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Volumn 349, Issue 5, 2005, Pages 1011-1023

Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element

Author keywords

Human immunodeficiency virus (HIV); NMR; Ribosomal frameshifting; RNA structure; RNA thermodynamics

Indexed keywords

PURINE; VIRUS RNA;

EID: 20344397919     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.03.038     Document Type: Article
Times cited : (78)

References (47)
  • 1
    • 0023870815 scopus 로고
    • Characterization of ribosomal frameshifting in HIV-1 gag-pol expression
    • T. Jacks, M.D. Power, F.R. Masiarz, P.A. Luciw, P.J. Barr, and H.E. Varmus Characterization of ribosomal frameshifting in HIV-1 gag-pol expression Nature 331 1988 280 283
    • (1988) Nature , vol.331 , pp. 280-283
    • Jacks, T.1    Power, M.D.2    Masiarz, F.R.3    Luciw, P.A.4    Barr, P.J.5    Varmus, H.E.6
  • 2
    • 0026717107 scopus 로고
    • Human immunodeficiency virus type 1 gag-pol frameshifting is dependent on downstream mRNA secondary structure: Demonstration by expression in vivo
    • N.T. Parkin, M. Chamorro, and H.E. Varmus Human immunodeficiency virus type 1 gag-pol frameshifting is dependent on downstream mRNA secondary structure: demonstration by expression in vivo J. Virol. 66 1992 5147 5151
    • (1992) J. Virol. , vol.66 , pp. 5147-5151
    • Parkin, N.T.1    Chamorro, M.2    Varmus, H.E.3
  • 3
    • 0026018243 scopus 로고
    • Overexpression of the gag-pol precursor from human immunodeficiency virus type 1 proviral genomes results in efficient proteolytic processing in the absence of virion production
    • J. Park, and C.D. Morrow Overexpression of the gag-pol precursor from human immunodeficiency virus type 1 proviral genomes results in efficient proteolytic processing in the absence of virion production J. Virol. 65 1991 5111 5117
    • (1991) J. Virol. , vol.65 , pp. 5111-5117
    • Park, J.1    Morrow, C.D.2
  • 4
    • 0035282697 scopus 로고    scopus 로고
    • Comparative mutational analysis of cis-acting RNA signals for translational frameshifting in HIV-1 and HTLV-2
    • Y.G. Kim, S. Maas, and A. Rich Comparative mutational analysis of cis-acting RNA signals for translational frameshifting in HIV-1 and HTLV-2 Nucl. Acids Res. 29 2001 1125 1131
    • (2001) Nucl. Acids Res. , vol.29 , pp. 1125-1131
    • Kim, Y.G.1    Maas, S.2    Rich, A.3
  • 5
    • 0035138477 scopus 로고    scopus 로고
    • Maintenance of the Gag/Gag-Pol ratio is important for human immunodeficiency virus type 1 RNA dimerization and viral infectivity
    • M. Shehu-Xhilaga, S.M. Crowe, and J. Mak Maintenance of the Gag/Gag-Pol ratio is important for human immunodeficiency virus type 1 RNA dimerization and viral infectivity J. Virol. 75 2001 1834 1841
    • (2001) J. Virol. , vol.75 , pp. 1834-1841
    • Shehu-Xhilaga, M.1    Crowe, S.M.2    Mak, J.3
  • 6
    • 0031901133 scopus 로고    scopus 로고
    • Importance of ribosomal frameshifting for human immunodeficiency virus type 1 particle assembly and replication
    • M. Hung, P. Patel, S. Davis, and S.R. Green Importance of ribosomal frameshifting for human immunodeficiency virus type 1 particle assembly and replication J. Virol. 72 1998 4819 4824
    • (1998) J. Virol. , vol.72 , pp. 4819-4824
    • Hung, M.1    Patel, P.2    Davis, S.3    Green, S.R.4
  • 8
    • 0036314316 scopus 로고    scopus 로고
    • Analysis of natural variants of the human immunodeficiency virus type 1 gag-pol frameshift stem-loop structure
    • A. Telenti, R. Martinez, M. Munoz, G. Bleiber, G. Greub, and D. Sanglard Analysis of natural variants of the human immunodeficiency virus type 1 gag-pol frameshift stem-loop structure J. Virol. 76 2002 7868 7873
