PL EN


Preferences help
enabled [disable] Abstract
Number of results
Journal
2005 | 54 | 2-3 | 155-162
Article title

Przewidywanie struktury białek: podejście boltzmannowskie i darwinowskie

Content
Title variants
EN
Protein structure prediction: boltzmannian and darwinian approaches
Languages of publication
PL EN
Abstracts
EN
Efforts to solve the problem of protein folding have been traditionally rooted in two schools of thought named Boltzmannian' and Darwinian', after the scientists who defined the fundamental principles of statistical thermodynamics and evolutionary biology, respectively. One approach to protein structure prediction is based on the principles of physics, e.g. on the thermodynamic hypothesis, according to which the native structure of a protein corresponds to the global minimum of its free energy under given conditions. Accordingly, the physics-based methods model the process of protein folding by simulating the conformational changes and searching for the free energy minimum. The other approach is based on the principles of evolution, in particular the empirical rule that evolutionarily related (homologous) proteins usually retain the same three-dimen-sional fold despite the accumulation of divergent mutations. Evolution-based methods attempt to map the sequence of the target protein to the structure of another protein (a template), model the overall fold of the target based on that of the template and infer how the target structures will change due to substitutions, insertions and deletions, as compared with the template. This review summarizes the basics of protein structure prediction by both types of approaches and discusses the issue of model quality evaluation.
Keywords
Journal
Year
Volume
54
Issue
2-3
Pages
155-162
Physical description
Dates
published
2005
References
  • ANFINSEN C. B., HABER E., SELA M., WHITE F. H., JR., 1961. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc. Natl. Acad. Sci. USA 47, 1309-1314.
  • BAKER D., AGARD D. A., 1994. Kinetics versus thermodynamics in protein folding. Biochemistry 33, 7505-7509.
  • BAKER D., SALI A., 2001. Protein structure prediction and structural genomics. Science 294, 93-96.
  • BENSON D. A., KARSCH-MIZRACHI I., LIPMAN D. J., OSTELL J., WHEELER D. L., 2005. GenBank. Nucleic Acids Res. 33, D34-38.
  • BERMAN H. M., WESTBROOK J., FENG Z., GILLILAND G., BHAT T. N., WEISSIG H., SHINDYALOV I. N., BOURNE P. E., 2000. The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
  • BUJNICKI J. M. 2005. Protein structure prediction by recombination of fragments. ChemBioChem (w druku).
  • BUJNICKI J. M., FISCHER D., 2004. 'Meta' approaches to protein structure prediction. [W:] Practical Bioinformatics. BUJNICKI J. M. (red.). Springer-Verlag, Berlin, 23-34.
  • BYSTROFF C., SHAO Y., 2004. Modeling protein folding pathways. [W:] Practical Bioinformatics. BUJNICKI J. M. (red.). Springer-Verlag, Berlin, 97-122.
  • CHOTHIA C., LESK A. M., 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823-826.
  • CYMERMAN I. A., FEDER M., PAWLOWSKI M., KUROWSKI M. A., BUJNICKI J. M., 2004. Computational methods for protein structure prediction and fold recognition. [W:] Practical Bioinformatics. BUJNICKI J. M. (red.). Springer-Verlag, Berlin, 1-21.
  • KARPLUS M., 1997. The Levinthal paradox: yesterday and today. Fold. Des. 2, S69-S75.
  • KOLINSKI A., 2004. Protein modeling and structure prediction with a reduced representation. Acta Biochim. Polon. 51, 349-371.
  • LAZARIDIS T., KARPLUS M., 2000. Effective energy functions for protein structure prediction. Curr. Opin. Struct. Biol. 10, 139-145.
  • LEO-MACIAS A., LOPEZ-ROMERO P., LUPYAN D., ZERBINO D., ORTIZ A. R., 2005. Core deformations in protein families: a physical perspective. Biophys. Chem. 115, 125-128.
  • LUPAS A. N., PONTING C. P., RUSSELL R. B., 2001. On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J. Struct. Biol. 134, 191-203.
  • MISURA K. M., BAKER D., 2005. Progress and challenges in high-resolution refinement of protein structure models. Proteins 59, 15-29.
  • SALI A., BLUNDELL T. L., 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815.
  • SASIN J. M., BUJNICKI J. M., 2004. COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res. 32, W586-W589.
  • SCHWEDE T., KOPP J., GUEX N., PEITSCH M. C., 2003. SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 31, 3381- 3385.
  • YE X., O'NEIL P. K., FOSTER A. N., GAJDA M. J., KOSINSKI J., KUROWSKI M. A., BUJNICKI J. M., FRIEDMAN A. M., BAILEY-KELLOGG C., 2004. Probabilistic crosslink analysis and experiment planning for high-throughput elucidation of protein structure. Protein Sci. 13, 3298-3313.
Document Type
Publication order reference
YADDA identifier
bwmeta1.element.bwnjournal-article-ksv54p155kz
Identifiers
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.