In silico Structural Study of Random Amino Acid Sequence Proteins Not Present in Nature
| Autor: | Zdzisław Wiśniowski, Fabio Polticelli, Monika Piwowar, Kinga Sałapa, Marek Kochańczyk, Maciej Malawski, Tomasz Szepieniec, Lukasz Flis, Giuseppe Minervini, Irena Roterman, Giovanni Evangelista, Katarzyna Prymula, Ewa Matczyńska |
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| Přispěvatelé: | Prymula, K, Piwowar, M, Kochanczyk, M, Flis, L, Malawski, M, Szepieniec, T, Evangelista, G, Minervini, G, Polticelli, Fabio, Wisniowski, Z, Salapa, K, Matczynska, E, Roterman, I. |
| Rok vydání: | 2009 |
| Předmět: |
Models
Molecular Protein Structure Secondary Structural similarity In silico Molecular Sequence Data Bioengineering Computational biology Biochemistry Protein Structure Secondary Protein sequencing Protein structure Models Algorithms Amino Acid Sequence Catalytic Domain Proteins Molecular Biology Peptide sequence chemistry.chemical_classification Molecular General Chemistry General Medicine Structural Classification of Proteins database Amino acid chemistry Molecular Medicine Threading (protein sequence) |
| Zdroj: | Chemistry & Biodiversity. 6:2311-2336 |
| ISSN: | 1612-1880 1612-1872 |
| DOI: | 10.1002/cbdv.200800338 |
| Popis: | f ),Zdzislaw Wisniowski a ),Kinga Salapa a a ) 1 ) a The three-dimensional structures of a set ofnever born proteins� (NBP, random amino acid sequence proteins with no significant homology with known proteins) were predicted using two methods: Rosetta and the one based on thefuzzy-oil-drop� (FOD) model. More than 3000 different random amino acid sequences have been generated, filtered against the non redundant protein sequence data base, to remove sequences with significant homology with known proteins, and subjected to three- dimensional structure prediction. Comparison between Rosetta and FOD predictions allowed to select the ten top (highest structural similarity) and the ten bottom (the lowest structural similarity) structures from the ranking list organized according to the RMS-D value. The selected structures were taken for detailed analysis to define the scale of structural accordance and discrepancy between the two methods. The structural similarity measurements revealed discrepancies between structures generated on the basis of the two methods. Their potential biological function appeared to be quite different as well. The ten bottom structures appeared to beunfoldablefor the FOD model. Some aspects of the general characteristics of the NBPs are also discussed. The calculations were performed on the EUChinaGRID grid platform to test the performance of this infrastructure for massive protein structure predictions. Introduction. - The search for techniques aimed at the generation of new proteins for pharmacological and biotechnological applications is widely developed nowadays (1 - 3). This involves the selection of proteins of desirable activity among those present in Nature, as well as the production of new polypeptide compounds resulting from libraries of peptides with random amino acid sequences (4) (5). The final aim of these |
| Databáze: | OpenAIRE |
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