메뉴 건너뛰기




Volumn 3, Issue 23, 2012, Pages 3616-3625

RNA under tension: Folding landscapes, kinetic partitioning mechanism, and molecular tensegrity

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR FUNCTION; CONFORMATIONAL CHANGE; CONFORMATIONAL DYNAMICS; KEY PARAMETERS; KINETIC PARTITIONING MECHANISMS; NON-CODING RNAS; RIBOSWITCHES; RNA MOLECULES; SINGLE-MOLECULE; TENSEGRITIES; TERTIARY INTERACTIONS;

EID: 84870802321     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz301537t     Document Type: Article
Times cited : (16)

References (59)
  • 1
    • 0037062949 scopus 로고    scopus 로고
    • The Chemical Repertoire of Natural Ribozymes
    • Doudna, J.; Cech, T. The Chemical Repertoire of Natural Ribozymes Nature 2002, 418, 222-228
    • (2002) Nature , vol.418 , pp. 222-228
    • Doudna, J.1    Cech, T.2
  • 2
    • 0034637161 scopus 로고    scopus 로고
    • The Structural Basis of Ribosome Activity in Peptide Bond Synthesis
    • Nissen, P.; Hansen, J.; Ban, N.; Moore, P.; Steitz, T. The Structural Basis of Ribosome Activity in Peptide Bond Synthesis Science 2000, 289, 920-930
    • (2000) Science , vol.289 , pp. 920-930
    • Nissen, P.1    Hansen, J.2    Ban, N.3    Moore, P.4    Steitz, T.5
  • 3
    • 10644237968 scopus 로고    scopus 로고
    • RNAi-Mediated Pathways in the Nucleus
    • Matke, M. A; Birchier, J. A. RNAi-Mediated Pathways in the Nucleus Nat. Rev. Genet. 2005, 6, 24-35
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 24-35
    • Matke, M.A.1    Birchier, J.A.2
  • 4
    • 27144527479 scopus 로고    scopus 로고
    • Regulation of Bacterial Gene Expression by Riboswitches
    • Winkler, W. C; Breaker, R. R. Regulation of Bacterial Gene Expression by Riboswitches Annu. Rev. Microbiol. 2005, 59, 487-517
    • (2005) Annu. Rev. Microbiol. , vol.59 , pp. 487-517
    • Winkler, W.C.1    Breaker, R.R.2
  • 5
    • 48249104039 scopus 로고    scopus 로고
    • Riboswitches: Emerging Themes in RNA Structure and Function
    • Montange, R. K; Batey, R. Riboswitches: Emerging Themes in RNA Structure and Function Annu. Rev Biophys. 2008, 37, 117-133
    • (2008) Annu. Rev Biophys. , vol.37 , pp. 117-133
    • Montange, R.K.1    Batey, R.2
  • 6
    • 16344371778 scopus 로고    scopus 로고
    • RNA and Protein folding: Common Themes and Variations
    • Thirumalai, D.; Hyeon, C. RNA and Protein folding: Common Themes and Variations Biochemistry 2005, 44, 4957-4970
    • (2005) Biochemistry , vol.44 , pp. 4957-4970
    • Thirumalai, D.1    Hyeon, C.2
  • 7
    • 14144252846 scopus 로고    scopus 로고
    • Extracting Stacking Interaction Parameters for RNA from the Data Set of Native Structures
    • Dima, R. I; Hyeon, C.; Thirumalai, D. Extracting Stacking Interaction Parameters for RNA from the Data Set of Native Structures J. Mol. Biol. 2005, 347, 53-69
    • (2005) J. Mol. Biol. , vol.347 , pp. 53-69
    • Dima, R.I.1    Hyeon, C.2    Thirumalai, D.3
  • 8
    • 0035946973 scopus 로고    scopus 로고
    • Role of Counterion Condensation in Folding of the Tetrahymena Ribozyme II. Counterion-Dependence of Folding Kinetics
    • Heilman-Miller, S.; Pan, J.; Thirumalai, D.; Woodson, S. Role of Counterion Condensation in Folding of the Tetrahymena Ribozyme II. Counterion-Dependence of Folding Kinetics J. Mol. Biol. 2001, 309, 57-68
    • (2001) J. Mol. Biol. , vol.309 , pp. 57-68
    • Heilman-Miller, S.1    Pan, J.2    Thirumalai, D.3    Woodson, S.4
  • 9
    • 36449009348 scopus 로고
    • Folding Kinetics of Proteins: A Model Study
