dipolar couplings. J. Am. Chem. Soc. 124 (2002) 5822-5833
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 5822-5833
    • Peti, W.1    Meiler, J.2    Bruschweiler, R.3    Griesinger, C.4
  • 14
    • 33845203743 scopus 로고    scopus 로고
    • Simultaneous determination of protein backbone structure and dynamics from residual dipolar couplings
    • Bouvignies G., Markwick P., Bruschweiler R., and Blackledge M. Simultaneous determination of protein backbone structure and dynamics from residual dipolar couplings. J. Am. Chem. Soc. 128 (2006) 15100-15101
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 15100-15101
    • Bouvignies, G.1    Markwick, P.2    Bruschweiler, R.3    Blackledge, M.4
  • 15
    • 4143079167 scopus 로고    scopus 로고
    • Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements
    • Clore G.M., and Schwieters C.D. Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements. Biochemistry 43 (2004) 10678-10691
    • (2004) Biochemistry , vol.43 , pp. 10678-10691
    • Clore, G.M.1    Schwieters, C.D.2
  • 17
    • 0037048594 scopus 로고    scopus 로고
    • A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy
    • Tolman J.R. A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy. J. Am. Chem. Soc. 124 (2002) 12020-12030
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 12020-12030
    • Tolman, J.R.1
  • 18
    • 0034820148 scopus 로고    scopus 로고
    • Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins
    • Meiler J., Prompers J.J., Peti W., Griesinger C., and Bruschweiler R. Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. J. Am. Chem. Soc. 123 (2001) 6098-6107
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 6098-6107
    • Meiler, J.1    Prompers, J.J.2    Peti, W.3    Griesinger, C.4    Bruschweiler, R.5
  • 19
    • 0042933782 scopus 로고    scopus 로고
    • De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy
    • Briggman K.B., and Tolman J.R. De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy. J. Am. Chem. Soc. 125 (2003) 10164-10165
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 10164-10165
    • Briggman, K.B.1    Tolman, J.R.2
  • 20
    • 37549017736 scopus 로고    scopus 로고
    • Visualizing spatially correlated dynamics that directs RNA conformational transitions
    • Zhang Q., Stelzer A.C., Fisher C.K., and Al-Hashimi H.M. Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature 450 (2007) 1263-1267
    • (2007) Nature , vol.450 , pp. 1263-1267
    • Zhang, Q.1    Stelzer, A.C.2    Fisher, C.K.3    Al-Hashimi, H.M.4
  • 21
    • 0042355704 scopus 로고    scopus 로고
    • Probing motions between equivalent RNA domains using magnetic field induced residual dipolar couplings: accounting for correlations between motions and alignment
    • Zhang Q., Throolin R., Pitt S.W., Serganov A., and Al-Hashimi H.M. Probing motions between equivalent RNA domains using magnetic field induced residual dipolar couplings: accounting for correlations between motions and alignment. J. Am. Chem. Soc. 125 (2003) 10530-10531
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 10530-10531
    • Zhang, Q.1    Throolin, R.2    Pitt, S.W.3    Serganov, A.4    Al-Hashimi, H.M.5
  • 22
    • 0034167156 scopus 로고    scopus 로고
    • Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings
    • Al-Hashimi H.M., Valafar H., Terrell M., Zartler E.R., Eidsness M.K., and Prestegard J.H. Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings. J. Magn. Reson. 143 (2000) 402-406
    • (2000) J. Magn. Reson. , vol.143 , pp. 402-406
    • Al-Hashimi, H.M.1    Valafar, H.2    Terrell, M.3    Zartler, E.R.4    Eidsness, M.K.5    Prestegard, J.H.6
  • 23
    • 0034685436 scopus 로고    scopus 로고
    • Prediction of sterically induced alignment in a dilute liquid crystalline phase; aid to protein structure determination by NMR
