메뉴 건너뛰기




Volumn 264, Issue 5, 1996, Pages 1164-1179

How to derive a protein folding potential? A new approach to an old problem

Author keywords

Fold recognition; Protein folding; Protein folding potential

Indexed keywords

PROTEIN;

EID: 0030596063     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0704     Document Type: Article
Times cited : (255)

References (50)
  • 1
    • 36448999595 scopus 로고
    • Free energy landscape for protein folding kinetics, intermediates, traps and multiple pathways in theory and lattice model simulations
    • Abkevich, V. I., Gutin, A. M. & Shakhnovich, E. I. (1994). Free energy landscape for protein folding kinetics, intermediates, traps and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101, 6052-6062.
    • (1994) J. Chem. Phys. , vol.101 , pp. 6052-6062
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 2
    • 0029155772 scopus 로고
    • Impact of local and non-local interactions on thermodynamics and kinetics of protein folding
    • Abkevich, V. I., Gutin, A. M. & Shakhnovich, E. I. (1995). Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J. Mol. Biol. 252, 460-471.
    • (1995) J. Mol. Biol. , vol.252 , pp. 460-471
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 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. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 4
    • 0027318317 scopus 로고
    • An empirical energy function for threading protein sequence through the folding motif
    • Bryant, S. H. & Lawrence, C. E. (1993). An empirical energy function for threading protein sequence through the folding motif. Proteins: Struct. Funct. Genet. 16, 92-112.
    • (1993) Proteins: Struct. Funct. Genet. , vol.16 , pp. 92-112
    • Bryant, S.H.1    Lawrence, C.E.2
  • 5
    • 0000997402 scopus 로고
    • When is a potential accurate enough for structure prediction?
    • Bryngelson, J. D. (1994). When is a potential accurate enough for structure prediction? J. Chem. Phys. 100, 6038-6045.
    • (1994) J. Chem. Phys. , vol.100 , pp. 6038-6045
    • Bryngelson, J.D.1
  • 6
    • 0028049306 scopus 로고
    • Low resolution models of polypeptide chain collapse
    • Covell, D. G. (1994). Low resolution models of polypeptide chain collapse. J. Mol. Biol. 25, 1032-1043.
    • (1994) J. Mol. Biol. , vol.25 , pp. 1032-1043
    • Covell, D.G.1
  • 8
    • 0028072364 scopus 로고
    • Pseudodihedrals: Simplified protein backbone representation with knowledge-based energy
    • De Witte, R. & Shakhnovich, E. (1994). Pseudodihedrals: simplified protein backbone representation with knowledge-based energy. Protein Sci. 3, 1570-1581.
    • (1994) Protein Sci. , vol.3 , pp. 1570-1581
    • DeWitte, R.1    Shakhnovich, E.2
  • 9
    • 0029085037 scopus 로고
    • Local moves: An efficient algorithm for simulation of protein folding
    • Elofson, A. Le Grand, S. & Eisenberg, D. (1995). Local moves: an efficient algorithm for simulation of protein folding. Proteins: Struct. Fund. Genet. 23, 73-82.
    • (1995) Proteins: Struct. Fund. Genet. , vol.23 , pp. 73-82
    • Elofson, A.1    Le Grand, S.2    Eisenberg, D.3
  • 10
    • 0026418178 scopus 로고
    • Search for the most stable folds of protein chains
    • Finkelstein, A. V. & Reva, B. A. (1991). Search for the most stable folds of protein chains. Nature, 351, 497-499.
    • (1991) Nature , vol.351 , pp. 497-499
    • Finkelstein, A.V.1    Reva, B.A.2
  • 11
    • 0027258419 scopus 로고
    • Why are the same protein folds used to perform different functions?
    • Finkelstein, A. V., Gutin, A. M. & Badretdinov, A. Ya. (1993). Why are the same protein folds used to perform different functions? FEBS Letters, 325, 23-28.
    • (1993) FEBS Letters , vol.325 , pp. 23-28
