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Volumn 31, Issue 3, 1998, Pages 299-308

Extracting contact energies from protein structures: A study using a simplified model

Author keywords

Energy landscape; Glass transition; Quasi chemical approximation; Statistical potential; Threading

Indexed keywords

ARTICLE; ENERGY; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; THERMODYNAMICS;

EID: 0032525182     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980515)31:3<299::AID-PROT6>3.0.CO;2-E     Document Type: Article
Times cited : (13)

References (59)
  • 1
    • 0029942661 scopus 로고    scopus 로고
    • Simple empirical potentials derived from structures and their use in protein simulations
    • Jernigan, R.L., Bahar, I. Simple empirical potentials derived from structures and their use in protein simulations. Curr. Opin. Struct. Biol. 6:195-209, 1996.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 195-209
    • Jernigan, R.L.1    Bahar, I.2
  • 2
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • Sippl, M.J. Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5:229-235, 1995.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 3
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie, J.U., Luthy, R., Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164-170, 1991.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 4
    • 0026690571 scopus 로고
    • Anew approach to protein fold recognition
    • Jones, D.T., Taylor, W.R., Thornton, J.M. Anew approach to protein fold recognition. Nature 358:86-89, 1992.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 5
    • 0026726481 scopus 로고
    • Topology fingerprint approach to the inverse folding problems
    • Godzik, A., Kolinski, A., Skolnick, J. Topology fingerprint approach to the inverse folding problems. J. Mol. Biol. 227:227-238, 1992.
    • (1992) J. Mol. Biol. , vol.227 , pp. 227-238
    • Godzik, A.1    Kolinski, A.2    Skolnick, J.3
  • 6
    • 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. 227:876-888, 1992.
    • (1992) J. Mol. Biol. , vol.227 , pp. 876-888
    • Maiorov, V.N.1    Crippen, G.M.2
  • 8
    • 0027318317 scopus 로고
    • An empirical energy function for threading protein sequence through the folding motif
    • Bryant, S.H., Lawrence, C.E. An empirical energy function for threading protein sequence through the folding motif. Proteins 16:92-112, 1993.
    • (1993) Proteins , vol.16 , pp. 92-112
    • Bryant, S.H.1    Lawrence, C.E.2
  • 10
    • 0028318094 scopus 로고
    • Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
    • Kocher, J.P., Rooman, M.J., Wodak, S.J. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235:1598-1613, 1994.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1598-1613
    • Kocher, J.P.1    Rooman, M.J.2    Wodak, S.J.3
  • 11
    • 0029912991 scopus 로고    scopus 로고
    • Global optimum protein threading with gapped alignment and empirical pair score functions
    • Lathrop, R.H., Smith, T.F. Global optimum protein threading with gapped alignment and empirical pair score functions. J. Mol. Biol. 255:641-665, 1996.
    • (1996) J. Mol. Biol. , vol.255 , pp. 641-665
    • Lathrop, R.H.1    Smith, T.F.2
  • 12
    • 0030067191 scopus 로고    scopus 로고
    • Assigning amino acid sequences to 3-dimensional protein folds
    • Fischer, D., Rice, D., Bowie, J.U., Eisenberg, D. Assigning amino acid sequences to 3-dimensional protein folds. FASEB J. 10:126-136, 1996
    • (1996) FASEB J. , vol.10 , pp. 126-136
    • Fischer, D.1    Rice, D.2    Bowie, J.U.3    Eisenberg, D.4
  • 13
    • 0025319917 scopus 로고
    • Conformations of folded proteins in restricted spaces
    • Covell, D.G., Jernigan, R.L. Conformations of folded proteins in restricted spaces. Biochemistry 29:3287-3294, 1990.
    • (1990) Biochemistry , vol.29 , pp. 3287-3294
    • Covell, D.G.1    Jernigan, R.L.2
  • 14
    • 0027503403 scopus 로고
    • Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms
    • Sun, S. Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms. Protein Sci. 2:762-785, 1993.
    • (1993) Protein Sci. , vol.2 , pp. 762-785
    • Sun, S.1
  • 15
    • 0027245418 scopus 로고
    • Genetic algorithms for protein folding simulations
    • Unger, R., Moult, J. Genetic algorithms for protein folding simulations. J. Mol. Biol. 231:75-81, 1993.
