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Volumn 5, Issue 1, 2015, Pages 294-320

What RNA world? Why a peptide/rna partnership merits renewed experimental attention

Author keywords

Catalysis; Enzyme superfamilies; Operational RNA code; Sense antisense genetic coding; tRNA acceptor stem recognition

Indexed keywords


EID: 84922022547     PISSN: None     EISSN: 20751729     Source Type: Journal    
DOI: 10.3390/life5010294     Document Type: Review
Times cited : (69)

References (99)
  • 1
    • 0000931002 scopus 로고
    • A Proposed Model for Interaction of Polypeptides with RNA
    • Carter, C.W., Jr.; Kraut, J. A Proposed Model for Interaction of Polypeptides with RNA. Proc. Natl. Acad. Sci. USA 1974, 71, 283-287.
    • (1974) Proc. Natl. Acad. Sci. USA , vol.71 , pp. 283-287
    • Carter, C.W.1    Kraut, J.2
  • 2
    • 84903905062 scopus 로고
    • Cradles for Molecular Evolution
    • 27 March
    • Carter, C.W., Jr. Cradles for Molecular Evolution. New Scientist, 27 March 1975, pp. 784-787.
    • (1975) New Scientist , pp. 784-787
    • Carter, C.W.1
  • 3
    • 33646080332 scopus 로고    scopus 로고
    • Progress Toward Understanding the Origin of the RNA World
    • 3rd ed.; Gesteland, R.F., Cech, T.R., Atkins, J., Eds.; Cold Spring Harbor Laboratory: Cold Spring Harbor, NY, USA
    • Joyce, G.; Orgel, L.E. Progress Toward Understanding the Origin of the RNA World. In The RNA World, 3rd ed.; Gesteland, R.F., Cech, T.R., Atkins, J., Eds.; Cold Spring Harbor Laboratory: Cold Spring Harbor, NY, USA, 2006.
    • (2006) The RNA World
    • Joyce, G.1    Orgel, L.E.2
  • 4
    • 84922035503 scopus 로고    scopus 로고
    • RNA World 2.0
    • 1 March
    • Akst, J. RNA World 2.0. The Scientist, 1 March 2014, pp. 34-40.
    • (2014) The Scientist , pp. 34-40
    • Akst, J.1
  • 5
    • 0038497542 scopus 로고
    • A Structure for Deoxyribose Nucleic Acid
    • Watson, J.D.; Crick, F.H.C. A Structure for Deoxyribose Nucleic Acid. Nature 1953, 171, 737-738.
    • (1953) Nature , vol.171 , pp. 737-738
    • Watson, J.D.1    Crick, F.H.C.2
  • 6
    • 36849148382 scopus 로고
    • The RNA World
    • Gilbert, W. The RNA World. Nature 1986, 319, 618.
    • (1986) Nature , vol.319 , pp. 618
    • Gilbert, W.1
  • 8
    • 0029436218 scopus 로고
    • Two Types of Aminoacyl-tRNA Synthetases Could be Originally Encoded by Complementary Strands of the Same Nucleic Acid
    • Rodin, S.N.; Ohno, S. Two Types of Aminoacyl-tRNA Synthetases Could be Originally Encoded by Complementary Strands of the Same Nucleic Acid. Orig. Life Evol. Biosph. 1995, 25, 565-589.
    • (1995) Orig. Life Evol. Biosph. , vol.25 , pp. 565-589
    • Rodin, S.N.1    Ohno, S.2
  • 9
    • 0025158208 scopus 로고
    • Partition of tRNA Synthetases into Two Classes Based on Mutually Exclusive Sets of Sequence Motifs
    • Eriani, G.; Delarue, M.; Poch, O.; Gangloff, J.; Moras, D. Partition of tRNA Synthetases into Two Classes Based on Mutually Exclusive Sets of Sequence Motifs. Nature 1990, 347, 203-206.
    • (1990) Nature , vol.347 , pp. 203-206
    • Eriani, G.1    Delarue, M.2    Poch, O.3    Gangloff, J.4    Moras, D.5
  • 10
    • 0025043116 scopus 로고
    • A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 Å
    • Cusack, S.; Berthet-Colominas, C.; Härtlein, M.; Nassar, N.; Leberman, R. A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 Å. Nature 1990, 347, 249-255.
    • (1990) Nature , vol.347 , pp. 249-255
    • Cusack, S.1    Berthet-Colominas, C.2    Härtlein, M.3    Nassar, N.4    Leberman, R.5
  • 11
    • 0026429275 scopus 로고
    • Class II Aminoacyl Transfer RNA Synthetases: Crystal Structure of Yeast Aspartyl-tRNA Synthetase Complexed with Trna (Asp)
    • Ruff, M.; Krishnaswamy, S.; Boeglin, M.; Poterszman, A.; Mitschler, A.; Podjarny, A.; Rees, B.; Thierry, J.C.; Moras, D. Class II Aminoacyl Transfer RNA Synthetases: Crystal Structure of Yeast Aspartyl-tRNA Synthetase Complexed with Trna (Asp). Science 1991, 252, 1682-1689.
    • (1991) Science , vol.252 , pp. 1682-1689
    • Ruff, M.1    Krishnaswamy, S.2    Boeglin, M.3    Poterszman, A.4    Mitschler, A.5    Podjarny, A.6    Rees, B.7    Thierry, J.C.8    Moras, D.9
  • 12
    • 84903893580 scopus 로고    scopus 로고
    • Urzymology: Experimental Access to a Key Transition in the Appearance of Enzymes
    • Carter, C.W., Jr. Urzymology: Experimental Access to a Key Transition in the Appearance of Enzymes. J. Biol. Chem. 2014, 289, 30213-30220.
