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Volumn 100, Issue 3, 2011, Pages 693-700

Accounting for protein-solvent contacts facilitates design of nonaggregating lattice proteins

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EID: 79551662403     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.11.088     Document Type: Article
Times cited : (22)

References (39)
  • 1
    • 0027191901 scopus 로고
    • A new substitution matrix for protein sequence searches based on contact frequencies in protein structures
    • Miyazawa, S., and R. L. Jernigan. 1993. A new substitution matrix for protein sequence searches based on contact frequencies in protein structures. Protein Eng. 6:267-278.
    • (1993) Protein Eng. , vol.6 , pp. 267-278
    • Miyazawa, S.1    Jernigan, R.L.2
  • 2
    • 0028270634 scopus 로고
    • Kinetics of protein folding: A lattice model study of the requirements for folding to the native state
    • Sali, A., E. Shakhnovich, and M. Karplus. 1994. Kinetics of protein folding: a lattice model study of the requirements for folding to the native state. J. Mol. Biol. 235:1614-1638.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1614-1638
    • Sali, A.1    Shakhnovich, E.2    Karplus, M.3
  • 3
    • 4243392673 scopus 로고
    • Proteins with selected sequences fold into unique native conformation
    • Shakhnovich, E. I. 1994. Proteins with selected sequences fold into unique native conformation. Phys. Rev. Lett. 72:3907-3910.
    • (1994) Phys. Rev. Lett. , vol.72 , pp. 3907-3910
    • Shakhnovich, E.I.1
  • 5
    • 0033582587 scopus 로고    scopus 로고
    • Thermodynamics of model prions and its implications for the problem of prion protein folding
    • Harrison, P. M., H. S. Chan, F. E. Cohen. 1999. Thermodynamics of model prions and its implications for the problem of prion protein folding. J. Mol. Biol. 286:593-606.
    • (1999) J. Mol. Biol. , vol.286 , pp. 593-606
    • Harrison, P.M.1    Chan, H.S.2    Cohen, F.E.3
  • 6
    • 0036228167 scopus 로고    scopus 로고
    • Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics
    • Dima, R. I., and D. Thirumalai. 2002. Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Protein Sci. 11:1036-1049.
    • (2002) Protein Sci. , vol.11 , pp. 1036-1049
    • Dima, R.I.1    Thirumalai, D.2
  • 7
    • 9244260521 scopus 로고    scopus 로고
    • Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
    • Nguyen, H. D., and C. K. Hall. 2004. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc. Natl. Acad. Sci. USA. 101:16180-16185.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 16180-16185
    • Nguyen, H.D.1    Hall, C.K.2
  • 8
    • 22044455269 scopus 로고    scopus 로고
    • A toy model for predicting the rate of amyloid formation from unfolded protein
    • Hall, D., N. Hirota, and C. M. Dobson. 2005. A toy model for predicting the rate of amyloid formation from unfolded protein. J. Mol. Biol. 351:195-205.
    • (2005) J. Mol. Biol. , vol.351 , pp. 195-205
    • Hall, D.1    Hirota, N.2    Dobson, C.M.3
  • 9
    • 57149102288 scopus 로고    scopus 로고
    • A generic mechanism of emergence of amyloid protofilaments from disordered oligomeric aggregates
    • Auer, S., F. Meersman, M. Vendruscolo. 2008. A generic mechanism of emergence of amyloid protofilaments from disordered oligomeric aggregates. PLoS. Comput. Biol. 4: e1000222.
    • (2008) PLoS. Comput. Biol. , vol.4
    • Auer, S.1    Meersman, F.2    Vendruscolo, M.3
  • 10
    • 0025319917 scopus 로고
    • Conformations of folded proteins in restricted spaces
    • Covell, D. G., and R. L. Jernigan. 1990. Conformations of folded proteins in restricted spaces. Biochemistry. 29:3287-3294.
    • (1990) Biochemistry , vol.29 , pp. 3287-3294
    • Covell, D.G.1    Jernigan, R.L.2
  • 12
    • 79551658975 scopus 로고    scopus 로고
    • Simple off-lattice model to study the folding and aggregation of peptides
    • Combe, N., and D. Frenkel. 2007. Simple off-lattice model to study the folding and aggregation of peptides. Mol. Phys. 1115:201312.
    • (2007) Mol. Phys. , vol.1115 , pp. 201312
    • Combe, N.1    Frenkel, D.2
  • 13
    • 33744827373 scopus 로고    scopus 로고
    • Side-chain interactions determine amyloid formation by model polyglutamine peptides in molecular dynamics simulations
    • Marchut, A. J., and C. K. Hall. 2006. Side-chain interactions determine amyloid formation by model polyglutamine peptides in molecular dynamics simulations. Biophys. J. 90:4574-4584.
