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Volumn 13, Issue 10, 2007, Pages 679-692

Loop propensity of the sequence YKGQP from staphylococcal nuclease: Implications for the folding of nuclease

Author keywords

Free energy landscape; GROMOS96; Loop; Peptide; Protein folding; Staphylococcal nuclease; Turn

Indexed keywords

ALANINE; GLYCINE; NUCLEASE; PEPTIDE; PROLINE; TYROSINE; WATER;

EID: 35348816793     PISSN: 10752617     EISSN: 10991387     Source Type: Journal    
DOI: 10.1002/psc.907     Document Type: Article
Times cited : (8)

References (61)
  • 1
    • 0021779081 scopus 로고    scopus 로고
    • Rose GD, Gierasch LM, Smith JA. Turns in peptides and proteins. Adv. Protein Chem. 1985; 37: 1-109.
    • Rose GD, Gierasch LM, Smith JA. Turns in peptides and proteins. Adv. Protein Chem. 1985; 37: 1-109.
  • 2
    • 14244267301 scopus 로고    scopus 로고
    • Multiple extracellular loops contribute to substrate binding and transport by the Escherichia coli cobalamin transporter BtuB
    • Fuller-Schaefer CA, Kadner RJ. Multiple extracellular loops contribute to substrate binding and transport by the Escherichia coli cobalamin transporter BtuB. J. Bacteriol. 2005; 187: 1732-1739.
    • (2005) J. Bacteriol , vol.187 , pp. 1732-1739
    • Fuller-Schaefer, C.A.1    Kadner, R.J.2
  • 3
    • 0028856717 scopus 로고
    • Destabilizing loop swaps in the CDRs of an immunoglobulin VL domain
    • Helms LR, Wetzel R. Destabilizing loop swaps in the CDRs of an immunoglobulin VL domain. Protein Sci. 1995; 4: 2073-2081.
    • (1995) Protein Sci , vol.4 , pp. 2073-2081
    • Helms, L.R.1    Wetzel, R.2
  • 5
    • 0026351935 scopus 로고
    • Conformation of beta hairpins in protein structures: Classification and diversity in homologous structures
    • Sibanda BL, Thornton JM. Conformation of beta hairpins in protein structures: classification and diversity in homologous structures. Methods Enzymol. 1991; 202: 59-82.
    • (1991) Methods Enzymol , vol.202 , pp. 59-82
    • Sibanda, B.L.1    Thornton, J.M.2
  • 6
    • 0024391832 scopus 로고
    • Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering
    • Sibanda BL, Blundell TL, Thornton JM. Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J. Mol. Biol. 1989; 206: 759-777.
    • (1989) J. Mol. Biol , vol.206 , pp. 759-777
    • Sibanda, B.L.1    Blundell, T.L.2    Thornton, J.M.3
  • 7
  • 8
    • 0017251893 scopus 로고
    • Protein-folding dynamics
    • Karplus M, Weaver DL. Protein-folding dynamics. Nature 1976; 260: 404-406.
    • (1976) Nature , vol.260 , pp. 404-406
    • Karplus, M.1    Weaver, D.L.2
  • 9
    • 0028327236 scopus 로고
    • Protein folding dynamics: The diffusion-collision model and experimental data
    • Karplus M, Weaver DL. Protein folding dynamics: the diffusion-collision model and experimental data. Protein Sci. 1994; 3: 650-668.
    • (1994) Protein Sci , vol.3 , pp. 650-668
    • Karplus, M.1    Weaver, D.L.2
  • 10
    • 0022423920 scopus 로고
    • Theory for the folding and stability of globular proteins
    • Dill KA. Theory for the folding and stability of globular proteins. Biochemistry 1985; 24: 1501-1509.
    • (1985) Biochemistry , vol.24 , pp. 1501-1509
    • Dill, K.A.1
  • 11
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill KA, Dominant forces in protein folding. Biochemistry 1990; 29: 7133-7155.
