Dissimilar sequence: similar structure of proteins

• Autorzy: Banach M. , Konieczny L. , Roterman I.

Identyfikatory

DOI

10.1515/bams-2016-0014

• Języki publikacji: EN

Abstrakty

EN

Sequence-to-structure relation is one of the major objects of the analysis of protein folding problem. The pair of two small proteins (domains) of similar structure (β-hairpin/α-helix/β-hairpin) generated by the chains of similar length (about 60 amino acids) with very low sequence similarity (15%) is the object of the comparable analysis of 3D structure. The criterion for similarity estimation is the status of polypeptide chain with respect to the hydrophobic core structure. The fuzzy oil drop model is applied to reveal the differentiated status of fragments of the well-defined secondary structure. This analysis allows the interpretation of the structure in other than the geometric form as it is made based on secondary structure classification. The two compared highly similar proteins appear to be different with respect to the hydrophobic core structure.

Słowa kluczowe

EN

hydrophobicity; protein structure; protein structure prediction; secondary structure

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2016
• Tom: Vol. 12, no. 3
• Strony: 117--121
• Opis fizyczny: Bibliogr. 14 poz., rys., wykr.

Twórcy

autor

Banach M.

• Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, 31-530 Krakow, Łazarza 16, Poland

autor

Konieczny L.

• Medical Biochemistry, Jagiellonian University Medical College, 31-034 Krakow, Kopernika 7, Poland

autor

Roterman I.

• Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, 31-530 Krakow, Łazarza 16, Poland

Bibliografia

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• 10. Kalinowska B, Banach M, Konieczny L, Roterman I. Application of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteins. Entropy 2015;17:1477–507.
• 11. Kalinowska B, Banach M, Konieczny L, Marchewka D, Roterman I. Intrinsically disordered proteins – relation to general model expressing the active role of the water environment. Adv Protein Chem Struct Biol 2014;94:315–46.
• 12. Banach M, Konieczny L, Roterman I. The fuzzy oil drop model, based on hydrophobicity density distribution, generalizes the influence of water environment on protein structure and function. J Theor Biol 2014;359:6–17.
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Uwagi

Opracowanie ze środków MNiSW w ramach umowy 812/P-DUN/2016 na działalność upowszechniającą naukę.