    • Zweckstetter M., and Bax A. Prediction of sterically induced alignment in a dilute liquid crystalline phase; aid to protein structure determination by NMR. J. Am. Chem. Soc. 122 (2000) 3791-3792
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 3791-3792
    • Zweckstetter, M.1    Bax, A.2
  • 24
    • 2942653357 scopus 로고    scopus 로고
    • Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases
    • Zweckstetter M., Hummer G., and Bax A. Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophys. J. 86 (2004) 3444-3460
    • (2004) Biophys. J. , vol.86 , pp. 3444-3460
    • Zweckstetter, M.1    Hummer, G.2    Bax, A.3
  • 25
    • 33745607601 scopus 로고    scopus 로고
    • Prediction of molecular alignment of nucleic acids in aligned media
    • Wu B., Petersen M., Girard F., Tessari M., and Wijmenga S.S. Prediction of molecular alignment of nucleic acids in aligned media. J. Biomol. NMR 35 (2006) 103-115
    • (2006) J. Biomol. NMR , vol.35 , pp. 103-115
    • Wu, B.1    Petersen, M.2    Girard, F.3    Tessari, M.4    Wijmenga, S.S.5
  • 26
    • 0035977613 scopus 로고    scopus 로고
    • Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex, relative orientation of G·(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation
    • Al-Hashimi H.M., Majumdar A., Gorin A., Kettani A., Skripkin E., and Patel D.J. Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex, relative orientation of G·(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation. J. Am. Chem. Soc. 123 (2001) 633-640
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 633-640
    • Al-Hashimi, H.M.1    Majumdar, A.2    Gorin, A.3    Kettani, A.4    Skripkin, E.5    Patel, D.J.6
  • 28
    • 38349001213 scopus 로고    scopus 로고
    • Comparison of alignment tensors generated for native tRNA(Val) using magnetic fields and liquid crystalline media
    • Latham M.P., Hanson P., Brown D.J., and Pardi A. Comparison of alignment tensors generated for native tRNA(Val) using magnetic fields and liquid crystalline media. J. Biomol. NMR 40 (2008) 83-94
    • (2008) J. Biomol. NMR , vol.40 , pp. 83-94
    • Latham, M.P.1    Hanson, P.2    Brown, D.J.3    Pardi, A.4
  • 29
    • 31944446215 scopus 로고    scopus 로고
    • Resolving the motional modes that code for RNA adaptation
    • Zhang Q., Sun X., Watt E.D., and Al-Hashimi H.M. Resolving the motional modes that code for RNA adaptation. Science 311 (2006) 653-656
    • (2006) Science , vol.311 , pp. 653-656
    • Zhang, Q.1    Sun, X.2    Watt, E.D.3    Al-Hashimi, H.M.4
  • 30
    • 35048901140 scopus 로고    scopus 로고
    • Modulating protein alignment in a liquid-crystalline medium through conservative mutagenesis
    • Yao L., and Bax A. Modulating protein alignment in a liquid-crystalline medium through conservative mutagenesis. J. Am. Chem. Soc. 129 (2007) 11326-11327
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 11326-11327
    • Yao, L.1    Bax, A.2
  • 31
    • 20444428018 scopus 로고    scopus 로고
    • Evidence that electrostatic interactions dictate the ligand-induced arrest of RNA global flexibility
    • Pitt S.W., Zhang Q., Patel D.J., and Al-Hashimi H.M. Evidence that electrostatic interactions dictate the ligand-induced arrest of RNA global flexibility. Angew. Chem. Int. Ed. Engl. 44 (2005) 3412-3415
    • (2005) Angew. Chem. Int. Ed. Engl. , vol.44 , pp. 3412-3415
    • Pitt, S.W.1    Zhang, Q.2    Patel, D.J.3    Al-Hashimi, H.M.4
  • 32
    • 34249898353 scopus 로고    scopus 로고
    • +-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition
    • +-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition. Biochemistry 46 (2007) 6525-6535
    • (2007) Biochemistry , vol.46 , pp. 6525-6535
    • Casiano-Negroni, A.1    Sun, X.2    Al-Hashimi, H.M.3
  • 33
    • 40149085374 scopus 로고    scopus 로고
    • Extending the NMR spatial resolution limit for RNA by motional couplings
