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Volumn 346, Issue 5, 2005, Pages 1409-1421

Folding studies on a knotted protein

Author keywords

Circular dichroism; Dimer thermodynamics; Fluorescence; Protein folding; Topological knot

Indexed keywords

CHAPERONE; KNOTTED PROTEIN; MONOMER; PROTEIN; UNCLASSIFIED DRUG; UREA; YIBK PROTEIN;

EID: 13844255609     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.12.055     Document Type: Article
Times cited : (117)

References (47)
  • 1
    • 0037686252 scopus 로고    scopus 로고
    • The present view of the mechanism of protein folding
    • V. Daggett, and A.R. Fersht The present view of the mechanism of protein folding Nature Rev. Mol. Cell. Biol. 4 2003 497 502
    • (2003) Nature Rev. Mol. Cell. Biol. , vol.4 , pp. 497-502
    • Daggett, V.1    Fersht, A.R.2
  • 2
    • 0037221599 scopus 로고    scopus 로고
    • Is there a unifying mechanism for protein folding?
    • V. Daggett, and A.R. Fersht Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28 2003 18 25
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 18-25
    • Daggett, V.1    Fersht, A.R.2
  • 3
    • 0037526102 scopus 로고    scopus 로고
    • Crystal structure of tRNA(m1G37)methyltransferase: Insights into tRNA recognition
    • H.J. Ahn, H.W. Kim, H.J. Yoon, B.I. Lee, S.W. Suh, and J.K. Yang Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition EMBO J. 22 2003 2593 2603
    • (2003) EMBO J. , vol.22 , pp. 2593-2603
    • Ahn, H.J.1    Kim, H.W.2    Yoon, H.J.3    Lee, B.I.4    Suh, S.W.5    Yang, J.K.6
  • 5
    • 0141704142 scopus 로고    scopus 로고
    • Functional assignment based on structural analysis: Crystal structure of the yggJ protein (HI0303) of Haemophilus influenzae reveals an RNA methyltransferase with a deep trefoil knot
    • F. Forouhar, J. Shen, R. Xiao, T.B. Acton, G.T. Montelione, and L. Tong Functional assignment based on structural analysis: crystal structure of the yggJ protein (HI0303) of Haemophilus influenzae reveals an RNA methyltransferase with a deep trefoil knot Proteins: Struct. Funct. Genet. 53 2003 329 332
    • (2003) Proteins: Struct. Funct. Genet. , vol.53 , pp. 329-332
    • Forouhar, F.1    Shen, J.2    Xiao, R.3    Acton, T.B.4    Montelione, G.T.5    Tong, L.6
  • 6
    • 0037375572 scopus 로고    scopus 로고
    • Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): A cofactor bound at a site formed by a knot
    • K. Lim, H. Zhang, A. Tempczyk, W. Krajewski, N. Bonander, and J. Toedt Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot Proteins: Struct. Funct. Genet. 51 2003 56 67
    • (2003) Proteins: Struct. Funct. Genet. , vol.51 , pp. 56-67
    • Lim, K.1    Zhang, H.2    Tempczyk, A.3    Krajewski, W.4    Bonander, N.5    Toedt, J.6
  • 7
    • 0036774065 scopus 로고    scopus 로고
    • The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot
    • G. Michel, V. Sauve, R. Larocque, Y. Li, A. Matte, and M. Cygler The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot Structure 10 2002 1303 1315
    • (2002) Structure , vol.10 , pp. 1303-1315
    • Michel, G.1    Sauve, V.2    Larocque, R.3    Li, Y.4    Matte, A.5    Cygler, M.6
  • 9
    • 1842607227 scopus 로고    scopus 로고
    • Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme
    • O. Nureki, K. Watanabe, S. Fukai, R. Ishii, Y. Endo, H. Hori, and S. Yokoyama Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme Structure 12 2004 593 602
    • (2004) Structure , vol.12 , pp. 593-602
    • Nureki, O.1    Watanabe, K.2    Fukai, S.3    Ishii, R.4    Endo, Y.5    Hori, H.6    Yokoyama, S.7
  • 11
    • 0029105847 scopus 로고
    • Topological features of protein structures - Knots and links
    • C.Z. Liang, and K. Mislow Topological features of protein structures - knots and links J. Am. Chem. Soc. 117 1995 4201 4213
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 4201-4213
