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Volumn 15, Issue 10, 2006, Pages 2278-2289

Design and NMR conformational study of a β-sheet peptide based on Betanova and WW domains

Author keywords

Antiparallel sheet; NMR; Peptide design; Peptide structure; WW domain

Indexed keywords

DISULFIDE;

EID: 33749341803     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062186506     Document Type: Article
Times cited : (17)

References (46)
  • 1
    • 0006393051 scopus 로고
    • Two-dimensional spectroscopy. Application to NMR
    • Aue, W.P., Bertholdi, E., and Ernst, R.R. 1976. Two-dimensional spectroscopy. application to NMR. J. Chem. Phys. 64: 2229-2246.
    • (1976) J. Chem. Phys. , vol.64 , pp. 2229-2246
    • Aue, W.P.1    Bertholdi, E.2    Ernst, R.R.3
  • 2
    • 0010285919 scopus 로고
    • Sensitivity-enhanced two-dimensional heteronuclear shift correlation NMR spectroscopy
    • Bax, A. and Subramanian, J. 1986. Sensitivity-enhanced two-dimensional heteronuclear shift correlation NMR spectroscopy. J. Magn. Reson. 67: 565-570.
    • (1986) J. Magn. Reson. , vol.67 , pp. 565-570
    • Bax, A.1    Subramanian, J.2
  • 4
    • 0033003335 scopus 로고    scopus 로고
    • Protein backbone angle restraints from searching a database for chemical shift and sequence homology
    • Cornilescu, G., Delaglio, F., and Bax, A. 1999. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13: 289-302.
    • (1999) J. Biomol. NMR , vol.13 , pp. 289-302
    • Cornilescu, G.1    Delaglio, F.2    Bax, A.3
  • 5
    • 0034724566 scopus 로고    scopus 로고
    • Mapping the transition state of the WW domain β-sheet
    • Crane, J.C., Koepf, E.K., Kelly, J.W., and Gruebele, M. 2000. Mapping the transition state of the WW domain β-sheet. J. Mol. Biol. 298: 283-292.
    • (2000) J. Mol. Biol. , vol.298 , pp. 283-292
    • Crane, J.C.1    Koepf, E.K.2    Kelly, J.W.3    Gruebele, M.4
  • 6
    • 0032540666 scopus 로고    scopus 로고
    • A designed three stranded β-sheet peptide as a multiple β-hairpin model
    • Das, C., Raghothama, S., and Balaram, P. 1998. A designed three stranded β-sheet peptide as a multiple β-hairpin model. J. Am. Chem. Soc. 120: 5812-5813.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 5812-5813
    • Das, C.1    Raghothama, S.2    Balaram, P.3
  • 7
    • 0032917075 scopus 로고    scopus 로고
    • De novo design of a monomeric three-stranded antiparallel β-sheet
    • de Alba, E., Santoro, J., Rico, M., and Jiménez, M.A. 1999. De novo design of a monomeric three-stranded antiparallel β-sheet. Protein Sci. 8: 854-865.
    • (1999) Protein Sci. , vol.8 , pp. 854-865
    • De Alba, E.1    Santoro, J.2    Rico, M.3    Jiménez, M.A.4
  • 8
    • 0037042295 scopus 로고    scopus 로고
    • The effect of backbone cyclization on the thermodynamics of β-sheet unfolding: Stability optimization of the PIN WW domain
    • Deechongkit, S. and Kelly, J.W. 2002. The effect of backbone cyclization on the thermodynamics of β-sheet unfolding: Stability optimization of the PIN WW domain. J. Am. Chem. Soc. 124: 4980-4986.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 4980-4986
    • Deechongkit, S.1    Kelly, J.W.2
  • 9
    • 3042848873 scopus 로고    scopus 로고
    • Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics
    • Deechongkit, S., Nguyen, H., Powers, E.T., Dawson, P.E., Gruebele, M., and Kelly, J.W. 2004. Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics. Nature 430: 101-105.
    • (2004) Nature , vol.430 , pp. 101-105
    • Deechongkit, S.1    Nguyen, H.2    Powers, E.T.3    Dawson, P.E.4    Gruebele, M.5    Kelly, J.W.6
  • 12
    • 0035085553 scopus 로고    scopus 로고
    • Computational estimation of specific side chain interaction energies in a helices