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 13
    • 0542397796 scopus 로고    scopus 로고
    • Kinetics and dynamics of loops, a-helixes, b-hairpins, and fast-folding proteins
    • Eaton WA, Munoz V, Thompson PA, Henry ER, Hofrichter J. Kinetics and dynamics of loops, a-helixes, b-hairpins, and fast-folding proteins. Acc. Chem. Res. 1998; 31: 745-753.
    • (1998) Acc. Chem. Res , vol.31 , pp. 745-753
    • Eaton, W.A.1    Munoz, V.2    Thompson, P.A.3    Henry, E.R.4    Hofrichter, J.5
  • 16
    • 0038385501 scopus 로고    scopus 로고
    • Role of local sequence in the folding of cellular retinoic abinding protein I: Structural propensities of reverse turns
    • Rotondi KS, Gierasch LM. Role of local sequence in the folding of cellular retinoic abinding protein I: structural propensities of reverse turns. Biochemistry 2003; 42: 7976-7985.
    • (2003) Biochemistry , vol.42 , pp. 7976-7985
    • Rotondi, K.S.1    Gierasch, L.M.2
  • 17
    • 0033871567 scopus 로고    scopus 로고
    • Critical role of beta-hairpin formation in protein G folding
    • McCallister EL, Alm E, Baker D. Critical role of beta-hairpin formation in protein G folding. Nat. Struct. Biol. 2000; 7: 669-673.
    • (2000) Nat. Struct. Biol , vol.7 , pp. 669-673
    • McCallister, E.L.1    Alm, E.2    Baker, D.3
  • 18
    • 0034964196 scopus 로고    scopus 로고
    • Computer-based redesign of a protein folding pathway
    • Nauli S, Kuhlman B, Baker D. Computer-based redesign of a protein folding pathway. Nat. Struct. Biol. 2001; 8: 602-605.
    • (2001) Nat. Struct. Biol , vol.8 , pp. 602-605
    • Nauli, S.1    Kuhlman, B.2    Baker, D.3
  • 19
    • 0031565981 scopus 로고    scopus 로고
    • Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein
    • Gu, Kim D, Baker D. Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein. J. Mol. Biol. 1997; 274: 588-596.
    • (1997) J. Mol. Biol , vol.274 , pp. 588-596
    • Gu1    Kim, D.2    Baker, D.3
  • 20
    • 0033548061 scopus 로고    scopus 로고
    • Using loop length variants to dissect the folding pathway of a four-helix-bundle protein
    • Nagi AD, Anderson KS, Regan L. Using loop length variants to dissect the folding pathway of a four-helix-bundle protein. J. Mol. Biol. 1999; 286: 257-265.
    • (1999) J. Mol. Biol , vol.286 , pp. 257-265
    • Nagi, A.D.1    Anderson, K.S.2    Regan, L.3
  • 21
    • 11444265452 scopus 로고    scopus 로고
    • Primary and secondary structure dependence of peptide flexibility assessed by fluorescence-based measurement of end-to-end collision rates
    • Huang F, Hudgins RR, Nau WM. Primary and secondary structure dependence of peptide flexibility assessed by fluorescence-based measurement of end-to-end collision rates. J. Am. Chem. Soc. 2004; 126: 16665-16675.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 16665-16675
    • Huang, F.1    Hudgins, R.R.2    Nau, W.M.3
  • 22
    • 14944346760 scopus 로고    scopus 로고
    • Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains
    • Krieger F, Moglich A, Kiefhaber T. Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains. J. Am Chem. Soc. 2005; 127: 3346-3352.
    • (2005) J. Am Chem. Soc , vol.127 , pp. 3346-3352
    • Krieger, F.1    Moglich, A.2    Kiefhaber, T.3
  • 23
    • 0028008617 scopus 로고
    • Staphylococcal nuclease folding intermediate characterized by hydrogen exchange and NMR spectroscopy
    • Jacobs MD, Fox RO. Staphylococcal nuclease folding intermediate characterized by hydrogen exchange and NMR spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 1994; 91: 449-453.