    • (2006) Biophys. J. , vol.90 , pp. 4574-4584
    • Marchut, A.J.1    Hall, C.K.2
  • 14
    • 55849105547 scopus 로고    scopus 로고
    • Probing the mechanisms of fibril formation using lattice models
    • Li, M. S., D. K. Klimov, D. Thirumalai. 2008. Probing the mechanisms of fibril formation using lattice models. J. Chem. Phys. 129:175101.
    • (2008) J. Chem. Phys. , vol.129 , pp. 175101
    • Li, M.S.1    Klimov, D.K.2    Thirumalai, D.3
  • 15
    • 0347357617 scopus 로고    scopus 로고
    • Protein folding and misfolding
    • Dobson, C. M. 2003. Protein folding and misfolding. Nature. 426:884-890.
    • (2003) Nature , vol.426 , pp. 884-890
    • Dobson, C.M.1
  • 16
    • 34247587012 scopus 로고    scopus 로고
    • Genetics. Getting closer to the whole picture
    • Sauer, U., M. Heinemann, and N. Zamboni. 2007. Genetics. Getting closer to the whole picture. Science. 316:550-551.
    • (2007) Science , vol.316 , pp. 550-551
    • Sauer, U.1    Heinemann, M.2    Zamboni, N.3
  • 17
    • 0027234766 scopus 로고
    • Engineering of stable and fast-folding sequences of model proteins
    • Shakhnovich, E. I., and A. M. Gutin. 1993. Engineering of stable and fast-folding sequences of model proteins. Proc. Natl. Acad. Sci. USA. 90:7195-7199.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 7195-7199
    • Shakhnovich, E.I.1    Gutin, A.M.2
  • 18
    • 0017021957 scopus 로고
    • Medium-and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
    • Tanaka, S., and H. A. Scheraga. 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
  • 19
    • 0030983768 scopus 로고    scopus 로고
    • Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?
    • Skolnick, J., L. Jaroszewski, A. Godzik. 1997. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci. 6:676-688.
    • (1997) Protein Sci. , vol.6 , pp. 676-688
    • Skolnick, J.1    Jaroszewski, L.2    Godzik, A.3
  • 20
    • 0001222466 scopus 로고
    • How accurate must potentials be for successful modeling of protein folding?
    • Pande, V. S., A. Y. Grosberg, and T. Tanaka. 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.S.1    Grosberg, A.Y.2    Tanaka, T.3
  • 21
    • 0029942661 scopus 로고    scopus 로고
    • Structure-derived potentials and protein simulations
    • Jernigan, R. L., and I. Bahar. 1996. Structure-derived potentials and protein simulations. Curr. Opin. Struct. Biol. 6:195-209.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 195-209
    • Jernigan, R.L.1    Bahar, I.2
  • 22
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: How accurate are they?
    • Thomas, P. D., and K. A. Dill. 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.D.1    Dill, K.A.2
  • 23
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasichemical approximation
    • Miyazawa, S., and R. L. Jernigan. 1985. Estimation of effective interresidue contact energies from protein crystal structures: quasichemical approximation. Macromolecules. 18:534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 24
    • 0033005899 scopus 로고    scopus 로고
    • Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
    • Betancourt, M. R., and D. Thirumalai. 1999. Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci. 8:361-369.
    • (1999) Protein Sci. , vol.8 , pp. 361-369
    • Betancourt, M.R.1    Thirumalai, D.2
  • 25
    • 0345490880 scopus 로고    scopus 로고
    • Solvent-amino acid interaction energies in 3-D-lattice MC simulations of model proteins. Aggregation thermodynamics and kinetics
    • Leonhard, K., J. M. Prausnitz, and C. J. Radke. 2003. Solvent-amino acid interaction energies in 3-D-lattice MC simulations of model proteins. Aggregation thermodynamics and kinetics. Phys. Chem. Chem. Phys. 5:5291-5299.
    • (2003) Phys. Chem. Chem. Phys. , vol.5 , pp. 5291-5299
    • Leonhard, K.1    Prausnitz, J.M.2    Radke, C.J.3
  • 26
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm, U., and C. Sander. 1994. Enlarged representative set of protein structures. Protein Sci. 3:522-524.
    • (1994) Protein Sci. , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 27
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 28
    • 84953648015 scopus 로고
    • New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles
    • Lyubartsev, A. P., A. A. Martsinovski, P. N. Vorontsov-Velyaminov. 1992. New approach to Monte Carlo calculation of the free energy: method of expanded ensembles. J. Chem. Phys. 96:1776-1783.