    • Fisinger, S., Serrano, L., and Lacroix, E. 2001. Computational estimation of specific side chain interaction energies in a helices. Protein Sci. 10: 809-818.
    • (2001) Protein Sci. , vol.10 , pp. 809-818
    • Fisinger, S.1    Serrano, L.2    Lacroix, E.3
  • 13
    • 0033824762 scopus 로고    scopus 로고
    • Structure, folding, and energetics of cooperative interactions between β-strands of a de novo designed three-stranded antiparallel β-sheet peptide
    • Griffiths-Jones, S.R. and Searle, M.S. 2000. Structure, folding, and energetics of cooperative interactions between β-strands of a de novo designed three-stranded antiparallel β-sheet peptide. J. Am. Chem. Soc. 122: 8350-8356.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 8350-8356
    • Griffiths-Jones, S.R.1    Searle, M.S.2
  • 14
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • Guntert, P., Mumenthaler, C., and Wüthrich, K. 1997. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273: 283-298.
    • (1997) J. Mol. Biol. , vol.273 , pp. 283-298
    • Guntert, P.1    Mumenthaler, C.2    Wüthrich, K.3
  • 15
    • 0031735020 scopus 로고    scopus 로고
    • Determinants of strand register in antiparallel β-sheets of proteins
    • Hutchinson, E.G., Sessions, R.B., Thornton, J.M., and Woolfson, D.N. 1998. Determinants of strand register in antiparallel β-sheets of proteins. Protein Sci. 7: 2287-2300.
    • (1998) Protein Sci. , vol.7 , pp. 2287-2300
    • Hutchinson, E.G.1    Sessions, R.B.2    Thornton, J.M.3    Woolfson, D.N.4
  • 17
    • 0343359244 scopus 로고
    • Investigation of exchange processes by two-dimensional NMR spectroscopy
    • Jeener, J., Meier, B.H., Bachmann, P., and Ernst, R.R. 1979. Investigation of exchange processes by two-dimensional NMR spectroscopy. J. Chem. Phys. 71: 4546-4553.
    • (1979) J. Chem. Phys. , vol.71 , pp. 4546-4553
    • Jeener, J.1    Meier, B.H.2    Bachmann, P.3    Ernst, R.R.4
  • 18
    • 0034976980 scopus 로고    scopus 로고
    • Increasing protein stability using a rational approach combining sequence homology and structural alignment: Stabilizing the WW domain
    • Jiang, X., Kowalski, J., and Kelly, J.W. 2001. Increasing protein stability using a rational approach combining sequence homology and structural alignment: Stabilizing the WW domain. Protein Sci. 10: 1454-1465.
    • (2001) Protein Sci. , vol.10 , pp. 1454-1465
    • Jiang, X.1    Kowalski, J.2    Kelly, J.W.3
  • 19
    • 0034805437 scopus 로고    scopus 로고
    • Incorporating beta-turns and a turn mimetic out of context in loop 1 of the WW domain affords cooperatively folded β-sheets
    • Kaul, R., Angeles, A.R., Jager, M., Powers, E.T., and Kelly, J.W. 2001. Incorporating beta-turns and a turn mimetic out of context in loop 1 of the WW domain affords cooperatively folded β-sheets. J. Am. Chem. Soc. 123: 5206-5212.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 5206-5212
    • Kaul, R.1    Angeles, A.R.2    Jager, M.3    Powers, E.T.4    Kelly, J.W.5
  • 20
    • 0032939806 scopus 로고    scopus 로고
    • WW: An isolated three-stranded antiparallel β-sheet domain that unfolds and refolds reversibly; evidence for a structured hydrophobic cluster in urea and GdnHCl and a disordered thermal unfolded state
    • Koepf, E.K., Petrassi, H.M., Sudol, M., and Kelly, J.W. 1999. WW: An isolated three-stranded antiparallel β-sheet domain that unfolds and refolds reversibly; evidence for a structured hydrophobic cluster in urea and GdnHCl and a disordered thermal unfolded state. Protein Sci. 8: 841-853.
    • (1999) Protein Sci. , vol.8 , pp. 841-853
    • Koepf, E.K.1    Petrassi, H.M.2    Sudol, M.3    Kelly, J.W.4
  • 21
    • 2642670311 scopus 로고    scopus 로고
    • Design of a 20-amino acid, three-stranded β-sheet protein
