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Volumn 28, Issue 3, 1997, Pages 344-359

Predicting helical segments in proteins by a helix-coil transition theory with parameters derived from a structural database of proteins

Author keywords

Helical boundaries; Helix stabilizing destabilizing interactions; Helix capping motifs; Structure prediction

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; DATA BASE; PRIORITY JOURNAL; PROTEIN CONFORMATION; STRUCTURE ANALYSIS;

EID: 0030926905     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199707)28:3<344::AID-PROT5>3.0.CO;2-C     Document Type: Article
Times cited : (12)

References (48)
  • 1
    • 0018110116 scopus 로고
    • Prediction of the secondary structure of proteins from their amino acid sequence
    • Chou, P.Y., Fasman, G.D. Prediction of the secondary structure of proteins from their amino acid sequence. Adv. Enzymol. 47:45-148, 1978.
    • (1978) Adv. Enzymol. , vol.47 , pp. 45-148
    • Chou, P.Y.1    Fasman, G.D.2
  • 3
    • 0023555768 scopus 로고
    • Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs
    • Gibrat, J.F., Garnier, J., Robson, B. Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J. Mol. Biol. 198:425-443, 1987.
    • (1987) J. Mol. Biol. , vol.198 , pp. 425-443
    • Gibrat, J.F.1    Garnier, J.2    Robson, B.3
  • 4
    • 0025881751 scopus 로고
    • Influence of the local amino acid sequence upon the zones of the torsional angles φ and ψ adopted by residues in proteins
    • Gibrat, J.F., Robson, B., Garnier, J. Influence of the local amino acid sequence upon the zones of the torsional angles φ and ψ adopted by residues in proteins. Biochemistry 230:1578-1586, 1991.
    • (1991) Biochemistry , vol.230 , pp. 1578-1586
    • Gibrat, J.F.1    Robson, B.2    Garnier, J.3
  • 5
    • 0025964419 scopus 로고
    • An extension of secondary structure prediction towards the prediction of the tertiary structure
    • Garratt, R.C., Thornton, J.M., Taylor, W.R. An extension of secondary structure prediction towards the prediction of the tertiary structure. FEBS Lett. 280:141-146, 1991.
    • (1991) FEBS Lett. , vol.280 , pp. 141-146
    • Garratt, R.C.1    Thornton, J.M.2    Taylor, W.R.3
  • 6
    • 0025334980 scopus 로고
    • Improvements in protein secondary structure prediction by an enhanced neural network
    • Kneller, D.G., Cohen, F.E., Langridge, R. Improvements in protein secondary structure prediction by an enhanced neural network. J. Mol. Biol. 214:171-182, 1990.
    • (1990) J. Mol. Biol. , vol.214 , pp. 171-182
    • Kneller, D.G.1    Cohen, F.E.2    Langridge, R.3
  • 7
    • 0025633838 scopus 로고
    • A machine learning approach for the prediction of protein secondary structure
    • King, R.D., Sternberg, M.J.E. A machine learning approach for the prediction of protein secondary structure. J. Mol. Biol. 216:441-457, 1990.
    • (1990) J. Mol. Biol. , vol.216 , pp. 441-457
    • King, R.D.1    Sternberg, M.J.E.2
  • 8
    • 0024078021 scopus 로고
    • Predictive sequence motifs limited by protein structure data base size
    • Rooman, M.J., Wodak, S.J. Predictive sequence motifs limited by protein structure data base size. Nature 335:45-49, 1988.
    • (1988) Nature , vol.335 , pp. 45-49
    • Rooman, M.J.1    Wodak, S.J.2
  • 9
    • 0028300741 scopus 로고
    • Combining evolutionary information and neural networks to predict protein secondary structure
    • Rost, B., Sander, C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19:55-72, 1994.
    • (1994) Proteins , vol.19 , pp. 55-72
    • Rost, B.1    Sander, C.2
  • 10
    • 0242677236 scopus 로고
    • Systematic sensitivity analyses in free energy perturbation calculations
    • Wong, C.F. Systematic sensitivity analyses in free energy perturbation calculations. J. Am. Chem. Soc. 113:3208-3209, 1991.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 3208-3209
    • Wong, C.F.1
  • 11
    • 0038369507 scopus 로고
    • Sensitivity Analysis and Principal Component Analysis in Free Energy Calculations
    • Wong, C.F., Rabitz, H. Sensitivity Analysis and Principal Component Analysis in Free Energy Calculations. J. Phys. Chem. 95:9628-9630, 1991.