    • (2014) J. Biol. Chem. , vol.289 , pp. 30213-30220
    • Carter, C.W.1
  • 13
    • 84884171822 scopus 로고    scopus 로고
    • Aminoacylating Urzymes Challenge the RNA World Hypothesis
    • Li, L.; Francklyn, C.; Carter, C.W., Jr. Aminoacylating Urzymes Challenge the RNA World Hypothesis. J. Biol. Chem. 2013, 288, 26856-26863.
    • (2013) J. Biol. Chem. , vol.288 , pp. 26856-26863
    • Li, L.1    Francklyn, C.2    Carter, C.W.3
  • 14
    • 79953187583 scopus 로고    scopus 로고
    • Histidyl-tRNA Synthetase Urzymes: Class I and II Aminoacyl-tRNA Synthetase Urzymes have Comparable Catalytic Activities for Cognate Amino Acid Activation
    • Li, L.; Weinreb, V.; Francklyn, C.; Carter, C.W., Jr. Histidyl-tRNA Synthetase Urzymes: Class I and II Aminoacyl-tRNA Synthetase Urzymes have Comparable Catalytic Activities for Cognate Amino Acid Activation. J. Biol. Chem. 2011, 286, 10387-10395.
    • (2011) J. Biol. Chem. , vol.286 , pp. 10387-10395
    • Li, L.1    Weinreb, V.2    Francklyn, C.3    Carter, C.W.4
  • 15
    • 33947266906 scopus 로고    scopus 로고
    • A Minimal TrpRS Catalytic Domain Supports Sense/Antisense Ancestry of Class I and II Aminoacyl-tRNA Synthetases
    • Pham, Y.; Li, L.; Kim, A.; Erdogan, O.; Weinreb, V.; Butterfoss, G.; Kuhlman, B.; Carter, C.W., Jr. A Minimal TrpRS Catalytic Domain Supports Sense/Antisense Ancestry of Class I and II Aminoacyl-tRNA Synthetases. Mol. Cell 2007, 25, 851-862.
    • (2007) Mol. Cell , vol.25 , pp. 851-862
    • Pham, Y.1    Li, L.2    Kim, A.3    Erdogan, O.4    Weinreb, V.5    Butterfoss, G.6    Kuhlman, B.7    Carter, C.W.8
  • 16
    • 0036809656 scopus 로고    scopus 로고
    • Did tRNA Synthetase Classes Arise on Opposite Strands of the Same Gene?
    • Carter, C.W., Jr.; Duax, W.L. Did tRNA Synthetase Classes Arise on Opposite Strands of the Same Gene? Mol. Cell 2002, 10, 705-708.
    • (2002) Mol. Cell , vol.10 , pp. 705-708
    • Carter, C.W.1    Duax, W.L.2
  • 17
    • 84879405227 scopus 로고    scopus 로고
    • Statistical Evaluation of the Rodin-Ohno Hypothesis: Sense/Antisense Coding of Ancestral Class I and II Aminoacyl-tRNA Synthetases
    • Chandrasekaran, S.N.; Yardimci, G.; Erdogan, O.; Roach, J.M.; Carter, C.W., Jr. Statistical Evaluation of the Rodin-Ohno Hypothesis: Sense/Antisense Coding of Ancestral Class I and II Aminoacyl-tRNA Synthetases. Mol. Biol. Evol. 2013, 30, 1588-1604.
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 1588-1604
    • Chandrasekaran, S.N.1    Yardimci, G.2    Erdogan, O.3    Roach, J.M.4    Carter, C.W.5
  • 19
    • 84908671076 scopus 로고    scopus 로고
    • Did Class 1 and Class 2 Aminoacyl-tRNA Synthetases Descend from Genetically Complementary, Catalytically Active ATP-Binding Motifs?
    • Jimenez, M.; Williams, T.; González-Rivera, A.K.; Li, L.; Erdogan, O.; Carter, C.W., Jr. Did Class 1 and Class 2 Aminoacyl-tRNA Synthetases Descend from Genetically Complementary, Catalytically Active ATP-Binding Motifs? Biophys. J. 2014, 106, 675a.
    • (2014) Biophys. J. , vol.106 , pp. 675
    • Jimenez, M.1    Williams, T.2    González-Rivera, A.K.3    Li, L.4    Erdogan, O.5    Carter, C.W.6
  • 20
    • 84902053224 scopus 로고    scopus 로고
    • The Rodin-Ohno Hypothesis That Two Enzyme Superfamilies Descended from One Ancestral Gene: An Unlikely Scenario for the Origins of Translation That Will Not Be Dismissed
    • Carter, C.W., Jr.; Li, L.; Weinreb, V.; Collier, M.; Gonzales-Rivera, K.; Jimenez-Rodriguez, M.; Erdogan, O.; Chandrasekharan, S.N. The Rodin-Ohno Hypothesis That Two Enzyme Superfamilies Descended from One Ancestral Gene: An Unlikely Scenario for the Origins of Translation That Will Not Be Dismissed. Biol. Direct 2014, 9, doi:10.1186/1745-6150-9-1.
