Adding backbone to protein folding: Why proteins are polypeptides

Folding and Design

Volumn 1, Issue 1, 1996, Pages

  Honig, Barry ^a   Cohen, Fred E ^b  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b Box 0450 ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEIN;

CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; HYDROGEN BOND; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; REVIEW; THERMODYNAMICS;

HYDROGEN BONDING; MODELS, CHEMICAL; MOLECULAR STRUCTURE; PEPTIDES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; THERMODYNAMICS;

EID: 0001842441     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(96)00005-3     Document Type: Article

References (35)

1. Brown, D. (1995). Washington Post October 1. p. A1.
2. Holden, C., ed. (1995). Folding proteins fast. Science 269, 1821.
3. Borman, S. (1995). Researchers advance ability to predict structures of folded proteins. Chem. Eng. News November 6. pp. 44-49.
4. Cohen, F.E. & Sternberg, M.J.E. (1980). On the prediction of protein structures: the significance of the root-mean-square deviation. J. Mol. Biol. 138, 321-333.
5. Hagler, AT. & Honig, B. (1978). On the formation of protein tertiary structures on a computer. Proc. Natl. Acad. Sci. USA 75, 554-558.
6. Lattman, E.E., ed. (1995). Protein structure prediction issue. Proteins 23, 295-462.
7. Levitt, M. & Warshel, A. (1975). Computer simulation of protein folding. Nature 253, 694-698.
8. Anfinsen, C.B. (1973). Principles that govern the folding of protein chains. Science 181, 223-230.
9. Levinthal, C. (1966). Molecular model-building by computer. Sci. Am. 214, 42-52.
10. Pauling, L., Corey, R.B. & Branson, H.R. (1951). The structure of proteins: two hydrogen bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. USA 37, 205-211.
11. Venkatchalam, C.M. & Ramachandran, G.N. (1969). Conformation of polypeptide chains. Annu. Rev. Biochem. 38, 45-82.
12. Sali, A., Shakhnovich, E. & Karplus, M. (1994). How does a protein fold? Nature 369, 248-251.
13. Bryngelson, J.D., Onuchic, J.N., Socci, N.D. & Wolynes, P.G. (1995). Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 21, 167-195.
14. Dill, K.A., et al., & Chan, H.S. (1995). Principles of protein folding - a perspective from simple exact models. Protein Sci. 4, 561-602.
15. Chan, H.S. (1995). Kinetics of protein folding [letter]. Nature 373, 664-665.
16. Doty, P. & Gratzer, W.B. (1962). Some recent observations on polypeptides in solution. In Polyamino Acids, Polypeptides and Proteins. (Stahman, M.A., ed.), pp. 111-118, University of Wisconsin Press, Madison, WI.
17. Kiefhaber, T., Labhardt, A.M. & Baldwin, R.L. (1995). Direct NMR evidence for an intermediate preceding the rate-limiting step in the unfolding of ribonuclease A. Nature 375, 513-515.
18. Auer, H.E. & Doty, P. (1966). The synthesis, structure, and optical properties of some copolypeptides containing nonpolar amino acid residues. Biochemistry 5, 1708-1715.
19. Applequist, J. & Doty, P. (1962). α-Helix formation in poly-ε-carbobenoxy-L-lysine and poly-L-Iysine. In Polyamino Acids, Polypeptides and Proteins. (Stahman, M.A., ed.), pp. 161-177, University of Wisconsin Press, Madison, WI.
20. Ingwall, R.T., Scheraga, H.A., Lotan, N., Berger A. & and Katchalski, E. (1968). Conformational studies of poly-L-alanine in water. Biopolymers 6, 331-368.
21. Zimm, B.H. & Bragg, J.K. (1959). Theory of the phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 31, 526-535.
22. Lifson, S. & Roig, A. (1961). On the theory of helix-coil transition in polypeptides. J. Chem. Phys. 34, 1963-1974.
23. Honig, B. & Yang, A.S. (1995). Free energy balance in protein folding. Adv. Protein Chem. 46, 27-58.
24. Yang, A. & Honig, B. (1995). Free energy determinants of secondary structure formation. 1. Alpha-helices. J. Mol. Biol. 252, 351-365.
25. Bixon, M., Scheraga, M.A. & Lifson, S. (1963). Effect of hydrophobia bonding on the stability of poly-L-alanine helices in water. Biopolymers 1, 419-429.
26. Skolnick, J. & Kolinski, A. (1991). Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. J. Mol. Biol. 221, 499-531.
27. Hao, M.-H. & Scheraga, H.A. (1994). Statistical thermodynamics of protein folding-sequence dependence. J. Phys. Chem. 98, 9882-9893.
28. Sun, S., Thomas, P.D. & Dill, K. (1995). A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng. 8, 769-778.
29. Wolynes, P.G., Onuchic, J.N. & Thirumalai, D. (1995). Navigating the folding routes. Science 267, 1619-1620.
30. Onuchic, J.N., Wolynes, P.G., Luthey-Schulten, Z. & Socci, N.D. (1995). Toward an outline of the topography of a realistic protein-folding funnel. Proc. Natl. Acad. Sci. USA 92, 3626-3630.
31. Luthey-Schulten, Z., Ramirez, B.E. & Wolynes, P.G. (1995). Helix-coil, liquid crystal and spin glass transitions of a collapsed heteropolymer. J. Phys. Chem. 99, 2177-2185.
32. Zwanzig, R., Szabo, A. & Bagchi, B. (1992). Levinthal's paradox. Proc. Natl. Acad. Sci. USA 89, 20-22.
33. Simon, R.J., et al., & Huebner, V.D. (1992). Peptoids-a modular approach to drug discovery. Proc. Natl. Acad. Sci. USA 89, 9367-9371.
34. Cho, C.Y., et al., & Sundaram, A. (1993). An unnatural biopolymer. Science 261, 1303-1305.
35. Egholm, M., Buchardt, O., Nielsen, P.E. & Berg, R.H. (1992). Peptide nucleic acids (PNA). Oligonucleotide analogues with an ahiral peptide backbone. J. Am. Chem. Soc. 114, 1895-1897.