To be folded or to be unfolded?

Protein Science

Volumn 13, Issue 11, 2004, Pages 2871-2877

  Garbuzynskiy, Sergiy O ^a   Lobanov, Michail Yu ^a   Galzitskaya, Oxana V ^a  

^a INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

Globular protein; Monte Carlo simulation; Natively unfolded protein; Number of contacts per residue

Indexed keywords

PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CALCULATION; HYDROPHOBICITY; MONTE CARLO METHOD; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; HYDROPHOBICITY; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING;

EID: 7244231503     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.04881304     Document Type: Article

References (17)

1. Bairoch, A. and Apweiler, R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28: 45-48.
2. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rogers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M. 1977. The Protein Data Bank. A computer-based archival file for macromolecular structures. Eur. J. Biochem. 80: 319-324.
3. Dunker, A.K., Garner, E., Guilliot, S., Romero, P., Albrecht, K., Hart, J., Obradovic, Z., Kissinger, C., and Villafranca, J.E. 1998. Protein disorder and the evolution of molecular recognition: Theory, predictions and observations. Pac. Symp. Biocomput. 473-484.
4. Dyson, H.J. and Wright, P.E. 2002. Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance. Adv. Protein Chem. 62: 311-340.
5. Fauchere, I.I. and Pliska, V. 1983. Hydrophobic parameters amino-acid side chains from partitioning of N-acetyl-amino-acid amides. Eur. J. Med. Chem.-Chim. Ther. 18: 369-375.
6. Galzitskaya, O.V., Surin, A.K., and Nakamura, H. 2000. Optimal region of average side-chain entropy for fast protein folding. Protein Sci. 9: 580-586.
7. Kyte, J. and Doolittle, R.F. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157: 105-132.
8. Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
9. Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P., Brown, C.J., and Dunker, A.K. 2003. Predicting intrinsic disorder from amino acid sequence. Proteins 53: 566-572.
10. Radivojac, P., Obradovic, Z., Smith, D.K., Zhu, G., Vucetic, S., Brown, C.J., Lawson, J.D., and Dunker, A.K. 2004. Protein flexibility and intrinsic disorder. Protein Sci. 13: 71-80.
11. Romero, P., Obradovic, Z., Kissinger, C.R., Villafranca, J.E., Garner, E., Guilliot, S., and Dunker, A.K. 1998. Thousands of proteins likely to have long disordered regions. Pac. Symp. Biocomput. 437-448.
12. Romero, P., Obradovic, Z., and Dunker, A.K. 1999. Folding minimal sequences: The lower bound for sequence complexity of globular proteins. FEBS Lett. 462: 363-367.
13. Uversky, V.N. 2002. What does it mean to be natively unfolded? Eur. J. Biochem. 269: 2-12.
14. Uversky, V.N., Gillespie, J.R., and Fink, A.L. 2000. Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins 41: 415-427.
15. Vucetic, S., Brown, C.J., Dunker, A.K., and Obradovic, Z. 2003. Flavors of protein disorder. Proteins 52: 573-584.
16. Wootton, J.C. 1994. Non-globular domains in protein sequences: Automated segmentation using complexity measures. Comput. Chem. 18: 269-285.
17. Wright, P.E. and Dyson, H.J. 1999. Intrinsically unstructured proteins: Reassessing the protein structure-function paradigm. J. Mol. Biol. 293: 321-331.