    • (2014) Biol. Direct , vol.9
    • Carter, C.W.1    Li, L.2    Weinreb, V.3    Collier, M.4    Gonzales-Rivera, K.5    Jimenez-Rodriguez, M.6    Erdogan, O.7    Chandrasekharan, S.N.8
  • 21
    • 78649653834 scopus 로고    scopus 로고
    • Tryptophanyl-tRNA synthetase Urzyme: A model to recapitulate molecular evolution and investigate intramolecular complementation
    • Pham, Y.; Kuhlman, B.; Butterfoss, G.L.; Hu, H.; Weinreb, V.; Carter, C.W., Jr. Tryptophanyl-tRNA synthetase Urzyme: A model to recapitulate molecular evolution and investigate intramolecular complementation. J. Biol. Chem. 2010, 285, 38590-38601.
    • (2010) J. Biol. Chem. , vol.285 , pp. 38590-38601
    • Pham, Y.1    Kuhlman, B.2    Butterfoss, G.L.3    Hu, H.4    Weinreb, V.5    Carter, C.W.6
  • 22
    • 34047227549 scopus 로고    scopus 로고
    • The Rate Enhancement Produced by the Ribosome: An Improved Model
    • Schroeder, G.K.; Wolfenden, R. The Rate Enhancement Produced by the Ribosome: An Improved Model. Biochemisty 2007, 46, 4037-4044.
    • (2007) Biochemisty , vol.46 , pp. 4037-4044
    • Schroeder, G.K.1    Wolfenden, R.2
  • 24
    • 72449152725 scopus 로고    scopus 로고
    • On Primordial Sense-Antisense Coding
    • Rodin, A.; Rodin, S.N.; Carter, C.W., Jr. On Primordial Sense-Antisense Coding. J. Mol. Evol. 2009, 69, 555-567.
    • (2009) J. Mol. Evol. , vol.69 , pp. 555-567
    • Rodin, A.1    Rodin, S.N.2    Carter, C.W.3
  • 25
    • 84894199948 scopus 로고    scopus 로고
    • Enhanced Amino Acid Selection in Fully-Evolved Tryptophanyl-tRNA Synthetase, Relative to its Urzyme, Requires Domain Movement Sensed by the D1 Switch, a Remote, Dynamic Packing Motif
    • Weinreb, V.; Li, L.; Chandrasekaran, S.N.; Koehl, P.; Delarue, M.; Carter, C.W., Jr. Enhanced Amino Acid Selection in Fully-Evolved Tryptophanyl-tRNA Synthetase, Relative to its Urzyme, Requires Domain Movement Sensed by the D1 Switch, a Remote, Dynamic Packing Motif. J. Biol. Chem. 2014, 289, 4367-4376.
    • (2014) J. Biol. Chem. , vol.289 , pp. 4367-4376
    • Weinreb, V.1    Li, L.2    Chandrasekaran, S.N.3    Koehl, P.4    Delarue, M.5    Carter, C.W.6
  • 26
    • 84888996933 scopus 로고    scopus 로고
    • Full Implementation of the Genetic Code by Tryptophanyl-tRNA Synthetase Requires Intermodular Coupling
    • Li, L.; Carter, C.W., Jr. Full Implementation of the Genetic Code by Tryptophanyl-tRNA Synthetase Requires Intermodular Coupling. J. Biol. Chem. 2013, 288, 34736-34745.
    • (2013) J. Biol. Chem. , vol.288 , pp. 34736-34745
    • Li, L.1    Carter, C.W.2
  • 27
    • 0026075798 scopus 로고
    • Structural Relationships and the Classification of Aminoacyl-tRNA Synthetases
    • Burbaum, J.; Schimmel, P. Structural Relationships and the Classification of Aminoacyl-tRNA Synthetases. J. Biol. Chem. 1991, 266, 16965-16968.
    • (1991) J. Biol. Chem. , vol.266 , pp. 16965-16968
    • Burbaum, J.1    Schimmel, P.2
  • 28
    • 0026032475 scopus 로고
    • Assembly of a Class I tRNA Synthetase from Products of an Artificially Split Gene
    • Burbaum, J.J.; Schimmel, P. Assembly of a Class I tRNA Synthetase from Products of an Artificially Split Gene. Biochemtry 1991, 30, 319-324.
    • (1991) Biochemtry , vol.30 , pp. 319-324
    • Burbaum, J.J.1    Schimmel, P.2
  • 29
    • 0025343160 scopus 로고
    • Understanding Structural Relationships in Proteins of Unsolved Three-Dimensional Structure
    • Burbaum, J.J.; Starzyk, R.M.; Schimmel, P. Understanding Structural Relationships in Proteins of Unsolved Three-Dimensional Structure. Protein. Struct. Funct. Genet. 1990, 7, 99-111.
    • (1990) Protein. Struct. Funct. Genet. , vol.7 , pp. 99-111
    • Burbaum, J.J.1    Starzyk, R.M.2    Schimmel, P.3
  • 30
    • 33747859373 scopus 로고    scopus 로고
    • RosettaDesign server for protein design
    • Liu, Y.; Kuhlman, B. RosettaDesign server for protein design. Nucleic Acids Res. 2006, 34, 235-238.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 235-238
    • Liu, Y.1    Kuhlman, B.2
  • 31
    • 0035543093 scopus 로고    scopus 로고
    • The Depth of Chemical Time and the Power of Enzymes as Catalysts
    • Wolfenden, R.; Snider, M.J. The Depth of Chemical Time and the Power of Enzymes as Catalysts. Acc. Chem. Res. 2001, 34, 938-945.