    • Guo, Z.; Thirumalai, D.; Honeycutt, J. D. Folding Kinetics of Proteins: A Model Study J. Chem. Phys. 1992, 97, 525-535
    • (1992) J. Chem. Phys. , vol.97 , pp. 525-535
    • Guo, Z.1    Thirumalai, D.2    Honeycutt, J.D.3
  • 10
    • 0029010695 scopus 로고
    • Kinetics of Protein Folding: Nucleation Mechanism, Time Scales, and Pathways
    • Guo, Z.; Thirumalai, D. Kinetics of Protein Folding: Nucleation Mechanism, Time Scales, and Pathways Biopolymers 1995, 36, 83-102
    • (1995) Biopolymers , vol.36 , pp. 83-102
    • Guo, Z.1    Thirumalai, D.2
  • 11
    • 0031576334 scopus 로고    scopus 로고
    • Folding of RNA Involves Parallel Pathways
    • Pan, J.; Thirumalai, D.; Woodson, S. A. Folding of RNA Involves Parallel Pathways J. Mol. Biol. 1997, 273, 7-13
    • (1997) J. Mol. Biol. , vol.273 , pp. 7-13
    • Pan, J.1    Thirumalai, D.2    Woodson, S.A.3
  • 13
    • 83055179382 scopus 로고    scopus 로고
    • Fast Folding of RNA Pseudoknots Initiated by Laser Temperature-Jump
    • Narayanan, R.; Velmurugu, Y.; Kuznetsov, S.; Ansari, A. Fast Folding of RNA Pseudoknots Initiated by Laser Temperature-Jump J. Am. Chem. Soc. 2011, 133, 18767-18774
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 18767-18774
    • Narayanan, R.1    Velmurugu, Y.2    Kuznetsov, S.3    Ansari, A.4
  • 15
    • 0035957720 scopus 로고    scopus 로고
    • Reversible Unfolding of Single RNA Molecules by Mechanical Force
    • Liphardt, J.; Onoa, B.; Smith, S. B; Tinoco, I., Jr.; Bustamante, C. Reversible Unfolding of Single RNA Molecules by Mechanical Force Science 2001, 292, 733-737
    • (2001) Science , vol.292 , pp. 733-737
    • Liphardt, J.1    Onoa, B.2    Smith, S.B.3    Tinoco Jr., I.4    Bustamante, C.5
  • 16
    • 0242417558 scopus 로고    scopus 로고
    • Identifying Kinetic Barriers to Mechanical Unfolding of the T. thermophila Ribozyme
    • Onoa, B.; Dumont, S.; Liphardt, J.; Smith, S. B; Tinoco, I., Jr.; Bustamante, C. Identifying Kinetic Barriers to Mechanical Unfolding of the T. thermophila Ribozyme Science 2003, 299, 1892-1895
    • (2003) Science , vol.299 , pp. 1892-1895
    • Onoa, B.1    Dumont, S.2    Liphardt, J.3    Smith, S.B.4    Tinoco Jr., I.5    Bustamante, C.6
  • 18
    • 80053391759 scopus 로고    scopus 로고
    • Capturing the Essence of Folding and Functions of Biomolecules Using Coarse-Grained Models
    • Hyeon, C.; Thirumalai, D. Capturing the Essence of Folding and Functions of Biomolecules Using Coarse-Grained Models Nat. Commun. 2011, 2, 487
    • (2011) Nat. Commun. , vol.2 , pp. 487
    • Hyeon, C.1    Thirumalai, D.2
  • 20
    • 0015497450 scopus 로고
    • Conformational Changes of Transfer Ribonucleic Acid. Equilibrium Phase Diagrams
    • Cole, P. E; Yang, S. K; Crothers, D. M. Conformational Changes of Transfer Ribonucleic Acid. Equilibrium Phase Diagrams Biochemistry 1972, 11, 4358-4368
    • (1972) Biochemistry , vol.11 , pp. 4358-4368
    • Cole, P.E.1    Yang, S.K.2    Crothers, D.M.3
  • 21
    • 0015846852 scopus 로고
    • Thermodynamics and Kinetics of the Helix-Coil Transition of Oligomers Containing GC Base Pairs
    • Pörschke, D.; Uhlenbeck, O.; Martin, F. Thermodynamics and Kinetics of the Helix-Coil Transition of Oligomers Containing GC Base Pairs Biopolymers 1973, 12, 1313-1335
    • (1973) Biopolymers , vol.12 , pp. 1313-1335
    • Pörschke, D.1    Uhlenbeck, O.2    Martin, F.3
  • 22
    • 0016257808 scopus 로고
    • Thermodynamic and Kinetic Parameters of an Oligonucleotide Hairpin Helix