    • (1993) J. Mol. Biol. , vol.231 , pp. 75-81
    • Unger, R.1    Moult, J.2
  • 16
    • 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
  • 17
    • 0028149160 scopus 로고
    • Exploring conformational space with a simple lattice model for protein structure
    • Hinds, D.A., Levitt, M.A. Exploring conformational space with a simple lattice model for protein structure. J. Mol. Biol. 243:668-682, 1994.
    • (1994) J. Mol. Biol. , vol.243 , pp. 668-682
    • Hinds, D.A.1    Levitt, M.A.2
  • 18
    • 0028897718 scopus 로고
    • Computer modeling of protein folding: Conformational and energetic analysis
    • Monge, A., Lathrop, E.J.P., Gunn, J.R., Shenkin, P.S., Friesner, R.A. Computer modeling of protein folding: Conformational and energetic analysis. J. Mol. Biol. 247:995-1012, 1995.
    • (1995) J. Mol. Biol. , vol.247 , pp. 995-1012
    • Monge, A.1    Lathrop, E.J.P.2    Gunn, J.R.3    Shenkin, P.S.4    Friesner, R.A.5
  • 19
    • 0030023960 scopus 로고    scopus 로고
    • Protein folding by a biased Monte Carlo procedure in the dihedral angle space
    • Lee, B., Kurochkina, N., Kang, H.S. Protein folding by a biased Monte Carlo procedure in the dihedral angle space. FASEB J. 10:119-125, 1996.
    • (1996) FASEB J. , vol.10 , pp. 119-125
    • Lee, B.1    Kurochkina, N.2    Kang, H.S.3
  • 20
    • 0029987862 scopus 로고
    • Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
    • Park, B.H., Levitt, M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J. Mol. Biol. 258:367-392, 1906.
    • (1906) J. Mol. Biol. , vol.258 , pp. 367-392
    • Park, B.H.1    Levitt, M.2
  • 21
    • 33845377127 scopus 로고
    • Estimation of effective inter-residue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa, S., Jernigan, R.L. Estimation of effective inter-residue 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
  • 22
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa, S., Jernigan, R.L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol, 256:623-644, 1996
    • (1996) J. Mol. Biol , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 23
    • 0028075953 scopus 로고
    • Protein stability for single substitution mutants and extent of local compactness in the denatured state
    • Miyazawa, S., Jernigan, R.L. Protein stability for single substitution mutants and extent of local compactness in the denatured state. Protein Eng. 7:1209-1220, 1994.
    • (1994) Protein Eng. , vol.7 , pp. 1209-1220
    • Miyazawa, S.1    Jernigan, R.L.2
  • 24
    • 0028332007 scopus 로고
    • A role for surface hydrophobicity in protein-protein recognition
    • Young, L., Jernigan, R.L., Covell, D.G. A role for surface hydrophobicity in protein-protein recognition. Protein Sci. 3:717-729, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 717-729
    • Young, L.1    Jernigan, R.L.2    Covell, D.G.3
  • 25
    • 0031552370 scopus 로고    scopus 로고
    • Determination of atomic desolvation energies from the structures of crystallized proteins
    • Zhang, C., Vasmatzis, G., Cornette, J.L., DeLisi, C. Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol. 267:707-726, 1997.
    • (1997) J. Mol. Biol. , vol.267 , pp. 707-726
    • Zhang, C.1    Vasmatzis, G.2    Cornette, J.L.3    DeLisi, C.4
  • 26
    • 0030945036 scopus 로고    scopus 로고
    • Consistency in the structural energetics of protein folding and peptide recognition
    • Zhang, C., Cornette, J.L., DeLisi, C. Consistency in the structural energetics of protein folding and peptide recognition. Protein Sci. 6:1057-1064, 1997.
    • (1997) Protein Sci. , vol.6 , pp. 1057-1064
    • Zhang, C.1    Cornette, J.L.2    DeLisi, C.3
  • 27
    • 0030292235 scopus 로고    scopus 로고
    • Computational determination of side chain specificity of pockets in class I MHC molecules
    • Vasmatzis, G., Zhang, C., Cornette, J.L., DeLisi, C. Computational determination of side chain specificity of pockets in class I MHC molecules. Mol. Immunol. 33:1231-1239, 1996.
    • (1996) Mol. Immunol. , vol.33 , pp. 1231-1239
    • Vasmatzis, G.1    Zhang, C.2    Cornette, J.L.3    DeLisi, C.4
  • 28
    • 0028801308 scopus 로고
    • Why do protein architectures have Boltzmann-like statistics?
