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Volumn 45, Issue 22, 2006, Pages 6940-6946

NMR characterization of a peptide model provides evidence for significant structure in the unfolded state of the villin headpiece helical subdomain

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; HYDROGEN BONDS; HYDROPHOBICITY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEINS; PROTONS;

EID: 33744960040     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi052484n     Document Type: Article
Times cited : (41)

References (48)
  • 1
    • 0030623698 scopus 로고    scopus 로고
    • Favourable native-like helical local interactions can accelerate protein folding
    • Viguera, A. R., Villegas, V., Aviles, F. X., and Serrano, L. (1997) Favourable native-like helical local interactions can accelerate protein folding, Folding Des. 2, 23-33.
    • (1997) Folding Des. , vol.2 , pp. 23-33
    • Viguera, A.R.1    Villegas, V.2    Aviles, F.X.3    Serrano, L.4
  • 2
    • 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. (1998) Contact order, transition state placement and the refolding rates of single domain proteins, J. Mol. Biol. 277, 985-94.
    • (1998) J. Mol. Biol. , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 3
    • 0002682169 scopus 로고    scopus 로고
    • Local versus nonlocal interactions in protein folding and stability: An experimentalists's point of view
    • Munoz, V., and Serrano, L. (1996) Local versus nonlocal interactions in protein folding and stability: An experimentalists's point of view, Folding Des. 1, R71-8.
    • (1996) Folding Des. , vol.1
    • Munoz, V.1    Serrano, L.2
  • 5
    • 0024293204 scopus 로고
    • Conformation of peptide fragments of proteins in aqueous solution: Implications for initiation of protein folding
    • Wright, P. E., Dyson, H. J., and Lerner, R. A. (1988) Conformation of peptide fragments of proteins in aqueous solution: Implications for initiation of protein folding, Biochemistry 27, 7167-75.
    • (1988) Biochemistry , vol.27 , pp. 7167-7175
    • Wright, P.E.1    Dyson, H.J.2    Lerner, R.A.3
  • 6
    • 0026768829 scopus 로고
    • Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. I. Myohemerythrin
    • Dyson, H. J., Merutka, G., Waltho, J. P., Lerner, R. A., and Wright, P. E. (1992) Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. I. Myohemerythrin, J. Mol. Biol. 226, 795-817.
    • (1992) J. Mol. Biol. , vol.226 , pp. 795-817
    • Dyson, H.J.1    Merutka, G.2    Waltho, J.P.3    Lerner, R.A.4    Wright, P.E.5
  • 7
    • 0026743136 scopus 로고
    • Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. II. Plastocyanin
    • Dyson, H. J., Sayre, J. R., Merutka, G., Shin, H. C., Lerner, R. A., and Wright, P. E. (1992) Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. II. Plastocyanin, J. Mol. Biol. 226, 819-35.
    • (1992) J. Mol. Biol. , vol.226 , pp. 819-835
    • Dyson, H.J.1    Sayre, J.R.2    Merutka, G.3    Shin, H.C.4    Lerner, R.A.5    Wright, P.E.6
  • 8
    • 0343059020 scopus 로고    scopus 로고
    • Conformational analysis of peptides corresponding to β-hairpins and a β-sheet that represent the entire sequence of the α-spectrin SH3 domain
    • Viguera, A. R., Jimenez, M. A., Rico, M., and Serrano, L. (1996) Conformational analysis of peptides corresponding to β-hairpins and a β-sheet that represent the entire sequence of the α-spectrin SH3 domain, J. Mol. Biol. 255, 507-21.
    • (1996) J. Mol. Biol. , vol.255 , pp. 507-521
    • Viguera, A.R.1    Jimenez, M.A.2    Rico, M.3    Serrano, L.4
  • 9
    • 0031576341 scopus 로고    scopus 로고
    • Complementation of peptide fragments of the single domain protein chymotrypsin inhibitor 2
    • Ladurner, A. G., Itzhaki, L. S., de Prat Gay, G., and Fersht, A. R. (1997) Complementation of peptide fragments of the single domain protein chymotrypsin inhibitor 2, J. Mol. Biol. 273, 317-29.