    • (1991) J. Phys. Chem. , vol.95 , pp. 9628-9630
    • Wong, C.F.1    Rabitz, H.2
  • 12
    • 36449008867 scopus 로고
    • Sensitivity analysis of water thermodynamics
    • Zhu S.-B., Wong, C.F. Sensitivity analysis of water thermodynamics. J. Chem. Phys. 98:8892-8899, 1993.
    • (1993) J. Chem. Phys. , vol.98 , pp. 8892-8899
    • Zhu, S.-B.1    Wong, C.F.2
  • 13
    • 0000315458 scopus 로고
    • Sensitivity analysis of distribution functions of liquid water
    • Zhu S.-B., Wong, C.F. Sensitivity analysis of distribution functions of liquid water. J. Chem. Phys. 99:9047-9053, 1993.
    • (1993) J. Chem. Phys. , vol.99 , pp. 9047-9053
    • Zhu, S.-B.1    Wong, C.F.2
  • 14
    • 0000471729 scopus 로고
    • Sensitivity analysis of a polariszable water model
    • Zhu, S.-B., Wong, C.F. Sensitivity analysis of a polariszable water model. J. Phys. Chem. 98:4695-4701, 1994.
    • (1994) J. Phys. Chem. , vol.98 , pp. 4695-4701
    • Zhu, S.-B.1    Wong, C.F.2
  • 15
    • 0028786896 scopus 로고
    • Parametric sensitivity analysis of avian pancreatic polypeptide (APP)
    • Zhang, H., Wong, C.F., Thacher, T., Rabitz, H. Parametric sensitivity analysis of avian pancreatic polypeptide (APP). Proteins 23:218-232, 1995.
    • (1995) Proteins , vol.23 , pp. 218-232
    • Zhang, H.1    Wong, C.F.2    Thacher, T.3    Rabitz, H.4
  • 17
    • 0027204024 scopus 로고
    • Helix stop signals in proteins and peptides: The capping box
    • Harper, E.T., Rose, G.D. Helix stop signals in proteins and peptides: The capping box. Biochemistry 32:7605-7609, 1993.
    • (1993) Biochemistry , vol.32 , pp. 7605-7609
    • Harper, E.T.1    Rose, G.D.2
  • 18
    • 0027986703 scopus 로고
    • Sequence determinants of the capping box, a stabilizing motif at the N-termini of α-helices
    • Seale, J.W., Srinivasan, R., Rose, G.D. Sequence determinants of the capping box, a stabilizing motif at the N-termini of α-helices. Protein Sci. 3:1741-1745, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 1741-1745
    • Seale, J.W.1    Srinivasan, R.2    Rose, G.D.3
  • 19
    • 0028173780 scopus 로고
    • Rules for α-helix termination by glycine
    • Aurora, R., Srinivasan, R., Rose, G.D. Rules for α-helix termination by glycine. Science 264:1126-1130, 1994.
    • (1994) Science , vol.264 , pp. 1126-1130
    • Aurora, R.1    Srinivasan, R.2    Rose, G.D.3
  • 20
    • 0000668407 scopus 로고
    • Theory of the phase transition between helix and random coil
    • Zimm, B.H., Bragg, J.K. Theory of the phase transition between helix and random coil. J. Chem. Phys. 31:526-535, 1959.
    • (1959) J. Chem. Phys. , vol.31 , pp. 526-535
    • Zimm, B.H.1    Bragg, J.K.2
  • 21
    • 0000333671 scopus 로고
    • On the theory of helix-coil transition in polypeptides
    • Lifson, S., Roig, A. On the theory of helix-coil transition in polypeptides. J. Chem. Phys. 34:1963-1974, 1961.
    • (1961) J. Chem. Phys. , vol.34 , pp. 1963-1974
    • Lifson, S.1    Roig, A.2
  • 22
    • 0026253633 scopus 로고
    • The helix-coil transition in heterogeneous peptides with specific side-chain interactions: Theory and comparison with CD spectral data
    • Gans, P.J., Lyu, P.C., Manning, M.C., Woody, R.W., Kallenbach, N.R. The helix-coil transition in heterogeneous peptides with specific side-chain interactions: Theory and comparison with CD spectral data. Biopolymers 31:1605-1614, 1991.
    • (1991) Biopolymers , vol.31 , pp. 1605-1614
    • Gans, P.J.1    Lyu, P.C.2    Manning, M.C.3    Woody, R.W.4    Kallenbach, N.R.5
  • 23
    • 0028289435 scopus 로고
    • Determination of free energies of N-capping in α-helices by modification of the Lifson-Roig helix-coil theory to include N- and C-capping
    • Doig, A.J., Chakrabartty, A., Klingler, T.M., Baldwin, R.L. Determination of free energies of N-capping in α-helices by modification of the Lifson-Roig helix-coil theory to include N-and C-capping. Biochemistry 33:3396-3403, 1994.
    • (1994) Biochemistry , vol.33 , pp. 3396-3403
    • Doig, A.J.1    Chakrabartty, A.2    Klingler, T.M.3    Baldwin, R.L.4
  • 24
    • 0028222235 scopus 로고
    • Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