    • (2001) Acc. Chem. Res. , vol.34 , pp. 938-945
    • Wolfenden, R.1    Snider, M.J.2
  • 32
    • 37049122234 scopus 로고
    • The Reactivity of Phosphate Esters. Reactions of Diesters with Nucleophiles
    • Kirby, A.J.; Younas, M. The Reactivity of Phosphate Esters. Reactions of Diesters with Nucleophiles. J. Chem. Soc. B Phys. Org. 1970, doi:10.1039/J29700001165.
    • (1970) J. Chem. Soc. B Phys. Org.
    • Kirby, A.J.1    Younas, M.2
  • 33
    • 69249106454 scopus 로고    scopus 로고
    • The Intrinsic Reactivity of ATP and the Catalytic Proficiencies of Kinases Acting on Glucose, N-Acetylgalactosamine, and Homeserine: A Thermodynamic Analysis
    • Stockbridge, R.B.; Wolfenden, R. The Intrinsic Reactivity of ATP and the Catalytic Proficiencies of Kinases Acting on Glucose, N-Acetylgalactosamine, and Homeserine: A Thermodynamic Analysis. J. Biol. Chem. 2009, 284, 22747-22757.
    • (2009) J. Biol. Chem. , vol.284 , pp. 22747-22757
    • Stockbridge, R.B.1    Wolfenden, R.2
  • 34
    • 0035912786 scopus 로고    scopus 로고
    • RNA-catalyzed amino acid activation
    • Kumar, R.K.; Yarus, M. RNA-catalyzed amino acid activation. Biochemtry 2001, 40, 6998-7004.
    • (2001) Biochemtry , vol.40 , pp. 6998-7004
    • Kumar, R.K.1    Yarus, M.2
  • 35
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32, 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 36
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: Selection of best-fit models of protein evolution
    • Abascal, F.; Zardoya, R.; Posada, D. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 2005, 21, 2104-2105.
    • (2005) Bioinformatics , vol.21 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 37
    • 84864453108 scopus 로고    scopus 로고
    • jModelTest 2: More models, new heuristics and parallel computing
    • Darriba, D.; Taboada, G.L.; Doallo, R.; Posada, D. jModelTest 2: More models, new heuristics and parallel computing. Nat. Meth. 2012, 9, doi:10.1038/nmeth.2109.
    • (2012) Nat. Meth. , vol.9
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 38
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: A program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. PAML 4: A program package for phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24, 1586-1591.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 40
    • 0022703916 scopus 로고
    • Are proteins made of modules
    • Traut, T.W. Are proteins made of modules. Mol. Cell. Biochem. 1986, 7, 3-10.
    • (1986) Mol. Cell. Biochem. , vol.7 , pp. 3-10
    • Traut, T.W.1
  • 41
    • 84868370084 scopus 로고    scopus 로고
    • The Origin of Life: Look Up and Look Down
    • Peters, J.W.; Williams, L.D. The Origin of Life: Look Up and Look Down. Astrobiology 2012, 12, 1087-1092.
    • (2012) Astrobiology , vol.12 , pp. 1087-1092
    • Peters, J.W.1    Williams, L.D.2
  • 43
    • 0013824051 scopus 로고
    • On the Origin of the Genetic Code
    • Woese, C.R. On the Origin of the Genetic Code. Proc. Natl. Acad. Sci. USA 1965, 54, 1546-1552.
    • (1965) Proc. Natl. Acad. Sci. USA , vol.54 , pp. 1546-1552
    • Woese, C.R.1
  • 46
    • 0026639881 scopus 로고
    • Unusual Resistance of Peptidyl Transferase to Protein Extraction Procedures
    • Noller, H.F.; Hoffarth, V.; Zimniak, L. Unusual Resistance of Peptidyl Transferase to Protein Extraction Procedures. Science 1992, 256, 1416-1419.
    • (1992) Science , vol.256 , pp. 1416-1419
    • Noller, H.F.1    Hoffarth, V.2    Zimniak, L.3
  • 47
    • 0037423764 scopus 로고    scopus 로고
    • Functional Fingerprints of Folds: Evidence for Correlated Structure-Function Evolution
    • Shakhnovich, B.E.; Dokholyan, N.V.; DeLisi, C.; Shacknovich, E. Functional Fingerprints of Folds: Evidence for Correlated Structure-Function Evolution. J. Mol. Biol. 2003, 326, 1-9.
    • (2003) J. Mol. Biol. , vol.326 , pp. 1-9
    • Shakhnovich, B.E.1    Dokholyan, N.V.2    DeLisi, C.3    Shacknovich, E.4
  • 48
  • 49
    • 0035823119 scopus 로고    scopus 로고
    • Understanding hierarchical protein evolution from first principles
    • Dokholyan, N.V.; Shakhnovich, E.I. Understanding hierarchical protein evolution from first principles. J. Mol. Biol. 2001, 312, 289-307.
    • (2001) J. Mol. Biol. , vol.312 , pp. 289-307
    • Dokholyan, N.V.1    Shakhnovich, E.I.2
  • 50
    • 0027171607 scopus 로고
    • Sequential Proton NMR Resonance Assignments, Circular Dichroism, and Structural Properties of a 50-Residue Substrate-Binding Peptide from DNA Polymerase I
    • Mullen, G.P.; Vaughn, J.B., Jr.; Mildvan, A.S. Sequential Proton NMR Resonance Assignments, Circular Dichroism, and Structural Properties of a 50-Residue Substrate-Binding Peptide from DNA Polymerase I. Arch. Biochem. Biophys. 1993, 301, 174-183.