    • Porschke, D. Thermodynamic and Kinetic Parameters of an Oligonucleotide Hairpin Helix Biophys. Chem. 1974, 1, 381-386
    • (1974) Biophys. Chem. , vol.1 , pp. 381-386
    • Porschke, D.1
  • 23
    • 38949141544 scopus 로고
    • The Molecular Mechanism of Thermal Unfolding of Escherichia coli Formylmethionine Transfer RNA
    • Crothers, D.; Cole, P.; Hilbers, C.; Shulman, R. The Molecular Mechanism of Thermal Unfolding of Escherichia coli Formylmethionine Transfer RNA J. Mol. Biol. 1974, 62, 383-401
    • (1974) J. Mol. Biol. , vol.62 , pp. 383-401
    • Crothers, D.1    Cole, P.2    Hilbers, C.3    Shulman, R.4
  • 26
    • 33846468971 scopus 로고    scopus 로고
    • DNA Folding and Melting Observed in Real Time Redefine the Energy Landscape
    • Ma, H.; Wan, C.; Wu, A.; Zewail, A. DNA Folding and Melting Observed in Real Time Redefine the Energy Landscape Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 712-716
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 712-716
    • Ma, H.1    Wan, C.2    Wu, A.3    Zewail, A.4
  • 28
    • 47749150330 scopus 로고    scopus 로고
    • Force Dependent Hopping Rates of RNA Hairpins Can Be Estimated from Accurate Measurement of the Folding Landscapes
    • Hyeon, C.; Morrison, G.; Thirumalai, D. Force Dependent Hopping Rates of RNA Hairpins Can Be Estimated from Accurate Measurement of the Folding Landscapes Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 9604-9606
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 9604-9606
    • Hyeon, C.1    Morrison, G.2    Thirumalai, D.3
  • 30
    • 38949165395 scopus 로고    scopus 로고
    • Multiple Probes Are Required to Explore and Control the Rugged Energy Landscape of RNA Hairpins
    • Hyeon, C.; Thirumalai, D. Multiple Probes Are Required to Explore and Control the Rugged Energy Landscape of RNA Hairpins J. Am. Chem. Soc. 2008, 130, 1538-1539
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 1538-1539
    • Hyeon, C.1    Thirumalai, D.2
  • 31
    • 79960305090 scopus 로고    scopus 로고
    • Measuring the Folding Landscape of a Harmonically Constrained Biopolymer
    • de Messieres, M.; Brawn-Cinani, B.; Porta, A. L. Measuring the Folding Landscape of a Harmonically Constrained Biopolymer Biophys. J. 2011, 100, 2736-2744
    • (2011) Biophys. J. , vol.100 , pp. 2736-2744
    • De Messieres, M.1    Brawn-Cinani, B.2    Porta, A.L.3
  • 32
    • 33846193288 scopus 로고    scopus 로고
    • Pathways and Kinetic Barriers in Mechanical Unfolding and Refolding of RNA and Proteins
    • Hyeon, C.; Dima, R. I; Thirumalai, D. Pathways and Kinetic Barriers in Mechanical Unfolding and Refolding of RNA and Proteins Structure 2006, 14, 1633-1645
    • (2006) Structure , vol.14 , pp. 1633-1645
    • Hyeon, C.1    Dima, R.I.2    Thirumalai, D.3
  • 33
    • 38349110269 scopus 로고    scopus 로고
    • Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin
    • Garcia, A. E; Paschek, D. Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin J. Am. Chem. Soc. 2008, 130, 815-817
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 815-817
    • Garcia, A.E.1    Paschek, D.2
  • 35
    • 33646203784 scopus 로고    scopus 로고
    • Forced-Unfolding and Force-Quench Refolding of RNA Hairpins
    • Hyeon, C.; Thirumalai, D. Forced-Unfolding and Force-Quench Refolding of RNA Hairpins Biophys. J. 2006, 90, 3410-3427
    • (2006) Biophys. J. , vol.90 , pp. 3410-3427
    • Hyeon, C.1    Thirumalai, D.2
  • 37