    • (1997) J. Mol. Biol. , vol.273 , pp. 317-329
    • Ladurner, A.G.1    Itzhaki, L.S.2    De Prat Gay, G.3    Fersht, A.R.4
  • 10
    • 0027136215 scopus 로고
    • Local conformations of peptides representing the entire sequence of bovine pancreatic trypsin inhibitor and their roles in folding
    • Kemmink, J., and Creighton, T. E. (1993) Local conformations of peptides representing the entire sequence of bovine pancreatic trypsin inhibitor and their roles in folding, J. Mol. Biol. 234, 861-78.
    • (1993) J. Mol. Biol. , vol.234 , pp. 861-878
    • Kemmink, J.1    Creighton, T.E.2
  • 11
    • 0028848469 scopus 로고
    • Search for nucleation sites in smaller fragments of chymotrypsin inhibitor 2
    • Itzhaki, L. S., Neira, J. L., Ruiz-Sanz, J., de Prat Gay, G., and Fersht, A. R. (1995) Search for nucleation sites in smaller fragments of chymotrypsin inhibitor 2, J. Mol. Biol. 254, 289-304.
    • (1995) J. Mol. Biol. , vol.254 , pp. 289-304
    • Itzhaki, L.S.1    Neira, J.L.2    Ruiz-Sanz, J.3    De Prat Gay, G.4    Fersht, A.R.5
  • 12
    • 0032905913 scopus 로고    scopus 로고
    • Conformational analysis of peptide fragments derived from the peripheral subunit-binding domain from the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus: Evidence for nonrandom structure in the unfolded state
    • Spector, S., Rosconi, M., and Raleigh, D. P. (1999) Conformational analysis of peptide fragments derived from the peripheral subunit-binding domain from the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus: Evidence for nonrandom structure in the unfolded state, Biopolymers 49, 29-40.
    • (1999) Biopolymers , vol.49 , pp. 29-40
    • Spector, S.1    Rosconi, M.2    Raleigh, D.P.3
  • 13
    • 0033605920 scopus 로고    scopus 로고
    • Conformational analysis of a set of peptides corresponding to the entire primary sequence of the N-terminal domain of the ribosomal protein L9: Evidence for stable native-like secondary structure in the unfolded state
    • Luisi, D. L., Wu, W. J., and Raleigh, D. P. (1999) Conformational analysis of a set of peptides corresponding to the entire primary sequence of the N-terminal domain of the ribosomal protein L9: Evidence for stable native-like secondary structure in the unfolded state, J. Mol. Biol. 287, 395-407.
    • (1999) J. Mol. Biol. , vol.287 , pp. 395-407
    • Luisi, D.L.1    Wu, W.J.2    Raleigh, D.P.3
  • 14
    • 0008501653 scopus 로고    scopus 로고
    • A thermostable 35-residue subdomain within villin headpiece
    • McKnight, C. J., Doering, D. S., Matsudaira, P. T., and Kim, P. S. (1996) A thermostable 35-residue subdomain within villin headpiece, J. Mol. Biol. 260, 126-34.
    • (1996) J. Mol. Biol. , vol.260 , pp. 126-134
    • McKnight, C.J.1    Doering, D.S.2    Matsudaira, P.T.3    Kim, P.S.4
  • 15
    • 0031058410 scopus 로고    scopus 로고
    • NMR structure of the 35-residue villin headpiece subdomain
    • McKnight, C. J., Matsudaira, P. T., and Kim, P. S. (1997) NMR structure of the 35-residue villin headpiece subdomain, Nat. Struct. Biol. 4, 180-4.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 180-184
    • McKnight, C.J.1    Matsudaira, P.T.2    Kim, P.S.3
  • 16
    • 0033579417 scopus 로고    scopus 로고
    • NMR structure of an F-actin-binding "headpiece" motif from villin
    • Vardar, D., Buckley, D. A., Frank, B. S., and McKnight, C. J. (1999) NMR structure of an F-actin-binding "headpiece" motif from villin, J. Mol. Biol. 294, 1299-310.