    • Finkelstein, A.V., Badretdinov, A.Y., Gutin, A.M. Why do protein architectures have Boltzmann-like statistics? Proteins 23:142-150, 1995.
    • (1995) Proteins , vol.23 , pp. 142-150
    • Finkelstein, A.V.1    Badretdinov, A.Y.2    Gutin, A.M.3
  • 29
    • 0030983768 scopus 로고    scopus 로고
    • Derivation and testing of pair potentials for protein folding. When is the quasi-chemical approximation correct?
    • Skolnick, J., Jaroszewski, L., Kolinski, A., Godzik, A. Derivation and testing of pair potentials for protein folding. When is the quasi-chemical approximation correct? Protein Sci. 6:676-688, 1997.
    • (1997) Protein Sci. , vol.6 , pp. 676-688
    • Skolnick, J.1    Jaroszewski, L.2    Kolinski, A.3    Godzik, A.4
  • 30
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: How accurate are they?
    • Thomas, P.D., Dill, K.A. Statistical potentials extracted from protein structures: How accurate are they? J. Mol. Biol. 257:457-469, 1996.
    • (1996) J. Mol. Biol. , vol.257 , pp. 457-469
    • Thomas, P.D.1    Dill, K.A.2
  • 31
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • Bahar, I., Jernigan, R.L. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266:195-214, 1997.
    • (1997) J. Mol. Biol. , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2
  • 32
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: A synthesis
    • Bryngelson, J.D., Onuchic, J.N., Socci, N.D., Wolynes, P.G. Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins 21:167-195, 1995.
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 33
    • 0029249945 scopus 로고
    • The nature of protein folding pathways: The classical versus the new view
    • Baldwin, R.L. The nature of protein folding pathways: The classical versus the new view. J. Biomol. NMR 5:103-109, 1995.
    • (1995) J. Biomol. NMR , vol.5 , pp. 103-109
    • Baldwin, R.L.1
  • 36
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill, K.A., Chan, H.S. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4:10-19, 1997.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 38
    • 33744825406 scopus 로고
    • 'Sequence space soup' of proteins and copolymers
    • Chan, H.S., Dill, K.A. 'Sequence space soup' of proteins and copolymers. J. Chem. Phys. 95:3775-3787, 1991.
    • (1991) J. Chem. Phys. , vol.95 , pp. 3775-3787
    • Chan, H.S.1    Dill, K.A.2
  • 39
    • 0024733407 scopus 로고
    • Intermediates and barrier crossing in a random energy model (with applications to protein folding)
    • Bryngelson, J.D., Wolynes, P.G. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93:6902-6915, 1989.
    • (1989) J. Phys. Chem. , vol.93 , pp. 6902-6915
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 40
    • 0026723063 scopus 로고
    • Protein folding funnels: A kinetic approach to the sequence-structure relationship
    • Leopold, P.E., Montai, M., Onuchic, J.N. Protein folding funnels: A kinetic approach to the sequence-structure relationship. Proc. Natl: Acad. Sci. USA 89:8721-8725, 1992.
    • (1992) Proc. Natl: Acad. Sci. USA , vol.89 , pp. 8721-8725
    • Leopold, P.E.1    Montai, M.2    Onuchic, J.N.3
  • 42
    • 0027318781 scopus 로고
    • Kinetics and thermodynamics of folding in model proteins
    • Camacho, C.J., Thirumalai, D. Kinetics and thermodynamics of folding in model proteins. Proc. Natl. Acad. Sci. USA 90:6369-6372, 1993.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 6369-6372
    • Camacho, C.J.1    Thirumalai, D.2
  • 44
    • 36449000646 scopus 로고
    • Transition states and folding dynamics of proteins and heteropolymers
    • Chan, H.S., Dill, K.A. Transition states and folding dynamics of proteins and heteropolymers. J. Chem. Phys. 100: 9238-9257, 1994.
    • (1994) J. Chem. Phys. , vol.100 , pp. 9238-9257
    • Chan, H.S.1    Dill, K.A.2
  • 45
    • 0030443105 scopus 로고    scopus 로고
    • Factors governing the foldability of proteins
    • Klimov, D.K., Thirumalai, D. Factors governing the foldability of proteins. Proteins 26:411-441, 1996.
    • (1996) Proteins , vol.26 , pp. 411-441
    • Klimov, D.K.1    Thirumalai, D.2
  • 46
    • 0007725036 scopus 로고
    • Folding kinetics of protein-like heteropolymers
    • Socci, N.D., Onuchic, J.N. Folding kinetics of protein-like heteropolymers. J. Chem. Phys. 101:1519-1528, 1994.