    • 33846820159 scopus 로고    scopus 로고
    • Mechanical Unfolding of RNA: From Hairpins to Structures with Internal Multiloops
    • Hyeon, C.; Thirumalai, D. Mechanical Unfolding of RNA: From Hairpins to Structures with Internal Multiloops Biophys. J. 2007, 92, 731-743
    • (2007) Biophys. J. , vol.92 , pp. 731-743
    • Hyeon, C.1    Thirumalai, D.2
  • 38
    • 33646131832 scopus 로고    scopus 로고
    • Probing the Mechanical Folding Kinetics of TAR RNA by Hopping, Force-Jump, and Force-Ramp Methods
    • Li, P. T. X; Collin, D.; Smith, S. B; Bustamante, C.; Tinoco, I., Jr. Probing the Mechanical Folding Kinetics of TAR RNA by Hopping, Force-Jump, and Force-Ramp Methods Biophys. J. 2006, 90, 250-260
    • (2006) Biophys. J. , vol.90 , pp. 250-260
    • Li, P.T.X.1    Collin, D.2    Smith, S.B.3    Bustamante, C.4    Tinoco Jr., I.5
  • 39
    • 34249855274 scopus 로고    scopus 로고
    • Real-Time Control of the Energy Landscape by Force Directs the Folding of RNA Molecules
    • Li, P. T. X; Bustamante, C.; Tinoco, I., Jr. Real-Time Control of the Energy Landscape by Force Directs the Folding of RNA Molecules Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 7039-7044
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 7039-7044
    • Li, P.T.X.1    Bustamante, C.2    Tinoco Jr., I.3
  • 40
    • 33645004171 scopus 로고    scopus 로고
    • Intrinsic Rates and Activation Free Energies from Single-Molecule Pulling Experiments
    • Dudko, O. K; Hummer, G.; Szabo, A. Intrinsic Rates and Activation Free Energies from Single-Molecule Pulling Experiments Phys. Rev. Lett. 2006, 96, 108101
    • (2006) Phys. Rev. Lett. , vol.96 , pp. 108101
    • Dudko, O.K.1    Hummer, G.2    Szabo, A.3
  • 41
    • 54849437727 scopus 로고    scopus 로고
    • Relative Stability of Helices Determines the Folding Landscape of Adenine Riboswitch Aptamers
    • Lin, J.; Thirumalai, D. Relative Stability of Helices Determines the Folding Landscape of Adenine Riboswitch Aptamers J. Am. Chem. Soc. 2008, 130, 14080-14081
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 14080-14081
    • Lin, J.1    Thirumalai, D.2
  • 42
    • 0001348245 scopus 로고
    • Kinetic Concept of the Strength of Solids
    • Zhurkov, S. N. Kinetic Concept of the Strength of Solids Int. J. Fract. Mech. 1965, 1, 311-322
    • (1965) Int. J. Fract. Mech. , vol.1 , pp. 311-322
    • Zhurkov, S.N.1
  • 43
    • 0018101150 scopus 로고
    • Models for the Specific Adhesion of Cells to Cells
    • Bell, G. I. Models for the Specific Adhesion of Cells to Cells Science 1978, 200, 618-627
    • (1978) Science , vol.200 , pp. 618-627
    • Bell, G.I.1
  • 44
    • 0001484374 scopus 로고
    • Kramers Problem in the Turnover Regime - The Role of the Stochastic Separatrix
    • Klosek, M. M; Matkowsky, B. J; Schuss, Z. Kramers Problem in the Turnover Regime-The Role of the Stochastic Separatrix Ber. Bunsenges. Phys. Chem. 1991, 95, 331
    • (1991) Ber. Bunsenges. Phys. Chem. , vol.95 , pp. 331
    • Klosek, M.M.1    Matkowsky, B.J.2    Schuss, Z.3
  • 45
    • 79960622883 scopus 로고    scopus 로고
    • Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments
    • Morrison, G.; Hyeon, C.; Hinczewski, M.; Thirumalai, D. Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments Phys. Rev. Lett. 2011, 106, 138102
    • (2011) Phys. Rev. Lett. , vol.106 , pp. 138102
    • Morrison, G.1    Hyeon, C.2    Hinczewski, M.3    Thirumalai, D.4
  • 46
    • 0037383404 scopus 로고    scopus 로고