    • (1999) J. Mol. Biol. , vol.294 , pp. 1299-1310
    • Vardar, D.1    Buckley, D.A.2    Frank, B.S.3    McKnight, C.J.4
  • 18
    • 0038288925 scopus 로고    scopus 로고
    • Dynamic NMR line-shape analysis demonstrates that the villin headpiece subdomain folds on the microsecond time scale
    • Wang, M., Tang, Y., Sato, S., Vugmeyster, L., McKnight, C. J., and Raleigh, D. P. (2003) Dynamic NMR line-shape analysis demonstrates that the villin headpiece subdomain folds on the microsecond time scale, J. Am. Chem. Soc. 125, 6032-3.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 6032-6033
    • Wang, M.1    Tang, Y.2    Sato, S.3    Vugmeyster, L.4    McKnight, C.J.5    Raleigh, D.P.6
  • 19
    • 0038054301 scopus 로고    scopus 로고
    • Experimental tests of villin subdomain folding simulations
    • Kubelka, J., Eaton, W. A., and Hofrichter, J. (2003) Experimental tests of villin subdomain folding simulations, J. Mol. Biol. 329, 625-30.
    • (2003) J. Mol. Biol. , vol.329 , pp. 625-630
    • Kubelka, J.1    Eaton, W.A.2    Hofrichter, J.3
  • 20
    • 28044438940 scopus 로고    scopus 로고
    • Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain
    • Brewer, S. H., Vu, D. M., Tang, Y., Li, Y., Franzen, S., Raleigh, D. P., and Dyer, R. B. (2005) Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain, Proc. Natl. Acad. Sci. U.S.A. 102, 16662-7.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 16662-16667
    • Brewer, S.H.1    Vu, D.M.2    Tang, Y.3    Li, Y.4    Franzen, S.5    Raleigh, D.P.6    Dyer, R.B.7
  • 21
    • 0036307683 scopus 로고    scopus 로고
    • Application of the diffusion-collision model to the folding of three-helix bundle proteins
    • Islam, S. A., Karplus, M., and Weaver, D. L. (2002) Application of the diffusion-collision model to the folding of three-helix bundle proteins, J. Mol. Biol. 318, 199-215.
    • (2002) J. Mol. Biol. , vol.318 , pp. 199-215
    • Islam, S.A.1    Karplus, M.2    Weaver, D.L.3
  • 22
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan, Y., and Kollman, P. A. (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution, Science 282, 740-4.
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 23
    • 0032544002 scopus 로고    scopus 로고
    • The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation
    • Duan, Y., Wang, L., and Kollman, P. A. (1998) The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation, Proc. Natl. Acad. Sci. U.S.A. 95, 9897-902.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 9897-9902
    • Duan, Y.1    Wang, L.2    Kollman, P.A.3
  • 24
    • 0037188018 scopus 로고    scopus 로고
    • Protein folding as biased Conformational diffusion
    • Sullivan, D. C., and Kuntz, I. D. (2002) Protein folding as biased Conformational diffusion, J. Phys. Chem. B 106, 3255-62.
    • (2002) J. Phys. Chem. B , vol.106 , pp. 3255-3262
    • Sullivan, D.C.1    Kuntz, I.D.2
  • 25
    • 0036892356 scopus 로고    scopus 로고
    • All-atom fast protein folding simulations: The villin headpiece
    • Shen, M. Y., and Freed, K. F. (2002) All-atom fast protein folding simulations: The villin headpiece, Proteins: Struct., Funct., Genet. 49, 439-45.
    • (2002) Proteins: Struct., Funct., Genet. , vol.49 , pp. 439-445
    • Shen, M.Y.1    Freed, K.F.2
  • 26
    • 0012216121 scopus 로고    scopus 로고
    • Folding and unfolding of chicken villin headpiece: Energy landscape of a single-domain model protein
    • Srinivas, G., and Bagchi, B. (2002) Folding and unfolding of chicken villin headpiece: Energy landscape of a single-domain model protein, Curr. Sci. 82, 179-85.
    • (2002) Curr. Sci. , vol.82 , pp. 179-185
    • Srinivas, G.1    Bagchi, B.2
  • 28
    • 0036428782 scopus 로고    scopus 로고
    • Simulation of folding of a small α-helical protein in atomistic detail using worldwide-distributed computing
    • Zagrovic, B., Snow, C. D., Shirts, M. R., and Pande, V. S. (2002) Simulation of folding of a small α-helical protein in atomistic detail using worldwide-distributed computing, J. Mol. Biol. 323, 927-37.