    • (1994) Proc. Natl. Acad. Sci. U.S.A , vol.91 , pp. 449-453
    • Jacobs, M.D.1    Fox, R.O.2
  • 24
    • 0036135965 scopus 로고    scopus 로고
    • Early formation of a beta hairpin during folding of staphylococcal nuclease H124L as detected by pulsed hydrogen exchange
    • Walkenhorst WF, Edwards JA, Markley JL, Roder H. Early formation of a beta hairpin during folding of staphylococcal nuclease H124L as detected by pulsed hydrogen exchange. Protein Sci. 2002; 11: 82-91.
    • (2002) Protein Sci , vol.11 , pp. 82-91
    • Walkenhorst, W.F.1    Edwards, J.A.2    Markley, J.L.3    Roder, H.4
  • 25
    • 33747873410 scopus 로고    scopus 로고
    • Beta-Hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease
    • Patel S, Sista P, Balaji PV, Sasidhar YU. Beta-Hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease. J. Mol. Graphics Modell. 2006; 25: 103-115.
    • (2006) J. Mol. Graphics Modell , vol.25 , pp. 103-115
    • Patel, S.1    Sista, P.2    Balaji, P.V.3    Sasidhar, Y.U.4
  • 26
    • 0024316597 scopus 로고
    • The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A
    • Loll PJ, Lattman EE. The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A. Proteins 1989; 5: 183-201.
    • (1989) Proteins , vol.5 , pp. 183-201
    • Loll, P.J.1    Lattman, E.E.2
  • 27
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • Pullman B ed, Reidel Publishing Company Dordrecht: The Netherlands
    • Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. In Inter Molecular Forces, Pullman B (ed.). Reidel Publishing Company Dordrecht: The Netherlands, 1981; 331-342.
    • (1981) Inter Molecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    van Gunsteren, W.F.3    Hermans, J.4
  • 28
    • 0035789518 scopus 로고    scopus 로고
    • Gromacs 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl E, Hess B, van der Spoel D. Gromacs 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 2001; 7: 306-317.
    • (2001) J. Mol. Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 32
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L. Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993; 98: 10089-10092.
    • (1993) J. Chem. Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 34
    • 33750587438 scopus 로고
    • Molecular dynamics with coupling to an external bath
    • Berendsen H, Postma J, DiNola A, Haak J. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984; 81: 3684-3690.
    • (1984) J. Chem. Phys , vol.81 , pp. 3684-3690
    • Berendsen, H.1    Postma, J.2    DiNola, A.3    Haak, J.4
  • 35
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983; 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 36
    • 0024279235 scopus 로고
    • Analysis and prediction of the different types of beta-turn in proteins
    • Wilmot CM, Thornton JM. Analysis and prediction of the different types of beta-turn in proteins. J. Mol. Biol. 1988; 203: 221-232.
    • (1988) J. Mol. Biol , vol.203 , pp. 221-232
    • Wilmot, C.M.1    Thornton, J.M.2
  • 41
    • 17844406143 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution: An extended phase space sampling by molecular dynamics simulations in explicit water
    • Daidone I, Amadei A, Di Nola A. Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution: an extended phase space sampling by molecular dynamics simulations in explicit water. Proteins 2005; 59: 510-518.
    • (2005) Proteins , vol.59 , pp. 510-518
    • Daidone, I.1    Amadei, A.2    Di Nola, A.3
  • 42
    • 0032802062 scopus 로고    scopus 로고
    • On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
    • Amadei A, Ceruso MA, Di Nola A. On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. Proteins 1999; 36: 419-424.
    • (1999) Proteins , vol.36 , pp. 419-424
    • Amadei, A.1    Ceruso, M.A.2    Di Nola, A.3
  • 44
    • 0017709445 scopus 로고
    • Beta-turns in proteins
    • Chou PY, Fasman GD. Beta-turns in proteins. J. Mol. Biol. 1977; 115: 135-175.