    • Liang, C.Z.1    Mislow, K.2
  • 13
    • 0028421135 scopus 로고
    • Are there knots in proteins?
    • M.L. Mansfield Are there knots in proteins? Nature Struct. Biol. 1 1994 213 214
    • (1994) Nature Struct. Biol. , vol.1 , pp. 213-214
    • Mansfield, M.L.1
  • 16
    • 0034710671 scopus 로고    scopus 로고
    • A deeply knotted protein structure and how it might fold
    • W.R. Taylor A deeply knotted protein structure and how it might fold Nature 406 2000 916 919
    • (2000) Nature , vol.406 , pp. 916-919
    • Taylor, W.R.1
  • 17
    • 0037413604 scopus 로고    scopus 로고
    • Protein knots: A tangled problem
    • W.R. Taylor, and K. Lin Protein knots: a tangled problem Nature 421 2003 25
    • (2003) Nature , vol.421 , pp. 25
    • Taylor, W.R.1    Lin, K.2
  • 19
    • 0036132209 scopus 로고    scopus 로고
    • SPOUT: A class of methyltransferases that includes SpoU and TrmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases
    • V. Anantharaman, E.V. Koonin, and L. Aravind SPOUT: a class of methyltransferases that includes SpoU and TrmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases J. Mol. Microbiol. Biotechnol. 4 2002 71 75
    • (2002) J. Mol. Microbiol. Biotechnol. , vol.4 , pp. 71-75
    • Anantharaman, V.1    Koonin, E.V.2    Aravind, L.3
  • 20
    • 0002394256 scopus 로고    scopus 로고
    • Influence of chain knotting on the rate of folding
    • A.V. Finkelstein, and A. Badretdinov Influence of chain knotting on the rate of folding Fold. Des. 3 1997 67 68
    • (1997) Fold. Des. , vol.3 , pp. 67-68
    • Finkelstein, A.V.1    Badretdinov, A.2
  • 21
    • 0028606077 scopus 로고
    • Conformational stability of dimeric proteins: Quantitative studies by equilibrium denaturation
    • K.E. Neet, and D.E. Timm Conformational stability of dimeric proteins: quantitative studies by equilibrium denaturation Protein Sci. 3 1994 2167 2174
    • (1994) Protein Sci. , vol.3 , pp. 2167-2174
    • Neet, K.E.1    Timm, D.E.2
  • 22
    • 0030925611 scopus 로고    scopus 로고
    • Urea and thermal equilibrium denaturation studies on the dimerization domain of Escherichia coli Trp repressor
    • L.M. Gloss, and C.R. Matthews Urea and thermal equilibrium denaturation studies on the dimerization domain of Escherichia coli Trp repressor Biochemistry 36 1997 5612 5623
    • (1997) Biochemistry , vol.36 , pp. 5612-5623
    • Gloss, L.M.1    Matthews, C.R.2
  • 23
    • 0036084703 scopus 로고    scopus 로고
    • Equilibrium denaturation studies of the Escherichia coli factor for inversion stimulation: Implications for in vivo function
    • S.A. Hobart, S. Ilin, D.F. Moriarty, R. Osuna, and W. Colon Equilibrium denaturation studies of the Escherichia coli factor for inversion stimulation: implications for in vivo function Protein Sci. 11 2002 1671 1680
    • (2002) Protein Sci. , vol.11 , pp. 1671-1680
    • Hobart, S.A.1    Ilin, S.2    Moriarty, D.F.3    Osuna, R.4    Colon, W.5
  • 24
    • 0037137182 scopus 로고    scopus 로고
    • From two-state to three-state: The effect of the P61A mutation on the dynamics and stability of the factor for inversion stimulation results in an altered equilibrium denaturation mechanism
    • S.A. Hobart, D.W. Meinhold, R. Osuna, and W. Colon From two-state to three-state: the effect of the P61A mutation on the dynamics and stability of the factor for inversion stimulation results in an altered equilibrium denaturation mechanism Biochemistry 41 2002 13744 13754
    • (2002) Biochemistry , vol.41 , pp. 13744-13754
    • Hobart, S.A.1    Meinhold, D.W.2    Osuna, R.3    Colon, W.4
  • 25
    • 0000022693 scopus 로고    scopus 로고
    • Dimeric tyrosyl-tRNA synthetase from Bacillus stearothermophilus unfolds through a monomeric intermediate. A quantitative analysis under equilibrium conditions