    • (1993) Arch. Biochem. Biophys. , vol.301 , pp. 174-183
    • Mullen, G.P.1    Vaughn, J.B.2    Mildvan, A.S.3
  • 51
    • 0026687134 scopus 로고
    • Two-Dimensional NMR, Circular Dichroism, and Fluorescence Studies of PP-50, a Synthetic ATP-Binding Peptide from the β-Subunit of Mitochondrial ATP Synthase
    • Chuang, W.-J.; Abeygunawardana, C.; Pedersen, P.L.; Mildvan, A.S. Two-Dimensional NMR, Circular Dichroism, and Fluorescence Studies of PP-50, a Synthetic ATP-Binding Peptide from the β-Subunit of Mitochondrial ATP Synthase. Biochem. 1992, 31, 7915-7921.
    • (1992) Biochem. , vol.31 , pp. 7915-7921
    • Chuang, W.-J.1    Abeygunawardana, C.2    Pedersen, P.L.3    Mildvan, A.S.4
  • 53
    • 0023896339 scopus 로고
    • Solution Structure of the 45-Residue MgATP-Binding Peptide of Adenylate Kinase As Examined by 2-D NMR, FTIR, and CD Spectroscopy
    • Fry, D.C.; Byler, D.M.; Sisu, H.; Brown, E.M.; Kuby, S.A.; Mildvan, A.S. Solution Structure of the 45-Residue MgATP-Binding Peptide of Adenylate Kinase As Examined by 2-D NMR, FTIR, and CD Spectroscopy. Biochem. 1988, 27, 3588-3598.
    • (1988) Biochem. , vol.27 , pp. 3588-3598
    • Fry, D.C.1    Byler, D.M.2    Sisu, H.3    Brown, E.M.4    Kuby, S.A.5    Mildvan, A.S.6
  • 54
    • 0021934074 scopus 로고
    • NMR Studies of the MgATP Binding Site of Adenylate Kinase and of a 45-Residue Peptide Fragment of the Enzyme
    • Fry, D.C.; Kuby, S.A.; Mildvan, A.S. NMR Studies of the MgATP Binding Site of Adenylate Kinase and of a 45-Residue Peptide Fragment of the Enzyme. Biochemtry 1985, 24, 4680-4694.
    • (1985) Biochemtry , vol.24 , pp. 4680-4694
    • Fry, D.C.1    Kuby, S.A.2    Mildvan, A.S.3
  • 55
    • 0027436686 scopus 로고
    • An operational RNA code for amino acids and possible relationship to genetic code
    • Schimmel, P.; Giegé, R.; Moras, D.; Yokoyama, S. An operational RNA code for amino acids and possible relationship to genetic code. Proc. Natl. Acad. Sci. USA 1993, 90, 8763-8768.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 8763-8768
    • Schimmel, P.1    Giegé, R.2    Moras, D.3    Yokoyama, S.4
  • 56
    • 84922035501 scopus 로고    scopus 로고
    • tRNA Acceptor-Stem and Anticodon Bases Form Independent Codes Related to Protein Folding
    • Submitted for publication
    • Carter, C.W., Jr.; Wolfenden, R. tRNA Acceptor-Stem and Anticodon Bases Form Independent Codes Related to Protein Folding. Proc. Natl. Acad. Sci. USA 2015, Submitted for publication.
    • (2015) Proc. Natl. Acad. Sci. USA
    • Carter, C.W.1    Wolfenden, R.2
  • 57
    • 0028568650 scopus 로고
    • Intrinsic Secondary Structure Propensities of the Amino Acids, Using Statistical Φ-Ψ matrices: Comparison with Experimental Scales
    • Muñoz, V.; Serrano, L. Intrinsic Secondary Structure Propensities of the Amino Acids, Using Statistical Φ-Ψ matrices: Comparison with Experimental Scales. Protein. Struct. Funct. Gen. 1994, 20, 301-311.
    • (1994) Protein. Struct. Funct. Gen. , vol.20 , pp. 301-311
    • Muñoz, V.1    Serrano, L.2
  • 58
    • 84859910800 scopus 로고    scopus 로고
    • Toward a Molecular Understanding of Protein Solubility: Increased Negative Surface Charge Correlates with Increased Solubility
    • Kramer, R.M.; Shende, V.R.; Motl, N.; Pace, C.N.; Scholtz, J.M. Toward a Molecular Understanding of Protein Solubility: Increased Negative Surface Charge Correlates with Increased Solubility. Biophys. J. 2014, 102, 1907-1915.
    • (2014) Biophys. J. , vol.102 , pp. 1907-1915
    • Kramer, R.M.1    Shende, V.R.2    Motl, N.3    Pace, C.N.4    Scholtz, J.M.5
  • 59
    • 0041341327 scopus 로고
    • Functional Properties of Succinylated and Acetylated Soy Protein
    • Franzen, K.L.; Kinsella, J.E. Functional Properties of Succinylated and Acetylated Soy Protein. J. Agric. Food Chem. 1976, 24, 788-795.
    • (1976) J. Agric. Food Chem. , vol.24 , pp. 788-795
    • Franzen, K.L.1    Kinsella, J.E.2
  • 60
    • 84864875884 scopus 로고    scopus 로고
    • The eightfold path to non-enzymatic RNA replication
    • Szostak, J. The eightfold path to non-enzymatic RNA replication. J. Syst. Chem. 2012, 3, doi:10.1186/1759-2208-3-2.