    • (2002) J. Virol. , vol.76 , pp. 7868-7873
    • Telenti, A.1    Martinez, R.2    Munoz, M.3    Bleiber, G.4    Greub, G.5    Sanglard, D.6
  • 9
    • 0041660967 scopus 로고    scopus 로고
    • Solution structure of the HIV-1 frameshift inducing stem-loop RNA
    • D.W. Staple, and S.E. Butcher Solution structure of the HIV-1 frameshift inducing stem-loop RNA Nucl. Acids Res. 31 2003 4326 4331
    • (2003) Nucl. Acids Res. , vol.31 , pp. 4326-4331
    • Staple, D.W.1    Butcher, S.E.2
  • 10
    • 0037370616 scopus 로고    scopus 로고
    • Replacement of murine leukemia virus readthrough mechanism by human immunodeficiency virus frameshift allows synthesis of viral proteins and virus replication
    • M.N. Brunelle, L. Brakier-Gingras, and G. Lemay Replacement of murine leukemia virus readthrough mechanism by human immunodeficiency virus frameshift allows synthesis of viral proteins and virus replication J. Virol. 77 2003 3345 3350
    • (2003) J. Virol. , vol.77 , pp. 3345-3350
    • Brunelle, M.N.1    Brakier-Gingras, L.2    Lemay, G.3
  • 11
    • 0030880945 scopus 로고    scopus 로고
    • In vivo HIV-1 frameshifting efficiency is directly related to the stability of the stem-loop stimulatory signal
    • L. Bidou, G. Stahl, B. Grima, H. Liu, M. Cassan, and J.P. Rousset In vivo HIV-1 frameshifting efficiency is directly related to the stability of the stem-loop stimulatory signal RNA 3 1997 1153 1158
    • (1997) RNA , vol.3 , pp. 1153-1158
    • Bidou, L.1    Stahl, G.2    Grima, B.3    Liu, H.4    Cassan, M.5    Rousset, J.P.6
  • 12
    • 0034724565 scopus 로고    scopus 로고
    • Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting
    • D.P. Giedroc, C.A. Theimer, and P.L. Nixon Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting J. Mol. Biol. 298 2000 167 185
    • (2000) J. Mol. Biol. , vol.298 , pp. 167-185
    • Giedroc, D.P.1    Theimer, C.A.2    Nixon, P.L.3
  • 13
    • 0028962374 scopus 로고
    • Structural and functional studies of retroviral RNA pseudoknots involved in ribosomal frameshifting: Nucleotides at the junction of the two stems are important for efficient ribosomal frameshifting
    • X. Chen, M. Chamorro, S.I. Lee, L.X. Shen, J.V. Hines, and I. Tinoco Jr Structural and functional studies of retroviral RNA pseudoknots involved in ribosomal frameshifting: nucleotides at the junction of the two stems are important for efficient ribosomal frameshifting EMBO J. 14 1995 842 852
    • (1995) EMBO J. , vol.14 , pp. 842-852
    • Chen, X.1    Chamorro, M.2    Lee, S.I.3    Shen, L.X.4    Hines, J.V.5    Tinoco Jr., I.6
  • 15
    • 0036924931 scopus 로고    scopus 로고
    • Characterization of the frameshift stimulatory signal controlling a programmed -1 ribosomal frameshift in the human immunodeficiency virus type 1
    • D. Dulude, M. Baril, and L. Brakier-Gingras Characterization of the frameshift stimulatory signal controlling a programmed -1 ribosomal frameshift in the human immunodeficiency virus type 1 Nucl. Acids Res. 30 2002 5094 5102
    • (2002) Nucl. Acids Res. , vol.30 , pp. 5094-5102
    • Dulude, D.1    Baril, M.2    Brakier-Gingras, L.3
  • 16
    • 0141631892 scopus 로고    scopus 로고
    • Efficiency of a programmed -1 ribosomal frameshift in the different subtypes of the human immunodeficiency virus type 1 group M
    • M. Baril, D. Dulude, K. Gendron, G. Lemay, and L. Brakier-Gingras Efficiency of a programmed -1 ribosomal frameshift in the different subtypes of the human immunodeficiency virus type 1 group M RNA 9 2003 1246 1253
    • (2003) RNA , vol.9 , pp. 1246-1253
    • Baril, M.1    Dulude, D.2    Gendron, K.3    Lemay, G.4    Brakier-Gingras, L.5
  • 17
    • 3342905119 scopus 로고    scopus 로고
