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Volumn 366, Issue 2, 2007, Pages 650-665

A Comparison of the Folding of Two Knotted Proteins: YbeA and YibK

Author keywords

chevron plot; dimer kinetics; global analysis; protein folding; topological knot

Indexed keywords

BACTERIAL PROTEIN; ESCHERICHIA COLI PROTEIN; MONOMER; PROTEIN YBEA; PROTEIN YIBK; UNCLASSIFIED DRUG; UREA;

EID: 33846362515     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.11.014     Document Type: Article
Times cited : (91)

References (48)
  • 1
    • 0037686252 scopus 로고    scopus 로고
    • The present view of the mechanism of protein folding
    • Daggett V., and Fersht A. 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.2
  • 2
    • 0036105533 scopus 로고    scopus 로고
    • The structure of the transition state for folding of domain-swapped dimeric p13suc1
    • Rousseau F., Schymkowitz J.W., Wilkinson H.R., and Itzhaki L.S. The structure of the transition state for folding of domain-swapped dimeric p13suc1. Structure 10 (2002) 649-657
    • (2002) Structure , vol.10 , pp. 649-657
    • Rousseau, F.1    Schymkowitz, J.W.2    Wilkinson, H.R.3    Itzhaki, L.S.4
  • 3
    • 33745126550 scopus 로고    scopus 로고
    • Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus
    • Pleshe E., Truesdell J., and Batey R.T. Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus. Acta Crystallog. sect. F 61 (2005) 722-728
    • (2005) Acta Crystallog. sect. F , vol.61 , pp. 722-728
    • Pleshe, E.1    Truesdell, J.2    Batey, R.T.3
  • 4
    • 0034710671 scopus 로고    scopus 로고
    • A deeply knotted protein structure and how it might fold
    • Taylor W.R. 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
  • 5
    • 0037413604 scopus 로고    scopus 로고
    • Protein knots: a tangled problem
    • Taylor W.R., and Lin K. Protein knots: a tangled problem. Nature 421 (2003) 25
    • (2003) Nature , vol.421 , pp. 25
    • Taylor, W.R.1    Lin, K.2
  • 6
    • 27844461604 scopus 로고    scopus 로고
    • A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome
    • Wagner J.R., Brunzelle J.S., Forest K.T., and Vierstra R.D. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 438 (2005) 325-331
    • (2005) Nature , vol.438 , pp. 325-331
    • Wagner, J.R.1    Brunzelle, J.S.2    Forest, K.T.3    Vierstra, R.D.4
  • 7
    • 0037526102 scopus 로고    scopus 로고
    • Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition
    • Ahn H.J., Kim H.W., Yoon H.J., Lee B.I., Suh S.W., and Yang J.K. 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
  • 9
    • 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
    • Forouhar F., Shen J., Xiao R., Acton T.B., Montelione G.T., and Tong L. 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
  • 10
    • 0037375572 scopus 로고    scopus 로고
    • Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot
    • Lim K., Zhang H., Tempczyk A., Krajewski W., Bonander N., Toedt J., et al. 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
  • 11
    • 0036774065 scopus 로고    scopus 로고
    • The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot
    • Michel G., Sauve V., Larocque R., Li Y., Matte A., and Cygler M. 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
  • 13
    • 1842607227 scopus 로고    scopus 로고
    • Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme
    • Nureki O., Watanabe K., Fukai S., Ishii R., Endo Y., Hori H., and Yokoyama S. 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
  • 15
    • 9644281537 scopus 로고    scopus 로고
    • Structure and function of the antibiotic resistance-mediating methyltransferase AviRb from Streptomyces viridochromogenes
    • Mosbacher T.G., Bechthold A., and Schulz G.E. Structure and function of the antibiotic resistance-mediating methyltransferase AviRb from Streptomyces viridochromogenes. J. Mol. Biol. 345 (2005) 535-545
    • (2005) J. Mol. Biol. , vol.345 , pp. 535-545
    • Mosbacher, T.G.1    Bechthold, A.2    Schulz, G.E.3
  • 18
    • 33749347406 scopus 로고    scopus 로고
    • Intricate knots in proteins: function and evolution
    • Virnau P., A.M. L., and Kardar M. Intricate knots in proteins: function and evolution. PLoS Comput. Biol. 2 (2006) 1074-1079
    • (2006) PLoS Comput. Biol. , vol.2 , pp. 1074-1079