    • (2012) J. Syst. Chem. , vol.3
    • Szostak, J.1
  • 61
    • 0042702356 scopus 로고    scopus 로고
    • METAL IONS IN BIOLOGICAL SYSTEMS
    • Glusker, J.P.; Katz, A.K.; Bock, C.W. METAL IONS IN BIOLOGICAL SYSTEMS. Rigaku J. 1999, 16, 8-16.
    • (1999) Rigaku J. , vol.16 , pp. 8-16
    • Glusker, J.P.1    Katz, A.K.2    Bock, C.W.3
  • 63
    • 0033167405 scopus 로고    scopus 로고
    • Non-Enzymatic RNA Hydrolysis Promoted by the Combined Catalytic Activity of Buffers and Magnesium Ions
    • AbouHaidar, M.G.; Ivanovb, I.G. Non-Enzymatic RNA Hydrolysis Promoted by the Combined Catalytic Activity of Buffers and Magnesium Ions. Z. Naturforsch. C 1999, 54, 542-548.
    • (1999) Z. Naturforsch. C , vol.54 , pp. 542-548
    • AbouHaidar, M.G.1    Ivanovb, I.G.2
  • 64
    • 0031007121 scopus 로고    scopus 로고
    • RNA-RNA Interactions Between Oligonucleotide Substrates for Aminoacylation
    • Henderson, B.S.; Schimmel, P. RNA-RNA Interactions Between Oligonucleotide Substrates for Aminoacylation. Bioorg. Med. Chem. 1997, 5, 1071-1079.
    • (1997) Bioorg. Med. Chem. , vol.5 , pp. 1071-1079
    • Henderson, B.S.1    Schimmel, P.2
  • 65
    • 79961119081 scopus 로고    scopus 로고
    • Polyphosphate-an ancient energy source and active metabolic regulator
    • Achbergerová, L.; Nahálka, J. Polyphosphate-an ancient energy source and active metabolic regulator. Microb. Cell Fact. 2011, 10, doi:10.1186/1475-2859-10-6.
    • (2011) Microb. Cell Fact. , vol.10
    • Achbergerová, L.1    Nahálka, J.2
  • 66
    • 0028967488 scopus 로고
    • Inorganic Polyphosphate: Toward Making a Forgotten Polymer Unforgettable
    • Kornberg, A. Inorganic Polyphosphate: Toward Making a Forgotten Polymer Unforgettable. J. Bact. 1995, 177, 491-496.
    • (1995) J. Bact. , vol.177 , pp. 491-496
    • Kornberg, A.1
  • 67
    • 0028943076 scopus 로고
    • Structure, Function and Evolution of Seryl-tRNA Synthetases: Implications for the Evolution of Aminoacyl-tRNA Synthetases and the Genetic Code
    • Härtlein, M.; Cusack, S. Structure, Function and Evolution of Seryl-tRNA Synthetases: Implications for the Evolution of Aminoacyl-tRNA Synthetases and the Genetic Code. J. Mol. Evol. 1995, 40, 519-530.
    • (1995) J. Mol. Evol. , vol.40 , pp. 519-530
    • Härtlein, M.1    Cusack, S.2
  • 68
    • 0028338701 scopus 로고
    • Phylogeny from function: Evidence from the molecular fossil record that tRNA originated in replication, not translation
    • Maizels, N.; Weiner, A.M. Phylogeny from function: Evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc. Natl. Acad. Sci. USA 1994, 91, 6729-6734.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 6729-6734
    • Maizels, N.1    Weiner, A.M.2
  • 69
    • 0023449816 scopus 로고
    • tRNA-like structures tag the 3' ends of genomic RNA molecules for replication: Implications for the origin of protein synthesis
    • Weiner, A.M.; Maizels, N. tRNA-like structures tag the 3' ends of genomic RNA molecules for replication: Implications for the origin of protein synthesis. Proc. Natl. Acad. Sci. USA 1987, 84, 7383-7387.
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 7383-7387
    • Weiner, A.M.1    Maizels, N.2
  • 70
    • 84922070316 scopus 로고    scopus 로고
    • The Place of RNA in the Origin and Early Evolution of the Genetic Machinery
    • Wächtershäuser, G. The Place of RNA in the Origin and Early Evolution of the Genetic Machinery. Life 2014, 4, 1050-1091.
    • (2014) Life , vol.4 , pp. 1050-1091
    • Wächtershäuser, G.1
  • 71
    • 17844405021 scopus 로고    scopus 로고
    • Coevolution theory of the genetic code at age thirty
    • Wong, J.T.-F. Coevolution theory of the genetic code at age thirty. BioEssays 2005, 27, 416-425.
    • (2005) BioEssays , vol.27 , pp. 416-425
    • Wong, J.T.-F.1
  • 72
    • 84887261289 scopus 로고    scopus 로고
    • Vesicle Extrusion Through Polycarbonate Track-etched Membranes using a Hand-held Mini-extruder
    • Zhu, T.F.; Budin, I.; Szostak, J.W. Vesicle Extrusion Through Polycarbonate Track-etched Membranes using a Hand-held Mini-extruder. Meth. Enzymol. 2013, 533, 275-282.