    • A reassessment of the response of the bacterial ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type 1
    • M. Leger, S. Sidani, and L. Brakier-Gingras A reassessment of the response of the bacterial ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type 1 RNA 10 2004 1225 1235
    • (2004) RNA , vol.10 , pp. 1225-1235
    • Leger, M.1    Sidani, S.2    Brakier-Gingras, L.3
  • 18
    • 11844292767 scopus 로고    scopus 로고
    • MRNA helicase activity of the ribosome
    • S. Takyar, R.P. Hickerson, and H.F. Noller mRNA helicase activity of the ribosome Cell 120 2005 49 58
    • (2005) Cell , vol.120 , pp. 49-58
    • Takyar, S.1    Hickerson, R.P.2    Noller, H.F.3
  • 19
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • T. Xia, J. SantaLucia Jr, M.E. Burkard, R. Kierzek, S.J. Schroeder, and X. Jiao Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs Biochemistry 37 1998 14719 14735
    • (1998) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1    SantaLucia Jr., J.2    Burkard, M.E.3    Kierzek, R.4    Schroeder, S.J.5    Jiao, X.6
  • 20
    • 0032012610 scopus 로고    scopus 로고
    • Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude
    • G.M. Clore, A.M. Gronenborn, and N. Tjandra Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude J. Magn. Reson. 131 1998 159 162
    • (1998) J. Magn. Reson. , vol.131 , pp. 159-162
    • Clore, G.M.1    Gronenborn, A.M.2    Tjandra, N.3
  • 21
    • 0035925113 scopus 로고    scopus 로고
    • Structural and dynamic analysis of residual dipolar coupling data for proteins
    • J.R. Tolman, H.M. Al-Hashimi, L.E. Kay, and J.H. Prestegard 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
  • 22
    • 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
    • H.M. Al-Hashimi, Y. Gosser, A. Gorin, W. Hu, A. Majumdar, and D.J. Patel 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
  • 25
    • 0037184536 scopus 로고    scopus 로고
    • Selection of tRNA by the ribosome requires a transition from an open to a closed form
    • J.M. Ogle, F.V. Murphy, M.J. Tarry, and V. Ramakrishnan Selection of tRNA by the ribosome requires a transition from an open to a closed form Cell 111 2002 721 732
    • (2002) Cell , vol.111 , pp. 721-732
    • Ogle, J.M.1    Murphy, F.V.2    Tarry, M.J.3    Ramakrishnan, V.4
  • 27
    • 0028910590 scopus 로고
    • The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus
    • L.X. Shen, and I. Tinoco Jr The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus J. Mol. Biol. 247 1995 963 978
    • (1995) J. Mol. Biol. , vol.247 , pp. 963-978
    • Shen, L.X.1    Tinoco Jr., I.2
  • 28
    • 0033010932 scopus 로고    scopus 로고
    • Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot
    • L. Su, L. Chen, M. Egli, J.M. Berger, and A. Rich Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot Nature Struct. Biol. 6 1999 285 292
    • (1999) Nature Struct. Biol. , vol.6 , pp. 285-292
    • Su, L.1    Chen, L.2    Egli, M.3    Berger, J.M.4    Rich, A.5
  • 29
    • 0030602904 scopus 로고    scopus 로고
    • A characteristic bent conformation of RNA pseudoknots promotes -1 frameshifting during translation of retroviral RNA
    • X. Chen, H. Kang, L.X. Shen, M. Chamorro, H.E. Varmus, and I. Tinoco Jr A characteristic bent conformation of RNA pseudoknots promotes -1 frameshifting during translation of retroviral RNA J. Mol. Biol. 260 1996 479 483
    • (1996) J. Mol. Biol. , vol.260 , pp. 479-483
    • Chen, X.1    Kang, H.2    Shen, L.X.3    Chamorro, M.4    Varmus, H.E.5    Tinoco Jr., I.6
  • 30
    • 9644310202 scopus 로고    scopus 로고
    • Untying the FIV frameshifting pseudoknot structure by MS3D
    • E.T. Yu, Q. Zhang, and D. Fabris Untying the FIV frameshifting pseudoknot structure by MS3D J. Mol. Biol. 345 2005 69 80
