Computations of protein hydrophobicity profile as virtual experiment in gridspace virtual laboratory

• Autorzy: Ciepiela E. , Jadczyk T. , Harężlak D. , Kasztelnik M. , Nowakowski P. , Dyk G. , Malawski M. , Bubak M. , Roterman I.
• Języki publikacji: EN

Abstrakty

EN

The terms like e-science, e-poster or e-health are nowadays commonly used. Special disciplines allowing fast development in these fields of science are commonly available. This paper presents e-paper [1] powered by the Collage Authoring Environment [2] e-publication system which is backed by the GridSpace2 [3] distributed computing platform. This e-publication in a form of WWW page, apart from the traditional textual and graphical content, embeds an on-line software tool for the analysis of the 3-D structure of protein based on the hydrophobicity distribution in protein body. The tool uses GridSpace2 platform in order to carry out computations on the PL-Grid [4] high-performance computing infrastructure. This work shows how this specific e-publication was accomplished utilizing above mentioned already existing information technologies and e-infrastructure. The tool employs the model called “fuzzy oil drop” that assumes the hydrophobicity distribution in proteins being in form of 3-D Gauss function. The protein of the hydrophobicity core structure accordant with the model with all hydrophobic residues buried in the central part of the protein body and hydrophilic residues exposed toward the water environment could be the protein very well soluble although representing no any form of activity. This is why the observed discrepancies between idealized and observed hydrophobicity distribution is presented in form of profile revealing the localization of residues representing local hydrophobicity excess as well as local hydrophobicity deficiency. The distribution of these discrepancies appeared to be specific and function related. The e-publication makes available the tool to calculate the profile of any protein under consideration. The interpretation of the final results is specific for particular protein.

Słowa kluczowe

EN

hydrophobicity distribution; tertiary structure of proteins; e-publication; virtual laboratory

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2012
• Tom: Vol. 8, no. 4
• Strony: 361--372
• Opis fizyczny: Bibliogr. 13 poz., rys.

Twórcy

autor

Ciepiela E.

• Academic Computer Centre CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland

autor

Jadczyk T.

• Academic Computer Centre CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland

autor

Harężlak D.

• Academic Computer Centre CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland

autor

Kasztelnik M.

• Academic Computer Centre CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland

autor

Nowakowski P.

• Academic Computer Centre CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland

autor

Dyk G.

• Academic Computer Centre CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland

autor

Malawski M.

• Department of Computer Science, AGH University of Science and Technology, al. Mickiewicza 30, 30-059 Kraków, Poland

autor

Bubak M.

• Academic Computer Centre CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland

autor

Roterman I.

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

Bibliografia

• [1] Jadczyk T, Malawski M, Bubak M, Roterman I. (2012) Protein Hydrophobicity Profile, e-publication hosted on GridSpace2 Executable Publications Portal, http://gs2.cyfronet.pl/epapers/hydrophobicity-profile/
• [2] Nowakowski P, Ciepiela E, Harężlak D, Kocot J, Kasztelnik M, Bartyński T, Meizner J, Dyk G, Malawski K. (2011) The Collage Authoring Environment. In: Proceedings of the International Conference on Computational Science, ICCS 2011
• [3] Ciepiela E, Nowakowski P, Kocot J, Harezlak D, Gubala T, Meizner J, Kasztelnik M, Bartynski T, Malawski M, Bubak M. (2012) Managing Entire Lifecycles of e-Science Applications in the GridSpace2 Virtual Laboratory - From Motivation through Idea to Operable Web-Accessible Environment Built on Top of PL-Grid e-Infrastructure. In: PL-Grid 2012, pp. 228-239
• [4] PL-Grid: Polish National Grid Initiative, http://www.plgrid.pl/en
• [5] Distributed Computing Environments (DICE) Team website – http://dice.cyfronet.pl/
• [6] Ciepiela E, Harezlak D, Kocot J, Bartynski T, Kasztelnik M, Nowakowski P, Gubała T, Malawski M, Bubak M. (2010) Exploratory Programming in the Virtual Laboratory. In: Proceedings of the International Multiconference on Computer Science and Information Technology, pp. 621-628.
• [7] Konieczny L, Bryliński M, Roterman I (2006) Gauss-function-based model of hydrophobicity density in proteins. InSilico Biol 6, pp. 5-22.
• [8] Levitt M (1976) A simplifed representation of protein conformations for rapid simulation of protein folding. J Mol Biol 104, pp. 59-107.
• [9] GridSpace2 Executable Publications Portal, http://gs2.cyfronet.pl/epapers/
• [10] Wordpress, web blog platform, http://wordpress.org/
• [11] Protein Data Bank (PDB), http://www.rcsb.org/pdb/
• [12] Roterman I. (2012) Identification of Ligand Binding Site and Protein-Protein Interaction Area, Springer
• [13] PL-Grid Portal – main information and management interface for PL-Grid users, https://portal.plgrid.pl/