    • Zhang Q., and Al-Hashimi H.M. Extending the NMR spatial resolution limit for RNA by motional couplings. Nat. Methods 5 (2008) 243-245
    • (2008) Nat. Methods , vol.5 , pp. 243-245
    • Zhang, Q.1    Al-Hashimi, H.M.2
  • 34
    • 56049118219 scopus 로고    scopus 로고
    • Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis
    • Dethoff E.A., Hansen A.L., Musselman C., Watt E.D., Andricioaei I., and Al-Hashimi H.M. Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis. Biophys. J. 95 (2008) 3906-3915
    • (2008) Biophys. J. , vol.95 , pp. 3906-3915
    • Dethoff, E.A.1    Hansen, A.L.2    Musselman, C.3    Watt, E.D.4    Andricioaei, I.5    Al-Hashimi, H.M.6
  • 35
    • 0031760503 scopus 로고    scopus 로고
    • Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions
    • Hansen M.R., Mueller L., and Pardi A. Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat. Struct. Biol. 5 (1998) 1065-1074
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 1065-1074
    • Hansen, M.R.1    Mueller, L.2    Pardi, A.3
  • 36
    • 0036290269 scopus 로고    scopus 로고
    • Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings
    • Al-Hashimi H.M., Gosser Y., Gorin A., Hu W., Majumdar A., and Patel D.J. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J. Mol. Biol. 315 (2002) 95-102
    • (2002) J. Mol. Biol. , vol.315 , pp. 95-102
    • Al-Hashimi, H.M.1    Gosser, Y.2    Gorin, A.3    Hu, W.4    Majumdar, A.5    Patel, D.J.6
  • 38
    • 0036306532 scopus 로고    scopus 로고
    • Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings
    • Al-Hashimi H.M., Gorin A., Majumdar A., Gosser Y., and Patel D.J. Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings. J. Mol. Biol. 318 (2002) 637-649
    • (2002) J. Mol. Biol. , vol.318 , pp. 637-649
    • Al-Hashimi, H.M.1    Gorin, A.2    Majumdar, A.3    Gosser, Y.4    Patel, D.J.5
  • 39
    • 33751248765 scopus 로고    scopus 로고
    • Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings
    • Musselman C., Pitt S.W., Gulati K., Foster L.L., Andricioaei I., and Al-Hashimi H.M. Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings. J. Biomol. NMR 36 (2006) 235-249
    • (2006) J. Biomol. NMR , vol.36 , pp. 235-249
    • Musselman, C.1    Pitt, S.W.2    Gulati, K.3    Foster, L.L.4    Andricioaei, I.5    Al-Hashimi, H.M.6
  • 40
    • 34250728646 scopus 로고    scopus 로고
    • Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings
    • Bailor M.H., Musselman C., Hansen A.L., Gulati K., Patel D.J., and Al-Hashimi H.M. Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings. Nat. Protoc. 2 (2007) 1536-1546
    • (2007) Nat. Protoc. , vol.2 , pp. 1536-1546
    • Bailor, M.H.1    Musselman, C.2    Hansen, A.L.3    Gulati, K.4    Patel, D.J.5    Al-Hashimi, H.M.6
  • 41
    • 42149130389 scopus 로고    scopus 로고
    • NMR: prediction of molecular alignment from structure using the PALES software
    • Zweckstetter M. NMR: prediction of molecular alignment from structure using the PALES software. Nat. Protoc. 3 (2008) 679-690
    • (2008) Nat. Protoc. , vol.3 , pp. 679-690
    • Zweckstetter, M.1
  • 42
    • 0035925113 scopus 로고    scopus 로고
    • Structural and dynamic analysis of residual dipolar coupling data for proteins
    • Tolman J.R., Al-Hashimi H.M., Kay L.E., and Prestegard J.H. Structural and dynamic analysis of residual dipolar coupling data for proteins. J. Am. Chem. Soc. 123 (2001) 1416-1424
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 1416-1424
    • Tolman, J.R.1    Al-Hashimi, H.M.2    Kay, L.E.3    Prestegard, J.H.4
  • 43
    • 34247185394 scopus 로고    scopus 로고
    • 2+ binding: role in the kissing-duplex structural transition
    • 2+ binding: role in the kissing-duplex structural transition. Nucleic Acids Res. 35 (2007) 1698-1713
    • (2007) Nucleic Acids Res. , vol.35 , pp. 1698-1713
    • Sun, X.1    Zhang, Q.2    Al-Hashimi, H.M.3


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