    • Y.C. Park, and H. Bedouelle Dimeric tyrosyl-tRNA synthetase from Bacillus stearothermophilus unfolds through a monomeric intermediate. A quantitative analysis under equilibrium conditions J. Biol. Chem. 273 1998 18052 18059
    • (1998) J. Biol. Chem. , vol.273 , pp. 18052-18059
    • Park, Y.C.1    Bedouelle, H.2
  • 26
    • 0022555885 scopus 로고
    • Determination and analysis of urea and guanidine hydrochloride denaturation curves
    • C.N. Pace Determination and analysis of urea and guanidine hydrochloride denaturation curves Methods Enzymol. 131 1986 266 280
    • (1986) Methods Enzymol. , vol.131 , pp. 266-280
    • Pace, C.N.1
  • 27
    • 0031808804 scopus 로고    scopus 로고
    • Chemical denaturation: Potential impact of undetected intermediates in the free energy of unfolding and m-values obtained from a two-state assumption
    • J.L. Soulages Chemical denaturation: potential impact of undetected intermediates in the free energy of unfolding and m-values obtained from a two-state assumption Biophys. J. 75 1998 484 492
    • (1998) Biophys. J. , vol.75 , pp. 484-492
    • Soulages, J.L.1
  • 28
    • 0028820703 scopus 로고
    • Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding
    • J.K. Myers, C.N. Pace, and J.M. Scholtz Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding Protein Sci. 4 1995 2138 2148
    • (1995) Protein Sci. , vol.4 , pp. 2138-2148
    • Myers, J.K.1    Pace, C.N.2    Scholtz, J.M.3
  • 30
    • 0029620316 scopus 로고
    • Modeling unfolded states of peptides and proteins
    • T.P. Creamer, R. Srinivasan, and G.D. Rose Modeling unfolded states of peptides and proteins Biochemistry 34 1995 16245 16250
    • (1995) Biochemistry , vol.34 , pp. 16245-16250
    • Creamer, T.P.1    Srinivasan, R.2    Rose, G.D.3
  • 31
    • 0030933329 scopus 로고    scopus 로고
    • Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility
    • T.P. Creamer, R. Srinivasan, and G.D. Rose Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility Biochemistry 36 1997 2832 2835
    • (1997) Biochemistry , vol.36 , pp. 2832-2835
    • Creamer, T.P.1    Srinivasan, R.2    Rose, G.D.3
  • 32
    • 0014718113 scopus 로고
    • Protein denaturation. Part C. Theoretical models for the mechanism of denaturation
    • C. Tanford Protein denaturation. Part C. Theoretical models for the mechanism of denaturation Advan. Protein Chem. 24 1970 1 95
    • (1970) Advan. Protein Chem. , vol.24 , pp. 1-95
    • Tanford, C.1
  • 33
    • 0027162959 scopus 로고
    • Folding of bacterial luciferase involves a non-native heterodimeric intermediate in equilibrium with the native enzyme and the unfolded subunits
    • A.C. Clark, J.F. Sinclair, and T.O. Baldwin Folding of bacterial luciferase involves a non-native heterodimeric intermediate in equilibrium with the native enzyme and the unfolded subunits J. Biol. Chem. 268 1993 10773 10779
    • (1993) J. Biol. Chem. , vol.268 , pp. 10773-10779
    • Clark, A.C.1    Sinclair, J.F.2    Baldwin, T.O.3
  • 34
  • 35
    • 0030711517 scopus 로고    scopus 로고
    • Organophosphorus hydrolase is a remarkably stable enzyme that unfolds through a homodimeric intermediate
    • J.K. Grimsley, J.M. Scholtz, C.N. Pace, and J.R. Wild Organophosphorus hydrolase is a remarkably stable enzyme that unfolds through a homodimeric intermediate Biochemistry 36 1997 14366 14374
    • (1997) Biochemistry , vol.36 , pp. 14366-14374
    • Grimsley, J.K.1    Scholtz, J.M.2    Pace, C.N.3    Wild, J.R.4
  • 36
    • 0034633885 scopus 로고    scopus 로고
    • Equilibrium folding of dimeric class mu glutathione transferases involves a stable monomeric intermediate
    • J.A. Hornby, J.K. Luo, J.M. Stevens, L.A. Wallace, W. Kaplan, R.N. Armstrong, and H.W. Dirr Equilibrium folding of dimeric class mu glutathione transferases involves a stable monomeric intermediate Biochemistry 39 2000 12336 12344
    • (2000) Biochemistry , vol.39 , pp. 12336-12344
