Stability of two natural homologous proteins with different folds

• Autorzy: Konieczny L. , Banach M. , Roterman I.
• Języki publikacji: EN

Abstrakty

EN

The applicability of the model for protein folding process simulation is presented using as the test two homologous proteins of different fold: helical in 3BD1 and β-structural form in 2PIJ [L. van Dorn, T. Newlove, S. Chang, W. Ingram, M. Cordes. Biochemistry 45, 10542 (2006)]. The folding process is assumed to be directed by hydrophobic core directing the hydrophobic residues toward the center of the molecule and exposing the hydrophilic residues on the surface. The “fuzzy oil drop” model is expressed by the 3-dimensional Gauss function which mimics the external force field. The value of Gauss function is interpreted as the hydrophobicity density calculated in any point of the space of the protein body. The accordance of idealized and observed hydrophobicity distributions (calculated according to Levitt function) measured using the Kullback-Leibler divergence entropy reveals good accordance in two homological proteins of different folds. The structural differences appeared to be easily explainable on the basis of “fuzzy oil drop” model.

Słowa kluczowe

EN

protein structure; homologous proteins; hydrophobicity; information theory

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2012
• Tom: Vol. 8, no. 2
• Strony: 185--193
• Opis fizyczny: Bibliogr. 16 poz., rys., tab., wykr.

Twórcy

autor

Konieczny L.

• Department of Bioinformatics and Telemedicine – Medical College – Jagiellonian University, Lazarza 16, 31-530 Kraków, Poland
• Chair of Medical Biochemistry, Medical College – Jagiellonian University, Kopernika 7, 31-034 Kraków, Poland

autor

Banach M.

• Department of Bioinformatics and Telemedicine – Medical College – Jagiellonian University, Lazarza 16, 31-530 Kraków, Poland
• Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland

autor

Roterman I.

• Department of Bioinformatics and Telemedicine – Medical College – Jagiellonian University, Lazarza 16, 31-530 Kraków, Poland

Bibliografia

• 1. L. van Dorn, T. Newlove, S. Chang, W. Ingram, M. Cordes, Relationship between sequence determinants of stability for two natural homologous proteins with different folds, Biochemistry 45 (2006) 10542- 10553.
• 2. C. Roessler,B. Hall, W. Anderson, W. Ingram, S. Roberts, W. Montfort, M. Cordes, Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds. Proc. Natl. Acad. Sci. USA 105 (2006) 2343-2348.
• 3. L. Konieczny, M. Brylinski, I. Roterman, Gauss-function-based model of hydrophobicity density in proteins, In Silico Biol 6,(2006) 0002.
• 4. R. F. Nalewajski. Information theory of molecular systems. Amsterdam [etc.]: Elsevier, 2006. ISBN 978-0-444-51966-5.
• 5. http://www.ebi.ac.uk/pdbsum
• 6. M. Levitt, A simplified representation of protein conformations for rapid simulation of protein folding, J Mol Biol 104 (1976) 59-107.
• 7. M. Brylinski, L. Konieczny, I. Roterman, Is the protein folding an aim-oriented process? Human haemoglobin as example. Int J Bioinform Res Appl. 3 (2007) 234-260.
• 8. W. Kauzmann, Some factors in the interpretation of protein denaturation Adv Protein Chem 14 (1959) 1-63.
• 9. M. Bryliński, L. Konieczny, I. Roterman, Hydrophobic collapse in (in silico) protein folding, Comp. Biol. Chem. 30 (2006) 255-267.
• 10. M. Brylinski, L. Konieczny, I. Roterman, Ligation site in proteins recognized in silico. Bioinformation 1 (2006) 127-129.
• 11. K. Prymula, K. Sałapa, I. Roterman, “Fuzzy Oil Drop” Model applied to individual small proteins built of 70 amino acids J. Mol. Model.16 (2010) 1269-1285.
• 12. M. Bryliński, M. Kochańczyk, E. Broniatowska, I. Roterman, Localization of ligand binding site in proteins identified in silico. J. Mol. Model. 13 (2007) 655-675.
• 13. M. Bryliński, K. Prymula, W. Jurkowski, M. Kochańczyk, E. Stawowczyk, L. Konieczny, I. Roterman, Prediction of functional sites based on the fuzzy oil drop model PLoS-Computational Biology (2007) E94
• 14. K. Prymula, I. Roterman, Structural entropy to characterize small proteins (70 aa) and their interactions. Entropy, 11 (2009) 62-84.
• 15. M. Banach, K. Stąpor, I. Roterman, Chaperonin structure – the large multi-subunit protein complex. Int. J. Mol. Sci. 10 (2009) 844-861.
• 16. V. Zobnina, I. Roterman, Application of the fuzzy-oil-drop model to membrane protein simulation Proteins 77 (2009) 378-394.