Instytut Podstawowych Problemów Techniki
Polskiej Akademii Nauk


K. Prymula

Ostatnie publikacje
1.  Prymula K., Piwowar M., Kochańczyk M., Flis Ł., Malawski M., Szepieniec T., Evangelista G., Minervini G., Polticelli F., Wiśniowski Z., Sałapa K., Matczyńska E., Roterman I., In silico Structural Study of Random Amino Acid Sequence Proteins Not Present in Nature, CHEMISTRY AND BIODIVERSITY, ISSN: 1612-1872, DOI: 10.1002/cbdv.200800338, Vol.6, No.12, pp.2311-2336, 2009

The three-dimensional structures of a set of ‘never 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 the ‘fuzzy-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 be ‘unfoldable’ for 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.

Afiliacje autorów:
Prymula K. - inna afiliacja
Piwowar M. - inna afiliacja
Kochańczyk M. - IPPT PAN
Flis Ł. - Jagiellonian University (PL)
Malawski M. - AGH University of Science and Technology (PL)
Szepieniec T. - Academic Computer Center CYFRONET (PL)
Evangelista G. - Universita degli Studi Roma Tre (IT)
Minervini G. - Universita degli Studi Roma Tre (IT)
Polticelli F. - Universita degli Studi Roma Tre (IT)
Wiśniowski Z. - Jagiellonian University (PL)
Sałapa K. - Jagiellonian University (PL)
Matczyńska E. - Jagiellonian University (PL)
Roterman I. - Jagiellonian University (PL)
2.  Bryliński M., Prymula K., Jurkowski W., Kochańczyk M., Stawowczyk E., Konieczny L., Roterman I., Prediction of Functional Sites Based on the Fuzzy Oil Drop Model, PLOS COMPUTATIONAL BIOLOGY, ISSN: 1553-7358, DOI: 10.1371/journal.pcbi.0030094, Vol.3, No.5, pp.e94-0909-0923, 2007

A description of many biological processes requires knowledge of the 3-D structure of proteins and, in particular, the defined active site responsible for biological function. Many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. Currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localization of active sites in proteins. This paper describes a computational model that can be used to identify potential areas that are able to interact with other molecules (ligands, substrates, inhibitors, etc.). The model for active site recognition is based on the analysis of hydrophobicity distribution in protein molecules. It is shown, based on the analyses of proteins with known biological activity and of proteins of unknown function, that the region of significantly irregular hydrophobicity distribution in proteins appears to be function related.

Słowa kluczowe:
Protein structure, Amino acid analysis, Isomerases, Protein structure prediction, Genomic databases, Structural genomics, Protein structure comparison, Oils

Afiliacje autorów:
Bryliński M. - inna afiliacja
Prymula K. - inna afiliacja
Jurkowski W. - inna afiliacja
Kochańczyk M. - IPPT PAN
Stawowczyk E. - inna afiliacja
Konieczny L. - inna afiliacja
Roterman I. - Jagiellonian University (PL)

Kategoria A Plus


logo ippt            ul. Pawińskiego 5B, 02-106 Warszawa
  +48 22 826 12 81 (centrala)
  +48 22 826 98 15

Znajdź nas

© Instytut Podstawowych Problemów Techniki Polskiej Akademii Nauk 2024