    • (2002) J. Mol. Biol. , vol.323 , pp. 927-937
    • Zagrovic, B.1    Snow, C.D.2    Shirts, M.R.3    Pande, V.S.4
  • 29
    • 0036394906 scopus 로고    scopus 로고
    • Native-like mean structure in the unfolded ensemble of small proteins
    • Zagrovic, B., Snow, C., Khaliq, S., Shirts, M., and Pande, V. (2002) Native-like mean structure in the unfolded ensemble of small proteins, J. Mol. Biol. 323, 153-64.
    • (2002) J. Mol. Biol. , vol.323 , pp. 153-164
    • Zagrovic, B.1    Snow, C.2    Khaliq, S.3    Shirts, M.4    Pande, V.5
  • 30
    • 0042171838 scopus 로고    scopus 로고
    • Parallel tempering simulations of HP-36
    • Lin, C. Y., Hu, C. K., and Hansmann, U. H. (2003) Parallel tempering simulations of HP-36, Proteins 52, 436-45.
    • (2003) Proteins , vol.52 , pp. 436-445
    • Lin, C.Y.1    Hu, C.K.2    Hansmann, U.H.3
  • 31
    • 0042378853 scopus 로고    scopus 로고
    • Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions
    • He, J. B., Zhang, Z. Y., Shi, Y. Y., and Liu, H. Y. (2003) Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions, J. Chem. Phys. 119, 4005-17.
    • (2003) J. Chem. Phys. , vol.119 , pp. 4005-4017
    • He, J.B.1    Zhang, Z.Y.2    Shi, Y.Y.3    Liu, H.Y.4
  • 32
    • 0345724787 scopus 로고    scopus 로고
    • Ab initio folding of helix bundle proteins using molecular dynamics simulations
    • Jang, S. M., Kim, E., Shin, S., and Pak, Y. (2003) Ab initio folding of helix bundle proteins using molecular dynamics simulations, J. Am. Chem. Soc. 125, 14841-6.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 14841-14846
    • Jang, S.M.1    Kim, E.2    Shin, S.3    Pak, Y.4
  • 33
    • 0242292035 scopus 로고    scopus 로고
    • Brute-force molecular dynamics simulations of Villin headpiece: Comparison with NMR parameters
    • van der Spoel, D., and Lindahl, E. (2003) Brute-force molecular dynamics simulations of Villin headpiece: Comparison with NMR parameters, J. Phys. Chem. B 107, 11178-87.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 11178-11187
    • Van Der Spoel, D.1    Lindahl, E.2
  • 34
    • 2542462060 scopus 로고    scopus 로고
    • Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH
    • Ripoll, D. R., Vila, J. A., and Scheraga, H. A. (2004) Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH, J. Mol. Biol. 339, 915-25.
    • (2004) J. Mol. Biol. , vol.339 , pp. 915-925
    • Ripoll, D.R.1    Vila, J.A.2    Scheraga, H.A.3
  • 35
    • 14744275152 scopus 로고    scopus 로고
    • Folding simulations of small proteins
    • Kim, S. Y., Lee, J., and Lee, J. (2005) Folding simulations of small proteins, Biophys. Chem. 115, 195-200.
    • (2005) Biophys. Chem. , vol.115 , pp. 195-200
    • Kim, S.Y.1    Lee, J.2    Lee, J.3
  • 36
    • 11344285181 scopus 로고    scopus 로고
    • Study of the villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics
    • De Mori, G. M. S., Colombo, G., and Micheletti, C. (2005) Study of the villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics, Proteins: Struct., Funct., Bioinf. 58, 459-71.
    • (2005) Proteins: Struct., Funct., Bioinf. , vol.58 , pp. 459-471
    • De Mori, G.M.S.1    Colombo, G.2    Micheletti, C.3
  • 37
    • 4344619300 scopus 로고    scopus 로고
    • All-atom folding simulations of the villin headpiece from stochastically selected coarse-grained structure
    • De Mori, G. M., Micheletti, C., and Colombo, G. (2004) All-atom folding simulations of the villin headpiece from stochastically selected coarse-grained structure, J. Phys. Chem. B 108, 12267-70.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 12267-12270
    • De Mori, G.M.1    Micheletti, C.2    Colombo, G.3
  • 38
    • 1542533572 scopus 로고    scopus 로고
    • Peptide models provide evidence for significant structure in the denatured state of a rapidly folding protein: The villin headpiece subdomain
    • Tang, Y. F., Rigotti, D. J., Fairman, R., and Raleigh, D. P. (2004) Peptide models provide evidence for significant structure in the denatured state of a rapidly folding protein: The villin headpiece subdomain, Biochemistry 43, 3264-72.