    • Chakrabartty, A., Kortemme, T., Baldwin, R.L. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 3:843-852, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 843-852
    • Chakrabartty, A.1    Kortemme, T.2    Baldwin, R.L.3
  • 25
    • 0028447768 scopus 로고
    • Elucidating the folding problem of helical peptides using empirical parameters
    • Muñoz, V., Serrano, L. Elucidating the folding problem of helical peptides using empirical parameters. Struct. Biol. 1:399-409, 1994.
    • (1994) Struct. Biol. , vol.1 , pp. 399-409
    • Muñoz, V.1    Serrano, L.2
  • 26
    • 0028873081 scopus 로고
    • Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides
    • Muñoz, V., Serrano, L. Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides. J. Mol. Biol. 245:275-296, 1995.
    • (1995) J. Mol. Biol. , vol.245 , pp. 275-296
    • Muñoz, V.1    Serrano, L.2
  • 27
    • 0028929583 scopus 로고
    • Free energy balance in protein folding
    • Honig, B., Yang, A.S. Free energy balance in protein folding. Adv. Protein Chem. 46:27-58, 1995.
    • (1995) Adv. Protein Chem. , vol.46 , pp. 27-58
    • Honig, B.1    Yang, A.S.2
  • 28
    • 0027141511 scopus 로고
    • A structure refinement method based on molecular dynamics in four spatial dimensions
    • van Schaik, R.C., Berendsen, H.J.C., Torda, A.E., van Gunsteren, W.F. A structure refinement method based on molecular dynamics in four spatial dimensions. J. Mol. Biol. 234:751-762, 1993.
    • (1993) J. Mol. Biol. , vol.234 , pp. 751-762
    • Van Schaik, R.C.1    Berendsen, H.J.C.2    Torda, A.E.3    Van Gunsteren, W.F.4
  • 29
    • 0028203492 scopus 로고
    • Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
    • Kolinski, A., Skolnick, J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18:338-352, 1994.
    • (1994) Proteins , vol.18 , pp. 338-352
    • Kolinski, A.1    Skolnick, J.2
  • 30
    • 0028326042 scopus 로고
    • Monte Carlo simulations of protein folding II. Application to protein A, ROP and crambin
    • Kolinski, A., Skolnick, J. Monte Carlo simulations of protein folding II. Application to protein A, ROP and crambin. Proteins 18:353-366, 1994.
    • (1994) Proteins , vol.18 , pp. 353-366
    • Kolinski, A.1    Skolnick, J.2
  • 31
    • 0028290433 scopus 로고
    • Prediction of the folding pathways and structure of the GCN4 leucine zipper
    • Vieth, M., Kolinski, A., Brooks III, C.L.B., Skolnick, J. Prediction of the folding pathways and structure of the GCN4 leucine zipper. J. Mol. Biol. 237:361-367, 1994.
    • (1994) J. Mol. Biol. , vol.237 , pp. 361-367
    • Vieth, M.1    Kolinski, A.2    Brooks III, C.L.B.3    Skolnick, J.4
  • 32
    • 0028892389 scopus 로고
    • Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets
    • Godzik, A., Kolinski, A., Skolnick, J. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. Protein Sci. 4:2107-2117, 1995.
    • (1995) Protein Sci. , vol.4 , pp. 2107-2117
    • Godzik, A.1    Kolinski, A.2    Skolnick, J.3
  • 33
    • 0017021957 scopus 로고
    • Medium- and long-range interaction parameters between aminoac acids for predicting three-dimensional structures of proteins
    • Tanaka, S., Scheraga, H.A. Medium-and long-range interaction parameters between aminoac acids for predicting three-dimensional structures of proteins. Macromolecules 9:945-950, 1976.
    • (1976) Macromolecules , vol.9 , pp. 945-950
    • Tanaka, S.1    Scheraga, H.A.2
  • 34
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa, S., Jernigan, R.L. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18:534-552, 1985.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 35
    • 0026785519 scopus 로고
    • Contact potential that recognizes the correct folding of globular proteins
    • Maiorov, V.N., Crippen, G.M. Contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol. 277:876-888, 1992.
    • (1992) J. Mol. Biol. , vol.277 , pp. 876-888
    • Maiorov, V.N.1    Crippen, G.M.2
  • 36
    • 0026519315 scopus 로고
    • A lattice model for protein structure prediction at low resolution
    • Hinds, D.A., Levitt, M. A lattice model for protein structure prediction at low resolution. Proc. Natl. Acad. Sci. U.S.A. 89:2536-2540, 1992.