    • Cell Structure and Hierarchical Systems Biology
    • Ingber, D. E.; Tensegrity, I. Cell Structure and Hierarchical Systems Biology J. Cell. Sci. 2003, 116, 1157-1173
    • (2003) J. Cell. Sci. , vol.116 , pp. 1157-1173
    • Ingber, D.E.1    Tensegrity, I.2
  • 50
  • 51
    • 38849204944 scopus 로고    scopus 로고
    • Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers
    • Greenleaf, W. J; Frieda, K. L; Foster, D. A. N; Woodside, M. T; Block, S. M. Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers Science 2008, 319, 630-633
    • (2008) Science , vol.319 , pp. 630-633
    • Greenleaf, W.J.1    Frieda, K.L.2    Foster, D.A.N.3    Woodside, M.T.4    Block, S.M.5
  • 53
    • 0038210214 scopus 로고    scopus 로고
    • Riboswitches Control Fundamental Biochemical Pathways in B acillus subtilis and Other Bacteria
    • Mandal, M.; Boese, B.; Barrick, J. E; Winkler, W. C; Breaker, R. R. Riboswitches Control Fundamental Biochemical Pathways in B acillus subtilis and Other Bacteria Cell 2003, 113, 577-586
    • (2003) Cell , vol.113 , pp. 577-586
    • Mandal, M.1    Boese, B.2    Barrick, J.E.3    Winkler, W.C.4    Breaker, R.R.5
  • 54
    • 0842334528 scopus 로고    scopus 로고
    • Adenine Riboswitches and Gene Activation by Disruption of a Transcription Terminator
    • Mandal, M.; Breaker, R. R. Adenine Riboswitches and Gene Activation by Disruption of a Transcription Terminator Nat. Struct. Mol. Biol. 2004, 11, 29-35
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 29-35
    • Mandal, M.1    Breaker, R.R.2
  • 55
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA Secondary Structure Server
    • Hofacker, I. Vienna RNA Secondary Structure Server Nucleic Acids Res. 2003, 31, 3429
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3429
    • Hofacker, I.1
  • 56
    • 80053216036 scopus 로고    scopus 로고
    • Single-Molecule Force Spectroscopy of the Add Adenine Riboswitch Relates Folding to Regulatory Mechanism
    • Neupane, K.; Daniel, H. Y; Foster, A. N; Wang, F.; Woodside, M. T. Single-Molecule Force Spectroscopy of the Add Adenine Riboswitch Relates Folding to Regulatory Mechanism Nucleic Acids Res. 2011, 39, 7677-7687
    • (2011) Nucleic Acids Res. , vol.39 , pp. 7677-7687
    • Neupane, K.1    Daniel, H.Y.2    Foster, A.N.3    Wang, F.4    Woodside, M.T.5
  • 57
    • 70350462752 scopus 로고    scopus 로고
    • Assembly Mechanisms of RNA Pseudoknots Are Determined by the Stabilities of Constituent Secondary Structures
    • Cho, S.; Pincus, D.; Thirumalai, D. Assembly Mechanisms of RNA Pseudoknots Are Determined by the Stabilities of Constituent Secondary Structures Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 17349
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 17349
    • Cho, S.1    Pincus, D.2    Thirumalai, D.3
  • 58
    • 84856710189 scopus 로고    scopus 로고
    • Chain Length Determines the Folding Rates of RNA
    • Hyeon, C.; Thirumalai, D. Chain Length Determines the Folding Rates of RNA Biophys. J. 2012, 102, L11-L13
    • (2012) Biophys. J. , vol.102
    • Hyeon, C.1    Thirumalai, D.2
  • 59
    • 0035913518 scopus 로고    scopus 로고
    • Lattice Model Studies of Force-Induced Unfolding of Protein
    • Klimov, D. K; Thirumalai, D. Lattice Model Studies of Force-Induced Unfolding of Protein J. Phys. Chem. B 2001, 105, 6648-6654
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6648-6654
    • Klimov, D.K.1    Thirumalai, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.