    • (2004) Biochemistry , vol.43 , pp. 3264-3272
    • Tang, Y.F.1    Rigotti, D.J.2    Fairman, R.3    Raleigh, D.P.4
  • 39
    • 33646115805 scopus 로고    scopus 로고
    • Efficient high level expression of peptides and proteins as fusion proteins with the N-terminal domain of L9: Application to the villin headpiece helical subdomain
    • Bi, Y., Tang, Y., Raleigh, D. P., and Cho, J. (2006) Efficient high level expression of peptides and proteins as fusion proteins with the N-terminal domain of L9: Application to the villin headpiece helical subdomain, Protein Expression Purif. 47, 234-40.
    • (2006) Protein Expression Purif. , vol.47 , pp. 234-240
    • Bi, Y.1    Tang, Y.2    Raleigh, D.P.3    Cho, J.4
  • 40
    • 45249128810 scopus 로고
    • Measurement of vicinal coupling from cross peaks in COSY spectra
    • Kim, Y., and Prestegard, J. H. (1989) Measurement of vicinal coupling from cross peaks in COSY spectra, J. Magn. Reson. 84, 9-13.
    • (1989) J. Magn. Reson. , vol.84 , pp. 9-13
    • Kim, Y.1    Prestegard, J.H.2
  • 41
    • 0029181728 scopus 로고
    • 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects
    • 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects, J. Biomol. NMR 5, 67-81.
    • (1995) J. Biomol. NMR , vol.5 , pp. 67-81
    • Wishart, D.S.1    Bigam, C.G.2    Holm, A.3    Hodges, R.S.4    Sykes, B.D.5
  • 42
    • 0026597879 scopus 로고
    • The chemical-shift index: A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy
    • Wishart, D. S., Sykes, B. D., and Richards, F. M. (1992) The chemical-shift index: A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy, Biochemistry 31, 1647-51.
    • (1992) Biochemistry , vol.31 , pp. 1647-1651
    • Wishart, D.S.1    Sykes, B.D.2    Richards, F.M.3
  • 43
    • 0030961391 scopus 로고    scopus 로고
    • Measurement of water-amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique
    • Mori, S., vanZijl, P. C. M., and Shortle, D. (1997) Measurement of water-amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique, Proteins: Struct., Funct., Genet. 28, 325-32.
    • (1997) Proteins: Struct., Funct., Genet. , vol.28 , pp. 325-332
    • Mori, S.1    Vanzijl, P.C.M.2    Shortle, D.3
  • 44
    • 0035005366 scopus 로고    scopus 로고
    • Preorganized secondary structure as an important determinant of fast protein folding
    • Myers, J. K., and Oas, T. G. (2001) Preorganized secondary structure as an important determinant of fast protein folding, Nat. Struct. Biol. 8, 552-8.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 552-558
    • Myers, J.K.1    Oas, T.G.2
  • 45
    • 2342655032 scopus 로고    scopus 로고
    • Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation
    • Jemth, P., Gianni, S., Day, R., Li, B., Johnson, C. M., Daggett, V., and Fersht, A. R. (2004) Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation, Proc. Natl. Acad. Sci. U.S.A. 101, 6450-5.
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 6450-6455
    • Jemth, P.1    Gianni, S.2    Day, R.3    Li, B.4    Johnson, C.M.5    Daggett, V.6    Fersht, A.R.7
  • 46
    • 19944382195 scopus 로고    scopus 로고
    • Denatured-state ensemble and the early-stage folding of the G29A mutant of the B-domain of protein A
    • Chowdhury, S., Lei, H. X., and Duan, Y. (2005) Denatured-state ensemble and the early-stage folding of the G29A mutant of the B-domain of protein A, J. Phys. Chem. B 109, 9073-81.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 9073-9081
    • Chowdhury, S.1    Lei, H.X.2    Duan, Y.3
  • 48
    • 0026244229 scopus 로고
    • Molscript: A Program to produce both detailed and schematic plots of protein structures
    • Kraulis, P. J. (1991) Molscript: A Program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallogr. 24, 946-50.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1


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