    • Kortemme, T., Ramírez-Alvarado, M., and Serrano, L. 1998. Design of a 20-amino acid, three-stranded β-sheet protein. Science 281: 253-256.
    • (1998) Science , vol.281 , pp. 253-256
    • Kortemme, T.1    Ramírez-Alvarado, M.2    Serrano, L.3
  • 22
    • 0019327003 scopus 로고
    • A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules
    • Kumar, A., Ernst, R.R., and Wüthrich, K. 1980. A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem. Biophys. Res. Commun. 95: 1-6.
    • (1980) Biochem. Biophys. Res. Commun. , vol.95 , pp. 1-6
    • Kumar, A.1    Ernst, R.R.2    Wüthrich, K.3
  • 24
    • 0034061258 scopus 로고    scopus 로고
    • Structural analysis of WW domains and design of a WW prototype
    • Macías, M.J., Gervais, V., Civera, C., and Oschkinat, H. 2000. Structural analysis of WW domains and design of a WW prototype. Nat. Struct. Biol. 7: 375-379.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 375-379
    • Macías, M.J.1    Gervais, V.2    Civera, C.3    Oschkinat, H.4
  • 25
    • 0027998757 scopus 로고
    • Context is a major determinant of β-sheet propensity
    • Minor Jr., D.L. and Kim, P.S. 1994a. Context is a major determinant of β-sheet propensity. Nature 371: 264-267.
    • (1994) Nature , vol.371 , pp. 264-267
    • Minor Jr., D.L.1    Kim, P.S.2
  • 26
    • 0028176595 scopus 로고
    • Measurement of the β-sheet-forming propensities of amino acids
    • _. 1994b. Measurement of the β-sheet-forming propensities of amino acids. Nature 367: 660-663.
    • (1994) Nature , vol.367 , pp. 660-663
  • 27
    • 0001071357 scopus 로고    scopus 로고
    • Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation
    • Nguyen, H., Jager, M., Moretto, A., Gruebele, M., and Kelly, J.W. 2003. Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation. Proc. Natl. Acad. Sci. 100: 3948-3953.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 3948-3953
    • Nguyen, H.1    Jager, M.2    Moretto, A.3    Gruebele, M.4    Kelly, J.W.5
  • 28
    • 33749073784 scopus 로고    scopus 로고
    • De novo design of monomeric β-hairpin and β-sheet peptides
    • (eds. R. Guerois and M. López de la Paz), Humana Press, Totowa, NJ
    • Pantoja-Uceda, D., Santiveri, C.M., and Jimenez, M.A. 2006. De novo design of monomeric β-hairpin and β-sheet peptides. In Protein design: Methods and applications (eds. R. Guerois and M. López de la Paz), Vol. 340, pp. 27-51. Humana Press, Totowa, NJ.
    • (2006) Protein Design: Methods and Applications , vol.340 , pp. 27-51
    • Pantoja-Uceda, D.1    Santiveri, C.M.2    Jimenez, M.A.3
  • 29
    • 0026951903 scopus 로고
    • Gradient-tailored excitation for single quantum NMR spectroscopy in aqueous solution
    • Piotto, M., Saudek, V., and Sklenar, V. 1992. Gradient-tailored excitation for single quantum NMR spectroscopy in aqueous solution. J. Biomol. NMR 6: 661-665.
    • (1992) J. Biomol. NMR , vol.6 , pp. 661-665
    • Piotto, M.1    Saudek, V.2    Sklenar, V.3
  • 30
    • 45949117739 scopus 로고
    • Improved techniques for homonuclear rotating-frame and isotropic mixing experiments
    • Rance, M. 1987. Improved techniques for homonuclear rotating-frame and isotropic mixing experiments. J. Magn. Reson. 74: 557-564.
    • (1987) J. Magn. Reson. , vol.74 , pp. 557-564
    • Rance, M.1
  • 31
    • 49549146155 scopus 로고
    • Quadrature Fourier detection: Simple multiplex for dual detection
    • Redfield, A.G. and Kuntz, S.D. 1975. Quadrature Fourier detection: Simple multiplex for dual detection. J. Magn. Reson. 19: 250-259.
    • (1975) J. Magn. Reson. , vol.19 , pp. 250-259
    • Redfield, A.G.1    Kuntz, S.D.2
  • 32
    • 0034744426 scopus 로고    scopus 로고