    • Finkelstein, A.V.1    Gutin, A.M.2    Badretdinov, A.Ya.3
  • 13
    • 0028892389 scopus 로고
    • Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets
    • Godzik, A., Kolinski, A. & Skolnick, J. (1995). Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. Protein Sci. 4, 2101-2117.
    • (1995) Protein Sci. , vol.4 , pp. 2101-2117
    • Godzik, A.1    Kolinski, A.2    Skolnick, J.3
  • 16
    • 0029945395 scopus 로고    scopus 로고
    • How optimization of potential function affects protein folding
    • Hao, M. & Scheraga, H. (1996a). How optimization of potential function affects protein folding. Proc. Natl Acad. Sci. USA, 93, 4984-4989.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 4984-4989
    • Hao, M.1    Scheraga, H.2
  • 17
    • 0000829596 scopus 로고    scopus 로고
    • Optimizing potential function for protein folding
    • Hao, M.-H. & Scheraga, H. A. (1996b). Optimizing potential function for protein folding. J. Phys. Chem. 100, 14540-14548.
    • (1996) J. Phys. Chem. , vol.100 , pp. 14540-14548
    • Hao, M.-H.1    Scheraga, H.A.2
  • 18
    • 0028149160 scopus 로고
    • Exploring conformational space with a simple lattice model for protein structure
    • Hinds, D. A. & Levitt, M. (1994). Exploring conformational space with a simple lattice model for protein structure. J. Mol. Biol. 243, 668-682.
    • (1994) J. Mol. Biol. , vol.243 , pp. 668-682
    • Hinds, D.A.1    Levitt, M.2
  • 19
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). A new approach to protein fold recognition. Nature, 358, 86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 20
    • 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. (1994). Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235, 1598-1613.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1598-1613
    • Kocher, J.P.1    Rooman, M.J.2    Wodak, S.J.3
  • 21
    • 0018509337 scopus 로고
    • Empirical torsional potential functions from protein structure data
    • Kolaskar, A. S. & Prashanth, D. (1979). Empirical torsional potential functions from protein structure data. Int. J. Pept. Protein Res. 14, 88-98.
    • (1979) Int. J. Pept. Protein Res. , vol.14 , pp. 88-98
    • Kolaskar, A.S.1    Prashanth, D.2
  • 22
    • 0000778903 scopus 로고
    • A general method for the prediction of three dimensional structure and folding pathway of globular proteins: Application of designed helical proteins
    • Kolinski, A. & Skolnick, J. (1993). A general method for the prediction of three dimensional structure and folding pathway of globular proteins: application of designed helical proteins. J. Chem. Phys. 98, 7420-7433.
    • (1993) J. Chem. Phys. , vol.98 , pp. 7420-7433
    • Kolinski, A.1    Skolnick, J.2
  • 23
    • 0028203492 scopus 로고
    • Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
    • Kolinski, A. & Skolnick, J. (1994). Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins: Struct. Funct. Genet 18, 338-352.
    • (1994) Proteins: Struct. Funct. Genet , vol.18 , pp. 338-352
    • Kolinski, A.1    Skolnick, J.2
  • 25
    • 0017157584 scopus 로고
    • A simplified representation of protein conformation for rapid simulation of protein folding
    • Levitt, M. (1976). A simplified representation of protein conformation for rapid simulation of protein folding. J. Mol. Biol. 104, 59-107.
    • (1976) J. Mol. Biol. , vol.104 , pp. 59-107
    • Levitt, M.1
  • 26
    • 0028818340 scopus 로고
    • Protein structure prediction by threading methods: Evaluation of current techniques
    • Lemer, C., Rooman, M. & Wodak, S. (1995). Protein structure prediction by threading methods: evaluation of current techniques. Proteins: Struct. Funct. Genet. 23, 321-332.