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 2536-2540
    • Hinds, D.A.1    Levitt, M.2
  • 39
    • 0028849248 scopus 로고
    • A molecular mechanics/continuum reaction field investigation of the interactions between polar amino acid side chains in water and in organic solvents
    • Langlet, J., Gresh, N., Giessner-Prettre, C. A molecular mechanics/continuum reaction field investigation of the interactions between polar amino acid side chains in water and in organic solvents. Biopolymers 36:765-780, 1995.
    • (1995) Biopolymers , vol.36 , pp. 765-780
    • Langlet, J.1    Gresh, N.2    Giessner-Prettre, C.3
  • 40
    • 0000103283 scopus 로고
    • Monte Carlo simulations on the like-charged guanidinium-guanidinium ion pair in water
    • Boudon, S., Wipff, G., Maigret, B. Monte Carlo simulations on the like-charged guanidinium-guanidinium ion pair in water. J. Phys. Chem. 94:6056-6061, 1990.
    • (1990) J. Phys. Chem. , vol.94 , pp. 6056-6061
    • Boudon, S.1    Wipff, G.2    Maigret, B.3
  • 41
    • 1842404385 scopus 로고
    • On the correlation between like ions in water
    • Dang, L.X., Pettitt, B.M., Rossky, P. On the correlation between like ions in water. J. Chem. Phys. 96:1333-1342, 1992.
    • (1992) J. Chem. Phys. , vol.96 , pp. 1333-1342
    • Dang, L.X.1    Pettitt, B.M.2    Rossky, P.3
  • 42
    • 0027391780 scopus 로고
    • Capping interactions in isolated alpha helices: Position-dependent substitution effects and structure of a serine-capped peptide helix
    • Lyu, P.C., Wemmer, D.E., Zhou, H.X., Pinker, R.J., Kallenbach, N.R. Capping interactions in isolated alpha helices: Position-dependent substitution effects and structure of a serine-capped peptide helix. Biochemistry 32:421-425, 1993.
    • (1993) Biochemistry , vol.32 , pp. 421-425
    • Lyu, P.C.1    Wemmer, D.E.2    Zhou, H.X.3    Pinker, R.J.4    Kallenbach, N.R.5
  • 43
    • 0028036221 scopus 로고
    • Alpha helix capping in synthetic model peptides by reciprocal side chain-main chain interactions: Evidence for an N terminal "capping box."
    • Zhou, H.X., Lyu, P., Wemmer, D.E., Kallenbach, N.R.Alpha helix capping in synthetic model peptides by reciprocal side chain-main chain interactions: Evidence for an N terminal "capping box." Proteins 18:1-7, 1994.
    • (1994) Proteins , vol.18 , pp. 1-7
    • Zhou, H.X.1    Lyu, P.2    Wemmer, D.E.3    Kallenbach, N.R.4
  • 44
    • 0027980822 scopus 로고
    • Contribution to global protein stabilization of the N-capping box in human growth hormone
    • Zhukovsky, E.A., Mulkerrin, M.G., Presta, L.G. Contribution to global protein stabilization of the N-capping box in human growth hormone. Biochemistry 33:9856-9864, 1994.
    • (1994) Biochemistry , vol.33 , pp. 9856-9864
    • Zhukovsky, E.A.1    Mulkerrin, M.G.2    Presta, L.G.3
  • 45
    • 0029009067 scopus 로고
    • The hydrophobic-staple motif and a role for loop-residues in α-helix stability and protein folding
    • Munoz, V., Blanco, F.J., Serrano, L. The hydrophobic-staple motif and a role for loop-residues in α-helix stability and protein folding. Nature Struct. Biol. 2:380-385, 1995.
    • (1995) Nature Struct. Biol. , vol.2 , pp. 380-385
    • Munoz, V.1    Blanco, F.J.2    Serrano, L.3
  • 46
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the end of α-helices
    • Richardson, J.S., Richardson, D.C. Amino acid preferences for specific locations at the end of α-helices. Science 240: 1648-1652, 1988.
    • (1988) Science , vol.240 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 47
    • 0242677229 scopus 로고
    • Sensitivity analysis of a 2-dimensional lattice model of protein folding
    • Bleil, R.E., Wong, C.F., Rabitz, H. Sensitivity analysis of a 2-dimensional lattice model of protein folding. J. Phys. Chem. 99:3379-3386, 1995.
    • (1995) J. Phys. Chem. , vol.99 , pp. 3379-3386
    • Bleil, R.E.1    Wong, C.F.2    Rabitz, H.3
  • 48
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews, B.W. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta. 304:442-451, 1975.
    • (1975) Biochim. Biophys. Acta , vol.304 , pp. 442-451
    • Matthews, B.W.1


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