    • Virnau, P.1    A.M., L.2    Kardar, M.3
  • 19
    • 13844255609 scopus 로고    scopus 로고
    • Folding studies on a knotted protein
    • Mallam A.L., and Jackson S.E. Folding studies on a knotted protein. J. Mol. Biol. 346 (2005) 1409-1421
    • (2005) J. Mol. Biol. , vol.346 , pp. 1409-1421
    • Mallam, A.L.1    Jackson, S.E.2
  • 20
    • 33745163582 scopus 로고    scopus 로고
    • Probing nature's knots: the folding pathway of a knotted homodimeric protein
    • Mallam A.L., and Jackson S.E. Probing nature's knots: the folding pathway of a knotted homodimeric protein. J. Mol. Biol. 359 (2006) 1420-1436
    • (2006) J. Mol. Biol. , vol.359 , pp. 1420-1436
    • Mallam, A.L.1    Jackson, S.E.2
  • 22
    • 13844299144 scopus 로고    scopus 로고
    • The family feud: do proteins with similar structures fold via the same pathway?
    • Zarrine-Afsar A., Larson S.M., and Davidson A.R. The family feud: do proteins with similar structures fold via the same pathway?. Curr. Opin. Struct. Biol. 15 (2005) 42-49
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 42-49
    • Zarrine-Afsar, A.1    Larson, S.M.2    Davidson, A.R.3
  • 23
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco K.W., Simons K.T., and Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277 (1998) 985-994
    • (1998) J. Mol. Biol. , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 24
    • 0034687123 scopus 로고    scopus 로고
    • Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics
    • Plaxco K.W., Simons K.T., Ruczinski I., and Baker D. Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry 39 (2000) 11177-11183
    • (2000) Biochemistry , vol.39 , pp. 11177-11183
    • Plaxco, K.W.1    Simons, K.T.2    Ruczinski, I.3    Baker, D.4
  • 25
    • 0034604105 scopus 로고    scopus 로고
    • A surprising simplicity to protein folding
    • Baker D. A surprising simplicity to protein folding. Nature 405 (2000) 39-42
    • (2000) Nature , vol.405 , pp. 39-42
    • Baker, D.1
  • 26
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • Jackson S.E. 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
  • 27
    • 0034308172 scopus 로고    scopus 로고
    • Discriminating between homodimeric and monomeric proteins in the crystalline state
    • Ponstingl H., Henrick K., and Thornton J.M. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins: Struct. Funct. Genet. 41 (2000) 47-57
    • (2000) Proteins: Struct. Funct. Genet. , vol.41 , pp. 47-57
    • Ponstingl, H.1    Henrick, K.2    Thornton, J.M.3
  • 28
    • 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
    • Hobart S.A., Meinhold D.W., Osuna R., and Colon W. 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
  • 29
    • 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
    • Soulages J.L. 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
  • 30
    • 0028820703 scopus 로고
    • Denaturant m-values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding
    • Myers J.K., Pace C.N., and Scholtz J.M. 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
  • 31
    • 0021113912 scopus 로고
    • Mechanism of folding of ribonuclease A. Slow refolding is a sequential reaction via structural intermediates
    • Schmid F.X. Mechanism of folding of ribonuclease A. Slow refolding is a sequential reaction via structural intermediates. Biochemistry 22 (1983) 4690-4696
    • (1983) Biochemistry , vol.22 , pp. 4690-4696
    • Schmid, F.X.1
  • 33
    • 0037058950 scopus 로고    scopus 로고
    • Sequential vs. parallel protein-folding mechanisms: experimental tests for complex folding reactions
    • Wallace L.A., and Matthews C.R. Sequential vs. parallel protein-folding mechanisms: experimental tests for complex folding reactions. Biophys. Chem. 101-102 (2002) 113-131
    • (2002) Biophys. Chem. , vol.101-102 , pp. 113-131
    • Wallace, L.A.1    Matthews, C.R.2
  • 34
    • 0030792287 scopus 로고    scopus 로고
    • New PC versions of the kinetic-simulation and fitting programs, KINSIM and FITSIM
    • Dang Q., and Frieden C. New PC versions of the kinetic-simulation and fitting programs, KINSIM and FITSIM. Trends Biochem. Sci. 22 (1997) 317
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 317
    • Dang, Q.1    Frieden, C.2
  • 35
    • 0029964867 scopus 로고    scopus 로고
    • Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding
    • Hagen S.J., Hofrichter J., Szabo A., and Eaton W.A. Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding. Proc. Natl Acad. Sci. USA 93 (1996) 11615-11617
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 11615-11617
    • Hagen, S.J.1    Hofrichter, J.2    Szabo, A.3    Eaton, W.A.4
  • 36
    • 0028325298 scopus 로고
    • P22 Arc repressor: folding kinetics of a single-domain, dimeric protein
    • Milla M.E., and Sauer R.T. P22 Arc repressor: folding kinetics of a single-domain, dimeric protein. Biochemistry 33 (1994) 1125-1133
    • (1994) Biochemistry , vol.33 , pp. 1125-1133
    • Milla, M.E.1    Sauer, R.T.2
  • 37
    • 0346500473 scopus 로고    scopus 로고
    • Folding and association of an extremely stable dimeric protein from Sulfolobus islandicus
    • Zeeb M., Lipps G., Lilie H., and Balbach J. Folding and association of an extremely stable dimeric protein from Sulfolobus islandicus. J. Mol. Biol. 336 (2004) 227-240
    • (2004) J. Mol. Biol. , vol.336 , pp. 227-240
    • Zeeb, M.1    Lipps, G.2    Lilie, H.3    Balbach, J.4
  • 38
    • 0032506048 scopus 로고    scopus 로고
    • Mechanism of folding of the dimeric core domain of Escherichia coli trp repressor: a nearly diffusion-limited reaction leads to the formation of an on-pathway dimeric intermediate
    • Gloss L.M., and Matthews C.R. Mechanism of folding of the dimeric core domain of Escherichia coli trp repressor: a nearly diffusion-limited reaction leads to the formation of an on-pathway dimeric intermediate. Biochemistry 37 (1998) 15990-15999
    • (1998) Biochemistry , vol.37 , pp. 15990-15999
    • Gloss, L.M.1    Matthews, C.R.2
  • 39
    • 4143073668 scopus 로고    scopus 로고
    • SecA folding kinetics: a large dimeric protein rapidly forms multiple native states
    • Doyle S.M., Bilsel O., and Teschke C.M. SecA folding kinetics: a large dimeric protein rapidly forms multiple native states. J. Mol. Biol. 341 (2004) 199-214
    • (2004) J. Mol. Biol. , vol.341 , pp. 199-214
    • Doyle, S.M.1    Bilsel, O.2    Teschke, C.M.3
  • 41
    • 0037447846 scopus 로고    scopus 로고
    • Detection and prevention of protein aggregation before, during, and after purification
    • Bondos S.E., and Bicknell A. Detection and prevention of protein aggregation before, during, and after purification. Anal. Biochem. 316 (2002) 223-231
    • (2002) Anal. Biochem. , vol.316 , pp. 223-231
    • Bondos, S.E.1    Bicknell, A.2
  • 42
    • 0032506169 scopus 로고    scopus 로고
    • The barriers in the bimolecular and unimolecular folding reactions of the dimeric core domain of Escherichia coli trp repressor are dominated by enthalpic contributions
    • Gloss L.M., and Matthews C.R. The barriers in the bimolecular and unimolecular folding reactions of the dimeric core domain of Escherichia coli trp repressor are dominated by enthalpic contributions. Biochemistry 37 (1998) 16000-16010
    • (1998) Biochemistry , vol.37 , pp. 16000-16010
    • Gloss, L.M.1    Matthews, C.R.2
  • 43
    • 10044293974 scopus 로고    scopus 로고
    • Three-state kinetic folding mechanism of the H2A/H2B histone heterodimer: the N-terminal tails affect the transition state between a dimeric intermediate and the native dimer
    • Placek B.J., and Gloss L.M. Three-state kinetic folding mechanism of the H2A/H2B histone heterodimer: the N-terminal tails affect the transition state between a dimeric intermediate and the native dimer. J. Mol. Biol. 345 (2005) 827-836
    • (2005) J. Mol. Biol. , vol.345 , pp. 827-836
    • Placek, B.J.1    Gloss, L.M.2
  • 44
    • 0001528720 scopus 로고    scopus 로고
    • Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules
    • Fraczkiewicz R., and Braun W. 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
  • 45
  • 46
    • 0029620316 scopus 로고
    • Modeling unfolded states of peptides and proteins
    • Creamer T.P., Srinivasan R., and Rose G.D. 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
  • 47
    • 0030933329 scopus 로고    scopus 로고
    • Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility
    • Creamer T.P., Srinivasan R., and Rose G.D. 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


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