    • (2005) J. Mol. Biol. , vol.345 , pp. 69-80
    • Yu, E.T.1    Zhang, Q.2    Fabris, D.3
  • 31
    • 0035958587 scopus 로고    scopus 로고
    • The path of messenger RNA through the ribosome
    • G.Z. Yusupova, M.M. Yusupov, J.H. Cate, and H.F. Noller The path of messenger RNA through the ribosome Cell 106 2001 233 241
    • (2001) Cell , vol.106 , pp. 233-241
    • Yusupova, G.Z.1    Yusupov, M.M.2    Cate, J.H.3    Noller, H.F.4
  • 34
    • 0037407032 scopus 로고    scopus 로고
    • Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification
    • N.J. Reiter, L.J. Nikstad, A.M. Allmann, R.J. Johnson, and S.E. Butcher Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification RNA 9 2003 533 542
    • (2003) RNA , vol.9 , pp. 533-542
    • Reiter, N.J.1    Nikstad, L.J.2    Allmann, A.M.3    Johnson, R.J.4    Butcher, S.E.5
  • 35
    • 0034130999 scopus 로고    scopus 로고
    • Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions
    • M.R. Hansen, P. Hanson, and A. Pardi 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
  • 36
    • 0037407032 scopus 로고    scopus 로고
    • Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification
    • N.J. Reiter, L.J. Nikstad, A.M. Allmann, R.J. Johnson, and S.E. Butcher Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification RNA 9 2003 533 542
    • (2003) RNA , vol.9 , pp. 533-542
    • Reiter, N.J.1    Nikstad, L.J.2    Allmann, A.M.3    Johnson, R.J.4    Butcher, S.E.5
  • 38
    • 1242340502 scopus 로고    scopus 로고
    • New applications of 2D filtered/edited NOESY for assignment and structure elucidation of RNA and RNA-protein complexes
    • R.D. Peterson, C.A. Theimer, H. Wu, and J. Feigon New applications of 2D filtered/edited NOESY for assignment and structure elucidation of RNA and RNA-protein complexes J. Biomol. NMR 28 2004 59 67
    • (2004) J. Biomol. NMR , vol.28 , pp. 59-67
    • Peterson, R.D.1    Theimer, C.A.2    Wu, H.3    Feigon, J.4
  • 41
    • 0032185144 scopus 로고    scopus 로고
    • Measurement of dipolar couplings for methylene and methyl sites in weakly oriented macromolecules and their use in structure determination
    • M. Ottiger, F. Delaglio, J.L. Marquardt, N. Tjandra, and A. Bax Measurement of dipolar couplings for methylene and methyl sites in weakly oriented macromolecules and their use in structure determination J. Magn. Reson. 134 1998 365 369
    • (1998) J. Magn. Reson. , vol.134 , pp. 365-369
    • Ottiger, M.1    Delaglio, F.2    Marquardt, J.L.3    Tjandra, N.4    Bax, A.5
  • 42
    • 0034685436 scopus 로고    scopus 로고
    • Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR
    • M. Zweckstetter, and A. Bax 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
  • 45
    • 0037433242 scopus 로고    scopus 로고
    • Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation
    • G.M. Clore, and J. Kuszewski Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation J. Am. Chem. Soc. 125 2003 1518 1525
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1518-1525
    • Clore, G.M.1    Kuszewski, J.2
  • 46
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • R. Koradi, M. Billeter, and K. Wuthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graph. 14 1996 51 55 see also 29-32
    • (1996) J. Mol. Graph. , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3
  • 47
    • 0029100232 scopus 로고
    • Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions
    • K.J. Breslauer Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions Methods Enzymol. 259 1995 221 242
    • (1995) Methods Enzymol. , vol.259 , pp. 221-242
    • Breslauer, K.J.1


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