    • (1977) J. Mol. Biol , vol.115 , pp. 135-175
    • Chou, P.Y.1    Fasman, G.D.2
  • 45
    • 0021844602 scopus 로고
    • Beta-hairpin families in globular proteins
    • Sibanda BL, Thornton JM. Beta-hairpin families in globular proteins. Nature 1985; 316: 170-174.
    • (1985) Nature , vol.316 , pp. 170-174
    • Sibanda, B.L.1    Thornton, J.M.2
  • 46
    • 1542314363 scopus 로고    scopus 로고
    • Local sequence information in cellular retinoic acid-binding protein I: Specific residue roles in b-turns
    • Rotondi KS, Gierasch LM. Local sequence information in cellular retinoic acid-binding protein I: specific residue roles in b-turns. Biopolymers 2003; 71: 638-651.
    • (2003) Biopolymers , vol.71 , pp. 638-651
    • Rotondi, K.S.1    Gierasch, L.M.2
  • 47
    • 0024278597 scopus 로고
    • Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn
    • Dyson HJ, Rance M, Houghten RA, Lerner RA, Wright PE. Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn. J. Mol. Biol. 1988; 201: 161-200.
    • (1988) J. Mol. Biol , vol.201 , pp. 161-200
    • Dyson, H.J.1    Rance, M.2    Houghten, R.A.3    Lerner, R.A.4    Wright, P.E.5
  • 48
    • 0028566270 scopus 로고
    • A revised set of potentials for beta-turn formation in proteins
    • Hutchinson EG, Thornton JM. A revised set of potentials for beta-turn formation in proteins. Protein Sci. 1994; 3: 2207-2216.
    • (1994) Protein Sci , vol.3 , pp. 2207-2216
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 49
    • 0032545165 scopus 로고    scopus 로고
    • Conformational interconversions in peptide beta-turns: Analysis of turns in proteins and computational estimates of barriers
    • Gunasekaran K, Gomathi L, Ramakrishnan C, Chandrasekhar J, Balaram P. Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers. J. Mol. Biol. 1998; 284: 1505-1516.
    • (1998) J. Mol. Biol , vol.284 , pp. 1505-1516
    • Gunasekaran, K.1    Gomathi, L.2    Ramakrishnan, C.3    Chandrasekhar, J.4    Balaram, P.5
  • 50
    • 0034710426 scopus 로고    scopus 로고
    • Folding studies of a linear pentamer peptide adopting a reverse turn conformation in aqueous solution through molecular dynamics simulation
    • Wu X, Wang S. Folding studies of a linear pentamer peptide adopting a reverse turn conformation in aqueous solution through molecular dynamics simulation. J. Phys. Chem. B 2000; 104: 8023-8034.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 8023-8034
    • Wu, X.1    Wang, S.2
  • 51
    • 0028157226 scopus 로고
    • Backbone flexibility and stability of reverse turn conformation in a model system
    • Scully J, Hermans J. Backbone flexibility and stability of reverse turn conformation in a model system. J. Mol. Biol. 1994; 235: 682-694.
    • (1994) J. Mol. Biol , vol.235 , pp. 682-694
    • Scully, J.1    Hermans, J.2
  • 52
    • 0030596522 scopus 로고    scopus 로고
    • Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding
    • Yang AS, Hitz B, Honig B. Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding. J. Mol. Biol. 1996; 259: 873-882.
    • (1996) J. Mol. Biol , vol.259 , pp. 873-882
    • Yang, A.S.1    Hitz, B.2    Honig, B.3
  • 53
    • 0015914783 scopus 로고
    • Conformation of twisted beta-pleated sheets in proteins
    • Chothia C. Conformation of twisted beta-pleated sheets in proteins. J. Mol. Biol. 1973; 75: 295-302.
    • (1973) J. Mol. Biol , vol.75 , pp. 295-302
    • Chothia, C.1
  • 54
    • 0028239910 scopus 로고
    • Analysis of two-residue turns in proteins
    • Mattos C, Petsko GA, Karplus M. Analysis of two-residue turns in proteins. J. Mol. Biol. 1994; 238: 733-747.