    • (1992) J. Chem. Phys. , vol.96 , pp. 1776-1783
    • Lyubartsev, A.P.1    Martsinovski, A.A.2    Vorontsov-Velyaminov, P.N.3
  • 29
    • 33644899039 scopus 로고
    • Simulated tempering: A new Monte Carlo scheme
    • Marinari, E., and G. Parisi. 1992. Simulated tempering: a new Monte Carlo scheme. Europhys. Lett. 19:451-458.
    • (1992) Europhys. Lett. , vol.19 , pp. 451-458
    • Marinari, E.1    Parisi, G.2
  • 30
    • 84950437936 scopus 로고
    • Annealing Markov chain Monte Carlo with applications to ancestral inference
    • Geyer, C. J., and E. A. Thompson. 1995. Annealing Markov chain Monte Carlo with applications to ancestral inference. J. Am. Stat. Assoc. 90:909-920.
    • (1995) J. Am. Stat. Assoc. , vol.90 , pp. 909-920
    • Geyer, C.J.1    Thompson, E.A.2
  • 31
    • 58149147308 scopus 로고    scopus 로고
    • Disordered flanks prevent peptide aggregation
    • Abeln, S., and D. Frenkel. 2008. Disordered flanks prevent peptide aggregation. PLOS Comput. Biol. 4: e1000241.
    • (2008) PLOS Comput. Biol. , vol.4
    • Abeln, S.1    Frenkel, D.2
  • 33
    • 0033596963 scopus 로고    scopus 로고
    • Pressure effect on the temperature-induced unfolding and tendency to aggregate of myoglobin
    • Smeller, L., P. Rubens, and K. Heremans. 1999. Pressure effect on the temperature-induced unfolding and tendency to aggregate of myoglobin. Biochemistry. 38:3816-3820.
    • (1999) Biochemistry , vol.38 , pp. 3816-3820
    • Smeller, L.1    Rubens, P.2    Heremans, K.3
  • 34
    • 55749087363 scopus 로고    scopus 로고
    • Direct characterization of amyloidogenic oligomers by single-molecule fluorescence
    • Orte, A., N. R. Birkett, D. Klenerman. 2008. Direct characterization of amyloidogenic oligomers by single-molecule fluorescence. Proc. Natl. Acad. Sci. USA. 105:14424-14429.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 14424-14429
    • Orte, A.1    Birkett, N.R.2    Klenerman, D.3
  • 35
    • 67649101377 scopus 로고    scopus 로고
    • Generic coarse-grained model for protein folding and aggregation
    • Bereau, T., and M. Deserno. 2009. Generic coarse-grained model for protein folding and aggregation. J. Chem. Phys. 130:235106.
    • (2009) J. Chem. Phys. , vol.130 , pp. 235106
    • Bereau, T.1    Deserno, M.2
  • 36
    • 63149196697 scopus 로고    scopus 로고
    • Topology-based potentials and the study of the competition between protein folding and aggregation
    • Prieto, L., and A. Rey. 2009. Topology-based potentials and the study of the competition between protein folding and aggregation. J. Chem. Phys. 130:115101.
    • (2009) J. Chem. Phys. , vol.130 , pp. 115101
    • Prieto, L.1    Rey, A.2
  • 37
    • 77950825396 scopus 로고    scopus 로고
    • Molecular structures of quiescently grown and brain-derived polymorphic fibrils of the Alzheimer amyloid Ab9-40 peptide: A comparison to agitated fibrils
    • Wu, C., M. T. Bowers, and J.-E. Shea. 2010. Molecular structures of quiescently grown and brain-derived polymorphic fibrils of the Alzheimer amyloid Ab9-40 peptide: a comparison to agitated fibrils. PLOS Comput. Biol. 6: e1000693.
    • (2010) PLOS Comput. Biol. , vol.6
    • Wu, C.1    Bowers, M.T.2    Shea, J.-E.3
  • 38
    • 74049165050 scopus 로고    scopus 로고
    • Atomic-scale simulations confirm that soluble β-sheet-rich peptide self-assemblies provide amyloid mimics presenting similar conformational properties
    • Yu, X., J. Wang, J. Zheng. 2010. Atomic-scale simulations confirm that soluble β-sheet-rich peptide self-assemblies provide amyloid mimics presenting similar conformational properties. Biophys. J. 98:27-36.
    • (2010) Biophys. J. , vol.98 , pp. 27-36
    • Yu, X.1    Wang, J.2    Zheng, J.3
  • 39
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequencestructure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi, J., T. L. Blundell, and K. Mizuguchi. 2001. FUGUE: sequencestructure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310:243-257.
    • (2001) J. Mol. Biol. , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3


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