    • (2013) Meth. Enzymol. , vol.533 , pp. 275-282
    • Zhu, T.F.1    Budin, I.2    Szostak, J.W.3
  • 73
    • 84906091500 scopus 로고    scopus 로고
    • Synthetic and Editing Mechanisms of Aminoacyl-tRNA Synthetases
    • Perona, J.J.; Gruic-Sovulj, I. Synthetic and Editing Mechanisms of Aminoacyl-tRNA Synthetases. Top. Curr. Chem. 2013, 344, 1-41.
    • (2013) Top. Curr. Chem. , vol.344 , pp. 1-41
    • Perona, J.J.1    Gruic-Sovulj, I.2
  • 74
    • 84868529168 scopus 로고    scopus 로고
    • Structural Diversity and Protein Engineering of the Aminoacyl-tRNA Synthetases
    • Perona, J.J.; Hadd, A. Structural Diversity and Protein Engineering of the Aminoacyl-tRNA Synthetases. Biochemistry 2013, 51, 8705-8729.
    • (2013) Biochemistry , vol.51 , pp. 8705-8729
    • Perona, J.J.1    Hadd, A.2
  • 75
    • 0037466332 scopus 로고    scopus 로고
    • Amino Acid Discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants
    • Bullock, T.; Uter, N.; Nissan, T.A.; Perona, J.J. Amino Acid Discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants. J. Mol. Biol. 2003, 328, 395-408.
    • (2003) J. Mol. Biol. , vol.328 , pp. 395-408
    • Bullock, T.1    Uter, N.2    Nissan, T.A.3    Perona, J.J.4
  • 76
    • 80054804699 scopus 로고    scopus 로고
    • Allosteric Communication in Cysteinyl tRNA Synthetase A NETWORK OF DIRECT AND INDIRECT READOUT
    • Ghosh, A.; Sakaguchi, R.; Liu, C.; Vishveshwara, S.; Hou, Y.-M. Allosteric Communication in Cysteinyl tRNA Synthetase A NETWORK OF DIRECT AND INDIRECT READOUT. J. Biol. Chem. 2011, 286, 37721-37731.
    • (2011) J. Biol. Chem. , vol.286 , pp. 37721-37731
    • Ghosh, A.1    Sakaguchi, R.2    Liu, C.3    Vishveshwara, S.4    Hou, Y.-M.5
  • 78
    • 0001185873 scopus 로고
    • An Essay towards solving a Problem in the Doctrine of Chance. By the late Rev. Mr. Bayes, F. R. S. communicated by Mr. Price, in a letter to John Canton, A. M. F. R. S
    • Bayes, T.; Price, R. An Essay towards solving a Problem in the Doctrine of Chance. By the late Rev. Mr. Bayes, F. R. S. communicated by Mr. Price, in a letter to John Canton, A. M. F. R. S. Philos. Trans. 1763, 53, 370-418.
    • (1763) Philos. Trans. , vol.53 , pp. 370-418
    • Bayes, T.1    Price, R.2
  • 80
    • 80052938979 scopus 로고    scopus 로고
    • The meaning of a minuscule ribozyme
    • Yarus, M. The meaning of a minuscule ribozyme. Phil. Trans. R. Soc. B 2011, 366, 2902-2909.
    • (2011) Phil. Trans. R. Soc. B , vol.366 , pp. 2902-2909
    • Yarus, M.1
  • 81
    • 79954508195 scopus 로고    scopus 로고
    • Catalyzed and Spontaneous Reactions on Ribozyme Ribose
    • Turk, R.M.; Illangasekare, M.; Yarus, M. Catalyzed and Spontaneous Reactions on Ribozyme Ribose. J. Am. Chem. Soc. 2011, 133, 6044-6050.
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 6044-6050
    • Turk, R.M.1    Illangasekare, M.2    Yarus, M.3
  • 82
    • 77949497062 scopus 로고    scopus 로고
    • Multiple translational products from a five-nucleotide ribozyme
    • Turk, R.M.; Chumachenkob, N.V.; Yarus, M. Multiple translational products from a five-nucleotide ribozyme. Proc. Natl. Acad. Sci. USA 2010, 107, 4585-4589.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 4585-4589
    • Turk, R.M.1    Chumachenkob, N.V.2    Yarus, M.3
  • 84
    • 72449163457 scopus 로고    scopus 로고
    • RNA-amino acid binding: A stereochemical era for the genetic code
    • Yarus, M.; Widmann, J.; Knight, R. RNA-amino acid binding: A stereochemical era for the genetic code. J. Mol. Evol. 2009, 69, 406-429.
    • (2009) J. Mol. Evol. , vol.69 , pp. 406-429
    • Yarus, M.1    Widmann, J.2    Knight, R.3
  • 85
    • 0030970582 scopus 로고    scopus 로고
    • 23S rRNA Similarity from Selection for Peptidyl Transferase Mimicry
    • Welch, M.; Majerfeld, I.; Yarus, M. 23S rRNA Similarity from Selection for Peptidyl Transferase Mimicry. Biochemistry 1997, 36, 6614-6623.
    • (1997) Biochemistry , vol.36 , pp. 6614-6623
    • Welch, M.1    Majerfeld, I.2    Yarus, M.3
  • 86
    • 0028957112 scopus 로고
    • An Inhibitor of Ribosomal Peptidyl Transferase Using Transition-State Analogy
    • Welch, M.; Chastang, J.; Yarus, M. An Inhibitor of Ribosomal Peptidyl Transferase Using Transition-State Analogy. Biochemtry 1995, 34, 385-390.