    • Hornby, J.A.1    Luo, J.K.2    Stevens, J.M.3    Wallace, L.A.4    Kaplan, W.5    Armstrong, R.N.6    Dirr, H.W.7
  • 37
    • 0036076144 scopus 로고    scopus 로고
    • Folding and stability of the ligand-binding domain of the glucocorticoid receptor
    • S.H. McLaughlin, and S.E. Jackson Folding and stability of the ligand-binding domain of the glucocorticoid receptor Protein Sci. 11 2002 1926 1936
    • (2002) Protein Sci. , vol.11 , pp. 1926-1936
    • McLaughlin, S.H.1    Jackson, S.E.2
  • 38
    • 0034718450 scopus 로고    scopus 로고
    • A change in the apparent m value reveals a populated intermediate under equilibrium conditions in Escherichia coli ribonuclease HI
    • G. Spudich, and S. Marqusee A change in the apparent m value reveals a populated intermediate under equilibrium conditions in Escherichia coli ribonuclease HI Biochemistry 39 2000 11677 11683
    • (2000) Biochemistry , vol.39 , pp. 11677-11683
    • Spudich, G.1    Marqusee, S.2
  • 39
    • 4143107222 scopus 로고    scopus 로고
    • Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers
    • K. Gunasekaran, C.J. Tsai, and R. Nussinov Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers J. Mol. Biol. 341 2004 1327 1341
    • (2004) J. Mol. Biol. , vol.341 , pp. 1327-1341
    • Gunasekaran, K.1    Tsai, C.J.2    Nussinov, R.3
  • 40
    • 0019872622 scopus 로고
    • Mechanism of protein stabilization by glycerol: Preferential hydration in glycerol-water mixtures
    • K. Gekko, and S.N. Timasheff Mechanism of protein stabilization by glycerol: preferential hydration in glycerol-water mixtures Biochemistry 20 1981 4667 4676
    • (1981) Biochemistry , vol.20 , pp. 4667-4676
    • Gekko, K.1    Timasheff, S.N.2
  • 41
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • S.E. Jackson How do small single-domain proteins fold? Fold. Des. 3 1998 81 91
    • (1998) Fold. Des. , vol.3 , pp. 81-91
    • Jackson, S.E.1
  • 42
    • 0024448151 scopus 로고
    • Calculation of protein extinction coefficients from amino acid sequence data
    • S.C. Gill, and P.H. von Hippel Calculation of protein extinction coefficients from amino acid sequence data Anal. Biochem. 182 1989 319 326
    • (1989) Anal. Biochem. , vol.182 , pp. 319-326
    • Gill, S.C.1    Von Hippel, P.H.2
  • 43
    • 33947482089 scopus 로고
    • Dithiothreitol, a new protective reagent for SH groups
    • W.W. Cleland Dithiothreitol, a new protective reagent for SH groups Biochemistry 35 1964 480 482
    • (1964) Biochemistry , vol.35 , pp. 480-482
    • Cleland, W.W.1
  • 44
    • 0002343673 scopus 로고
    • Measuring the conformational stability of a protein
    • T.E. Creighton Oxford University Press Oxford
    • C.N. Pace, B.A. Shirley, and J.A. Thomson Measuring the conformational stability of a protein T.E. Creighton Protein Structure. A Practical Approach 1990 Oxford University Press Oxford 311 330
    • (1990) Protein Structure. a Practical Approach , pp. 311-330
    • Pace, C.N.1    Shirley, B.A.2    Thomson, J.A.3
  • 45
    • 0000722070 scopus 로고
    • Spectral methods of characterizing protein conformation and conformational changes
    • T.E. Creighton Oxford University Press Oxford
    • F.X. Schmid Spectral methods of characterizing protein conformation and conformational changes T.E. Creighton Protein Structure. A Practical Approach 1990 Oxford University Press Oxford 251 285
    • (1990) Protein Structure. a Practical Approach , pp. 251-285
    • Schmid, F.X.1
  • 46
    • 0001528720 scopus 로고    scopus 로고
    • Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules
    • R. Fraczkiewicz, and W. Braun Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules J. Comput. Chem. 19 1998 319 333
    • (1998) J. Comput. Chem. , vol.19 , pp. 319-333
    • Fraczkiewicz, R.1    Braun, W.2


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