SEARCH

SEARCH BY CITATION

References and Notes

  • 1
    Chow, C.; Chow, C.; Rhagunathan, V.; Huppert, T.; Kimball, E.; Cavagnero, S. The chain length dependence of apomyoglobin folding: structural evolution from misfolded sheets to native helices. Biochemistry 2003, 42 (23), 70907099.
  • 2
    Cavagnero, S.; Kurt, N. Folding and misfolding as a function of polypeptide chain elongation: conformational trends and implications for intracellular events. In Misbehaving Proteins: Protein (Mis)folding, Aggregation and Stability; Murphy, R., Tsai, A., Eds.; Springer: New York, 2006; pp 217246.
  • 3
    Flanagan, J. M.; Kataoka, M.; Shortle, D.; Engelman, D. M. Truncated staphylococcal nuclease is compact but disordered. Proc. Natl. Acad. Sci. U.S.A. 1992, 89 (2), 748752.
  • 4
    Kurt, N.; Cavagnero, S. The burial of solvent-accessible surface area is a predictor of polypeptide folding and misfolding as a function of chain elongation. J. Am. Chem. Soc. 2005, 127, 1569015691.
  • 5
    de Marco, A.; Deuerling, E.; Mogk, A.; Tomoyasu, T.; Bukau, B. Chaperone-based procedure to increase yields of soluble recombinant proteins produced in E. Coli. BMC Biotechnology 2007, 7.
  • 6
    Plaxco, K. W.; Simons, K. T.; Baker, D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 1998, 277 (4), 985994.
  • 7
    Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28 (1), 235242.
  • 8
    Orengo, C. A.; Michie, A. D.; Jones, S.; Jones, D. T.; Swindells, M. B.; Thornton, J. M. CATH — a hierarchic classification of protein domain structures. Structure 1997, 5 (8), 10931108.
  • 9
    Noguchi, T.; Akiyama, Y. PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. Nucleic Acids Res. 2003, 31 (1), 492493.
  • 10
    Gromiha, M. M.; Selvaraj, S. Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: Applications of long-range order to folding rate prediction. J. Mol. Biol. 2001, 310 (1), 2732.
  • 11
    Kihara, D. The effect of long-range interactions on the secondary structure formation of proteins. Protein Sci. 2005, 14 (8), 19551963.
  • 12
    Krishna, M.; Englander, S. The N-terminal to C-terminal motif in protein folding and function. Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (4), 10531058.
  • 13
    Flory, P. J. Statistical Mechanics of Chain Molecules; Wiley: New York, 1969.
  • 14
    Ivankov, D. N.; Garbuzynskiy, S. O.; Alm, E.; Plaxco, K. W.; Baker, D.; Finkelstein, A. V. Contact order revisited: Influence of protein size on the folding rate. Protein Sci. 2003, 12 (9), 20572062.
  • 15
    de Prat Gay, G.; Ruiz-Sanz, J.; Neira, J. L.; Corrales, F. J.; Otzen, D. E.; Ladurner, A. G.; Fersht, A. R. Conformational pathway of the polypeptide chain of chymotrypsin inhibitor-2 growing from its N terminus in vitro. Parallels with the protein folding pathway. J. Mol. Biol. 1995, 254, 968979.
  • 16
    Itzhaki, L. S.; Neira, J. L.; Ruizsanz, J.; Gay, G. D.; Fersht, A. R. Search for nucleation sites in smaller fragments of chymotrypsin inhibitor-2. J. Mol. Biol. 1995, 254 (2), 289304.
  • 17
    Neira, J. L.; Fersht, A. R. Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments. J. Mol. Biol. 1999, 285, 13091333.
  • 18
    Shortle, D.; Meeker, A. K. Residual structure in large fragments of staphylococcal nuclease: Effects of amino acid substitution. Biochemistry 1989, 28, 936944.
  • 19
    Tian, K.; Zhou, B.; Geng, F.; Jing, G. Folding of SNase R begins early during synthesis: the conformational feature of two short N-terminal fragments of staphylococcal nuclease R. Int. J. Biol. Macromol. 1998, 23, 199206.
  • 20
    Caflisch, A. Computational models for the prediction of polypeptide aggregation propensity. Curr. Opin. Chem. Biol. 2006, 10 (5), 437444.
  • 21
    Conchillo-Sole, O.; de Groot, N. S.; Aviles, F. X.; Vendrell, J.; Daura, X.; Ventura, S. AGGRESCAN: a server for the prediction and evaluation of “hot spots” of aggregation in polypeptides. BMC Bioinformatics 2007, 8.
  • 22
    Dubay, K. F.; Pawar, A. P.; Chiti, F.; Zurdo, J.; Dobson, C. M.; Vendruscolo, M. Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains. J. Mol. Biol. 2004, 341 (5), 13171326.
  • 23
    Fernandez-Escamilla, A. M.; Rousseau, F.; Schymkowitz, J.; Serrano, L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat. Biotechnol. 2004, 22 (10), 13021306.
  • 24
    Trovato, A.; Seno, F.; Tosatto, S. C. E. The PASTA server for protein aggregation prediction. Protein Eng. Design Selection 2007, 20 (10), 521523.