    • (1995) Biochemtry , vol.34 , pp. 385-390
    • Welch, M.1    Chastang, J.2    Yarus, M.3
  • 87
    • 67649662135 scopus 로고    scopus 로고
    • A flexizyme that selectively charges amino acids activated by a water-friendly leaving group
    • Niwa, N.; Yamagishi, Y.; Murakami, H.; Suga, H. A flexizyme that selectively charges amino acids activated by a water-friendly leaving group. Bioorg. Med. Chem. Lett. 2009, 19, 3892-3894.
    • (2009) Bioorg. Med. Chem. Lett. , vol.19 , pp. 3892-3894
    • Niwa, N.1    Yamagishi, Y.2    Murakami, H.3    Suga, H.4
  • 88
    • 84911474212 scopus 로고    scopus 로고
    • A cross-chiral RNA polymerase ribozyme
    • Sczepanski, J.T.; Joyce, G.F. A cross-chiral RNA polymerase ribozyme. Nature 2014, 515, 440-442.
    • (2014) Nature , vol.515 , pp. 440-442
    • Sczepanski, J.T.1    Joyce, G.F.2
  • 89
    • 61349193830 scopus 로고    scopus 로고
    • Self-Sustained Replication of an RNA Enzyme
    • Lincoln, T.A.; Joyce, G.F. Self-Sustained Replication of an RNA Enzyme. Science 2009, 323, 1229-1232.
    • (2009) Science , vol.323 , pp. 1229-1232
    • Lincoln, T.A.1    Joyce, G.F.2
  • 90
    • 80052475860 scopus 로고    scopus 로고
    • The structural basis of RNA-catalyzed RNA polymerization
    • Shechner, D.M.; Bartel, D.P. The structural basis of RNA-catalyzed RNA polymerization. Nat. Struct. Mol. Biol. 2011, 18, 1036-1042.
    • (2011) Nat. Struct. Mol. Biol. , vol.18 , pp. 1036-1042
    • Shechner, D.M.1    Bartel, D.P.2
  • 91
    • 0035906978 scopus 로고    scopus 로고
    • RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension
    • Johnston, W.K.; Unrau, P.J.; Lawrence, M.S.; Glasner, M.E.; Bartel, D.P. RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension. Science 2001, 292, 1319-1325.
    • (2001) Science , vol.292 , pp. 1319-1325
    • Johnston, W.K.1    Unrau, P.J.2    Lawrence, M.S.3    Glasner, M.E.4    Bartel, D.P.5
  • 93
    • 79953809654 scopus 로고    scopus 로고
    • Ribozyme-Catalyzed Transcription of an Active Ribozyme
    • Wochner, A.; Attwater, J.; Coulson, A.; Holliger, P. Ribozyme-Catalyzed Transcription of an Active Ribozyme. Science 2011, 332, 209-212.
    • (2011) Science , vol.332 , pp. 209-212
    • Wochner, A.1    Attwater, J.2    Coulson, A.3    Holliger, P.4
  • 94
    • 9344271130 scopus 로고    scopus 로고
    • The driving force for molecular evolution of translation
    • Noller, H. The driving force for molecular evolution of translation. RNA 2004, 10, 1833-1837.
    • (2004) RNA , vol.10 , pp. 1833-1837
    • Noller, H.1
  • 95
    • 0034637111 scopus 로고    scopus 로고
    • The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution
    • Ban, N.; Nissen, P.; Hansen, J.; Moore, P.; Steitz, T.A. The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution. Science 2000, 289, 905-919.
    • (2000) Science , vol.289 , pp. 905-919
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.4    Steitz, T.A.5
  • 96
    • 65649084094 scopus 로고    scopus 로고
    • RNA-dependent RNA switches in bacteria
    • Henkin, T.M. RNA-dependent RNA switches in bacteria. Meth. Mol. Biol. 2009, 540, 207-214.
    • (2009) Meth. Mol. Biol. , vol.540 , pp. 207-214
    • Henkin, T.M.1
  • 97
    • 0037143628 scopus 로고    scopus 로고
    • tRNA-mediated transcription antitermination in vitro: Codon-anticodon pairing independent of the ribosome
    • Grundy, F.J.; Winkler, W.C.; Henkin, T.M. tRNA-mediated transcription antitermination in vitro: Codon-anticodon pairing independent of the ribosome. Proc. Natl. Acad. Sci. USA 2002, 99, 11121-11126.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 11121-11126
    • Grundy, F.J.1    Winkler, W.C.2    Henkin, T.M.3
  • 98
    • 84860788078 scopus 로고    scopus 로고
    • Gas-liquid transfer data used to analyze hydrophobic hydration and find the nature of the Kauzmann-Tanford hydrophobic factor
    • Baldwin, R.L. Gas-liquid transfer data used to analyze hydrophobic hydration and find the nature of the Kauzmann-Tanford hydrophobic factor. Proc. Natl. Acad. Sci. USA 2012, 109, 7310-7313.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 7310-7313
    • Baldwin, R.L.1
  • 99
    • 0008863560 scopus 로고
    • Some Factors in the Interpretation of Protein Denaturation
    • Kauzmann, W. Some Factors in the Interpretation of Protein Denaturation. Adv. Protein Chem. 1959, 14, 1-63.
    • (1959) Adv. Protein Chem. , vol.14 , pp. 1-63
    • Kauzmann, W.1


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