    • 13Cβ chemical shifts as a tool to delineate β-hairpin structures in peptides
    • 13Cβ chemical shifts as a tool to delineate β-hairpin structures in peptides. J. Biomol. NMR 19: 331-345.
    • (2001) J. Biomol. NMR , vol.19 , pp. 331-345
    • Santiveri, C.M.1    Rico, M.2    Jiménez, M.A.3
  • 34
    • 1842611349 scopus 로고    scopus 로고
    • Factors involved in the stability of isolated β-sheets: Turn sequence, β-sheet twisting, and hydrophobic surface burial
    • Santiveri, C.M., Santoro, J., Rico, M., and Jiménez, M.A. 2004. Factors involved in the stability of isolated β-sheets: Turn sequence, β-sheet twisting, and hydrophobic surface burial. Protein Sci. 13: 1134-1147.
    • (2004) Protein Sci. , vol.13 , pp. 1134-1147
    • Santiveri, C.M.1    Santoro, J.2    Rico, M.3    Jiménez, M.A.4
  • 36
    • 0043122630 scopus 로고    scopus 로고
    • Use of a designed triple-stranded antiparallel β-sheet to probe β-sheet cooperativity in aqueous solution
    • Schenck, H.L. and Gellman, S.H. 1998. Use of a designed triple-stranded antiparallel β-sheet to probe β-sheet cooperativity in aqueous solution. J. Am. Chem. Soc. 120: 4869-4870.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 4869-4870
    • Schenck, H.L.1    Gellman, S.H.2
  • 38
    • 0032479010 scopus 로고    scopus 로고
    • Cooperative interaction between the three strands of a designed antiparallel β-sheet
    • Sharman, G.J. and Searle, M.S. 1998. Cooperative interaction between the three strands of a designed antiparallel β-sheet. J. Am. Chem. Soc. 120: 5291-5300.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 5291-5300
    • Sharman, G.J.1    Searle, M.S.2
  • 39
    • 0028175780 scopus 로고
    • A thermodynamic scale for the β-sheet forming tendencies of the amino acids
    • Smith, C.K., Withka, J.M., and Regan, L. 1994. A thermodynamic scale for the β-sheet forming tendencies of the amino acids. Biochemistry 33: 5510-5517.
    • (1994) Biochemistry , vol.33 , pp. 5510-5517
    • Smith, C.K.1    Withka, J.M.2    Regan, L.3
  • 41
    • 0030424581 scopus 로고    scopus 로고
    • Structure and function of the WW domain
    • Sudol, M. 1996. Structure and function of the WW domain. Prog. Biophys. Mol. Biol. 65: 113-132.
    • (1996) Prog. Biophys. Mol. Biol. , vol.65 , pp. 113-132
    • Sudol, M.1
  • 42
    • 0026410969 scopus 로고
    • Relationship between nuclear magnetic resonance chemical shift and protein secondary structure
    • Wishart, D.S., Sykes, B.D., and Richards, F.M. 1991. Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J. Mol. Biol. 222: 311-333.
    • (1991) J. Mol. Biol. , vol.222 , pp. 311-333
    • Wishart, D.S.1    Sykes, B.D.2    Richards, F.M.3
  • 43
    • 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
  • 44
    • 0029058159 scopus 로고
    • An analysis of side chain interactions and pair correlations within antiparallel β-sheets: The differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs
    • Wouters, M.A. and Curmi, P.M. 1995. An analysis of side chain interactions and pair correlations within antiparallel β-sheets: The differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs. Proteins 22: 119-131.
    • (1995) Proteins , vol.22 , pp. 119-131
    • Wouters, M.A.1    Curmi, P.M.2
  • 46
    • 0021764802 scopus 로고
    • Polypeptide secondary structure determination by nuclear magnetic resonance observation of short proton-proton distances
    • Wüthrich, K., Billeter, M., and Braun, W. 1984. Polypeptide secondary structure determination by nuclear magnetic resonance observation of short proton-proton distances. J. Mol. Biol. 180: 715-740.
    • (1984) J. Mol. Biol. , vol.180 , pp. 715-740
    • Wüthrich, K.1    Billeter, M.2    Braun, W.3


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