    • (1994) J. Mol. Biol , vol.238 , pp. 733-747
    • Mattos, C.1    Petsko, G.A.2    Karplus, M.3
  • 55
    • 0025743641 scopus 로고
    • 3r Nanosecond time scale folding dynamics of a pentapeptide in water
    • Tobias DJ, Mertz JE, Brooks CL. 3r Nanosecond time scale folding dynamics of a pentapeptide in water. Biochemistry 1991; 30: 6054-6058.
    • (1991) Biochemistry , vol.30 , pp. 6054-6058
    • Tobias, D.J.1    Mertz, J.E.2    Brooks, C.L.3
  • 56
    • 0030627746 scopus 로고    scopus 로고
    • Dynamics of a type VI reverse turn in a linear peptide in aqueous solution
    • Demchuk E, Bashford D, Case DA. Dynamics of a type VI reverse turn in a linear peptide in aqueous solution. Fold. Des. 1997; 2: 35-46.
    • (1997) Fold. Des , vol.2 , pp. 35-46
    • Demchuk, E.1    Bashford, D.2    Case, D.A.3
  • 57
    • 0031587288 scopus 로고    scopus 로고
    • Kinetics of peptide folding: Computer simulations of SYPFDV and peptide variants in water
    • Mohanty D, Elber R, Thirumalai D, Beglov D, Roux B. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J. Mol. Biol. 1997; 272: 423-442.
    • (1997) J. Mol. Biol , vol.272 , pp. 423-442
    • Mohanty, D.1    Elber, R.2    Thirumalai, D.3    Beglov, D.4    Roux, B.5
  • 58
    • 0033398684 scopus 로고    scopus 로고
    • Solution conformation of phakellistatin 8 investigated by molecular dynamics simulations
    • Galzitskaya O, Caflisch A. Solution conformation of phakellistatin 8 investigated by molecular dynamics simulations. J. Mol. Graphics Modell. 1999; 17: 19-27.
    • (1999) J. Mol. Graphics Modell , vol.17 , pp. 19-27
    • Galzitskaya, O.1    Caflisch, A.2
  • 59
    • 33646165448 scopus 로고    scopus 로고
    • Kinetics and thermodynamics of type VIII beta-turn formation: A CD, NMR, and microsecond explicit molecular dynamics study of the GDNP tetrapeptide
    • Fuchs PF, Bonvin AM, Bochicchio B, Pepe A, Alix AJ, Tamburro AM. Kinetics and thermodynamics of type VIII beta-turn formation: a CD, NMR, and microsecond explicit molecular dynamics study of the GDNP tetrapeptide. Biophys. J. 2006; 90: 2745-2759.
    • (2006) Biophys. J , vol.90 , pp. 2745-2759
    • Fuchs, P.F.1    Bonvin, A.M.2    Bochicchio, B.3    Pepe, A.4    Alix, A.J.5    Tamburro, A.M.6
  • 60
    • 0034635351 scopus 로고    scopus 로고
    • Free energy landscapes of peptides by enhanced conformational sampling
    • Nakajima N, Higo J, Kidera A, Nakamura H. Free energy landscapes of peptides by enhanced conformational sampling. J. Mol. Biol. 2000; 296: 197-216.
    • (2000) J. Mol. Biol , vol.296 , pp. 197-216
    • Nakajima, N.1    Higo, J.2    Kidera, A.3    Nakamura, H.4
  • 61
    • 0031080855 scopus 로고    scopus 로고
    • A pentapeptide model for an early folding step in the refolding of staphylococcal nuclease: The role of its turn propensity
    • Ramakrishna V, Sasidhar YU. A pentapeptide model for an early folding step in the refolding of staphylococcal nuclease: the role of its turn propensity. Biopolymers 1997; 41: 181-191.
    • (1997) Biopolymers , vol.41 , pp. 181-191
    • Ramakrishna, V.1    Sasidhar, Y.U.2


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