2013 Fiscal Year Research-status Report
New insights into protein folding based on bioinformatics analysis of cell-free protein synthesis
| Project/Area Number |
25440023
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Research Institution | Kobe University |
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Principal Investigator |
TOKMAKOV A・A 神戸大学, 学内共同利用施設等, 研究員 (20301278)
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| Project Period (FY) |
2013-04-01 – 2016-03-31
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| Keywords | protein folding / cell-free synthesis / bioinformatics |
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| Research Abstract |
Presently, an approach aimed at identification of numerous physicochemical, structural and functional properties of amino acid sequences, including the sites of multiple PTMs, associated with soluble expression of eukaryotic proteins in bacterial cell-free extracts has been finalized and published [1]. The developed method is intended for analysis of output from a cell-free protein production pipeline. It includes: 1) categorical assessment of expression data; 2) calculation and prediction of multiple properties of expressed sequences; 3) correlation of the individual properties with the expression scores; and 4) evaluation of statistical significance of the observed correlations.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
At present, the method for identification of numerous physicochemical, structural and functional properties of amino acid sequences, including the sites of multiple PTMs, associated with soluble expression of eukaryotic proteins in bacterial cell-free extracts has been published [1]. The prototype of the prediction algorithm for assessment of protein amenability to cell-free expression is being evaluated by its ability to correctly classify new targets not present in the initial training set. The developed discriminant function is being applied to the test set of the expressed proteins, and prediction accuracy is estimated for this set.
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| Strategy for Future Research Activity |
During the second year of study (2014) recombinant proteins will be expressed in the eukaryotic cell-free system. A complete dataset of cell-free expressed proteins will comprise a number of non-redundant (at 90% identity) amino acid sequences. The proteins of different functional and structural classes will be represented in the dataset, with the unbiased target selection in this regard. All the proteins will be expressed in the extracts under the same uniform set of conditions minimizing the influence of sequence-independent factors. The scores A, C, and N will be designated to all experimentally expressed proteins as follows: A - soluble proteins, C - expressed, but insoluble proteins, and N - non-expressed proteins. Multiple features of the expression sequences will be predicted using available bioinformatics tools.
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Research Products
(6 results)
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[Presentation] mRNA degradation in apoptotic Xenopus eggs2013
Author(s)
1. Alexander A. Tokmakov, Takanori Hashimoto, Yushi Hasegawa, Sho Iguchi, Tetsushi Iwasaki and Yasuo Fukami
Organizer
Cold Spring Harbor symposium on Eukaryotic mRNA processing
Place of Presentation
Cold Spring Harbor, New York, USA
Year and Date
20130820-20130824