    • (1994) J. Chem. Phys. , vol.101 , pp. 1519-1528
    • Socci, N.D.1    Onuchic, J.N.2
  • 47
    • 0001538320 scopus 로고
    • Kinetics of protein-like models: The energy landscape factors that determine folding
    • Betancourt, M.R., Onuchic, J.N. Kinetics of protein-like models: The energy landscape factors that determine folding. J. Chem. Phys. 103:773-787, 1995.
    • (1995) J. Chem. Phys. , vol.103 , pp. 773-787
    • Betancourt, M.R.1    Onuchic, J.N.2
  • 48
    • 4243861085 scopus 로고
    • Random energy model: An exactly solvable model of disordered systems
    • Derrida, B. Random energy model: An exactly solvable model of disordered systems. Phys. Rev. 24:2613-2624, 1981.
    • (1981) Phys. Rev. , vol.24 , pp. 2613-2624
    • Derrida, B.1
  • 49
    • 0028929556 scopus 로고
    • Principles of protein folding: A perspective from simple exact models
    • Dill, K.A., Bromberg, S., Yue, K., et al. Principles of protein folding: A perspective from simple exact models. Protein Sci. 4:561-602, 1995.
    • (1995) Protein Sci. , vol.4 , pp. 561-602
    • Dill, K.A.1    Bromberg, S.2    Yue, K.3
  • 50
    • 0029909384 scopus 로고    scopus 로고
    • An iterative method for extracting energy-like quantities from protein structures
    • Thomas, P.D., Dill, K.A. An iterative method for extracting energy-like quantities from protein structures. Proc. Natl. Acad. Sci. USA 93:11628-11633, 1996.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 11628-11633
    • Thomas, P.D.1    Dill, K.A.2
  • 51
    • 0030596063 scopus 로고    scopus 로고
    • How to derive a protein folding potential? A new approach to an old problem
    • Mirny, L.A., Shakhnovich, E.I. How to derive a protein folding potential? A new approach to an old problem. J. Mol. Biol. 264:1164-1179, 1996.
    • (1996) J. Mol. Biol. , vol.264 , pp. 1164-1179
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 53
    • 0017157584 scopus 로고
    • A simplified representation of protein conformation for rapid simulation of protein folding
    • Levitt, M. A simplified representation of protein conformation for rapid simulation of protein folding. J. Mol. Biol. 104:59-107, 1976.
    • (1976) J. Mol. Biol. , vol.104 , pp. 59-107
    • Levitt, M.1
  • 54
    • 0022423920 scopus 로고
    • Theory for the folding and stability of globular proteins
    • Dill, K.A. Theory for the folding and stability of globular proteins. Biochemistry 24:1501-1509, 1985.
    • (1985) Biochemistry , vol.24 , pp. 1501-1509
    • Dill, K.A.1
  • 55
    • 0023449962 scopus 로고
    • Spin glasses and the statistical mechanics of protein folding
    • Bryngelson, J.D., Wolynes, P.G. Spin glasses and the statistical mechanics of protein folding. Proc. Natl. Acad. Sci. USA 84:7524-7528, 1987.
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 7524-7528
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 56
    • 0029772552 scopus 로고    scopus 로고
    • Emergence of preferred structures in a simple model of protein folding
    • Li, H., Helling, R., Tang, C., Wingreen, N. Emergence of preferred structures in a simple model of protein folding. Science 273:666-669, 1996.
    • (1996) Science , vol.273 , pp. 666-669
    • Li, H.1    Helling, R.2    Tang, C.3    Wingreen, N.4
  • 57
    • 0028949547 scopus 로고
    • Theoretical studies of protein folding and unfolding
    • Karplus, M., Sali, A. Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5:58-73, 1995.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 58-73
    • Karplus, M.1    Sali, A.2
  • 58
    • 0029028698 scopus 로고
    • Modeling the role of disulfide bonds in protein folding: Entropie barriers and pathways
    • Camacho, C.J., Thirumalai, D. Modeling the role of disulfide bonds in protein folding: Entropie barriers and pathways. Proteins 22:27-40, 1995.
    • (1995) Proteins , vol.22 , pp. 27-40
    • Camacho, C.J.1    Thirumalai, D.2
  • 59
    • 6144238579 scopus 로고    scopus 로고
    • Entropie barriers, frustration, and order: Basic ingredients in protein folding
    • Camacho, C.J. Entropie barriers, frustration, and order: Basic ingredients in protein folding. Phys. Rev. Lett. 77: 2324-2327, 1996.
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 2324-2327
    • Camacho, C.J.1


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