    • (1995) Proteins: Struct. Funct. Genet. , vol.23 , pp. 321-332
    • Lemer, C.1    Rooman, M.2    Wodak, S.3
  • 27
    • 0026785519 scopus 로고
    • Contact potential that recognizes the correct folding of globular proteins
    • Maiorov, V. N. & Grippen, G. M. (1992). Contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol. 227, 876-888.
    • (1992) J. Mol. Biol. , vol.227 , pp. 876-888
    • Maiorov, V.N.1    Grippen, G.M.2
  • 28
    • 0030443368 scopus 로고    scopus 로고
    • Protein fold recognition and dynamics in the space of contact maps
    • In the press
    • Mirny, L. & Domany, E. (1996). Protein fold recognition and dynamics in the space of contact maps. Proteins: Struct. Funct. Genet. In the press.
    • (1996) Proteins: Struct. Funct. Genet.
    • Mirny, L.1    Domany, E.2
  • 29
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa, S. & Jernigan, R. L. (1985). Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules, 18, 534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 30
    • 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. (1996). 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) J. Mol. Biol. , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.2
  • 31
    • 0027504808 scopus 로고
    • Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies
    • Nishikawa, K. & Matsuo, Y. (1993). Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies. Protein Eng. 6, 811-820.
    • (1993) Protein Eng. , vol.6 , pp. 811-820
    • Nishikawa, K.1    Matsuo, Y.2
  • 32
    • 0001222466 scopus 로고
    • How accurate must potentials be for successful modeling of protein folding?
    • Pande, V., Grosberg, A. & Tanaka, T. (1995). How accurate must potentials be for successful modeling of protein folding? J. Chem. Phys. 103, 9482-9491.
    • (1995) J. Chem. Phys. , vol.103 , pp. 9482-9491
    • Pande, V.1    Grosberg, A.2    Tanaka, T.3
  • 33
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near native folds from well-constructed decoys
    • Park, B. & Levitt, M. (1996). Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J. Mol. Biol. 258, 367-392.
    • (1996) J. Mol. Biol. , vol.258 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 34
    • 0026447086 scopus 로고
    • Extracting information on folding from aminoacid sequence: Accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions
    • Rooman, M., Kocher, J. A. & Wodak, S. (1992). Extracting information on folding from aminoacid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochemistry, 32, 10226-10238.
    • (1992) Biochemistry , vol.32 , pp. 10226-10238
    • Rooman, M.1    Kocher, J.A.2    Wodak, S.3
  • 35
    • 0028270634 scopus 로고
    • Kinetics of protein folding. A lattice model study of the requirements for folding to the native state
    • Sali, A. Shakhnovich, E. I. & Karplus, M. (1994a). Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. J. Mol. Biol. 235, 1614-1636.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1614-1636
    • Sali, A.1    Shakhnovich, E.I.2    Karplus, M.3
  • 36
    • 0025809473 scopus 로고
    • Influence of point mutations on protein structure. Probability of a neutral mutation
    • Shakhnovich, E. I. & Gutin, A. M. (1991). Influence of point mutations on protein structure. Probability of a neutral mutation. J. Theoret. Biol. 149, 537-546.
    • (1991) J. Theoret. Biol. , vol.149 , pp. 537-546
    • Shakhnovich, E.I.1    Gutin, A.M.2
  • 38
    • 0027234766 scopus 로고
    • Engineering of stable and fast-folding sequences of model proteins
    • Shakhnovich, E. I. & Gutin, A. M. (1993a). Engineering of stable and fast-folding sequences of model proteins. Proc. Natl Acad. Sci. USA, 90, 7195-7198.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 7195-7198
