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1 Bio-Algorithms and Med-Systems

1 2012

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

Ciepiela E., Jadczyk T., Harężlak D., Kasztelnik M., Nowakowski P., Dyk G., Malawski M., Bubak M., Roterman I.

Bio-Algorithms and Med-Systems

2012

Vol. 8, no. 4

361--372

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.