    • Shakhnovich, E.I.1    Gutin, A.M.2
  • 39
    • 0027438090 scopus 로고
    • A novel approach to design of stable proteins
    • Shakhnovich, E. I. & Gutin, A. M. (1993b). A novel approach to design of stable proteins. Protein Eng. 6, 793-800.
    • (1993) Protein Eng. , vol.6 , pp. 793-800
    • Shakhnovich, E.I.1    Gutin, A.M.2
  • 40
    • 4243392673 scopus 로고
    • Proteins with selected sequences fold to their unique native conformation
    • Shakhnovich, E. I. (1994). Proteins with selected sequences fold to their unique native conformation. Phys. Rev. Letters 72, 3907-3910.
    • (1994) Phys. Rev. Letters , vol.72 , pp. 3907-3910
    • Shakhnovich, E.I.1
  • 41
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl, M. J. (1990). Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213, 859-883.
    • (1990) J. Mol. Biol. , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 42
    • 0025608908 scopus 로고
    • Simulations of the folding of a globular protein
    • Skolnick, J. & Kolinski, A. (1990). Simulations of the folding of a globular protein. Science, 250, 1121-1125.
    • (1990) Science , vol.250 , pp. 1121-1125
    • Skolnick, J.1    Kolinski, A.2
  • 43
    • 0007725036 scopus 로고
    • Folding kinetics of protein-like heteropolymers
    • Socci, N. D. & Onuchic, J. N. (1994). Folding kinetics of protein-like heteropolymers. J. Chem. Phys. 101, 1519-1528.
    • (1994) J. Chem. Phys. , vol.101 , pp. 1519-1528
    • Socci, N.D.1    Onuchic, J.N.2
  • 44
    • 0017021957 scopus 로고
    • Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
    • Tanaka, S. & Scheraga, H. A. (1976). Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules, 9, 945-950.
    • (1976) Macromolecules , vol.9 , pp. 945-950
    • Tanaka, S.1    Scheraga, H.A.2
  • 45
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: How accurate are they?
    • Thomas, P. & Dill, K. (1996). Statistical potentials extracted from protein structures: How accurate are they? J. Mol. Biol. 257, 457-469.
    • (1996) J. Mol. Biol. , vol.257 , pp. 457-469
    • Thomas, P.1    Dill, K.2
  • 46
    • 0017842051 scopus 로고
    • Studies of protein folding, unfolding and fluctuations by computer simulations. II. A three-dimensional lattice model of lysozyme
    • Ueda, Y., Taketomi, H. & Go, N. (1978). Studies of protein folding, unfolding and fluctuations by computer simulations. II. A three-dimensional lattice model of lysozyme. Biopolymers, 17, 1531-1548.
    • (1978) Biopolymers , vol.17 , pp. 1531-1548
    • Ueda, Y.1    Taketomi, H.2    Go, N.3
  • 47
    • 0001290941 scopus 로고
    • Conformational energy calculations on polypeptides and proteins
    • Vasques, M., Nemethy, G. & Scheraga, H. (1994). Conformational energy calculations on polypeptides and proteins. Chem. Rev. 94, 2183-2239.
    • (1994) Chem. Rev. , vol.94 , pp. 2183-2239
    • Vasques, M.1    Nemethy, G.2    Scheraga, H.3
  • 48
    • 0024435638 scopus 로고
    • Computer model to dynamically simulate protein folding: Studies with crambin
    • Wilson, C. & Doniach, S. (1989). Computer model to dynamically simulate protein folding: studies with crambin. Proteins: Struct. Funct. Genet. 6, 193-209.
    • (1989) Proteins: Struct. Funct. Genet. , vol.6 , pp. 193-209
    • Wilson, C.1    Doniach, S.2
  • 49
    • 0027413658 scopus 로고
    • Generating and testing protein folds
    • Wodak, S. & Rooman, M. (1993). Generating and testing protein folds. Curr. Opin. Struct. Biol. 3, 247-259.
    • (1993) Curr. Opin. Struct. Biol. , vol.3 , pp. 247-259
    • Wodak, S.1    Rooman, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.