Pallab Bhowmick
I did my 4 years undergraduate from Westbengal University of Technology on Biotechnology where course comprises Chemistry, Microbiology, Genetics, Genetic Engineering, Protein Engineering among others. During my Undergraduate I decided to focus on Bioinformatics more and I went in Cardiff university to do my Post Graduate Certificate on Bioinformatics where I learned various computational application interest of biology. I designed Protein Database using Java Programme by SQL command where the objective was to design and apply a small relational database by using the MySQL RDBMS at server side. After finishing my Post grad certificate successfully, I moved to Birkbeck, University of London for doing MSc in Bioinformatics with Systems Biology and I worked at Dr Andrew Martin's group, Research Department of Structural and Molecular Biology, UCL where my main task was looking at preferred pairing of mouse antibody germline sequences using Abysis which is my Msc thesis as well as. Currently I am now in Vlaams Instituut voor Biotechnologie (VIB) in Brussels (Department of Structural Biology) and working under supervision of Peter Tompa.
| Researcher |
Pallab Bhowmick |
| Project Topic |
Improved bioinformatic tools for identifying disordered proteins |
| Project Description |
Intrinsic structural disorder brings functional diversity in human Ubiquitin network
The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with a single E1 (ubiquitin activating), few dozen of E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes serving the entire proteome. Disordered regions in E3s may serve as linkers, when they allow an “intramolecular diffusion” of substrate- and E2 binding regions to each other. They are also often involved in molecular recognition, as shown by the elevated level of disorder in E3s of multiple interaction partners. Furthermore, a search in PDB has uncovered distinct examples of human E3 interactions, where the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In all, our data are consistent with the primary role of structural disorder in the complex function of E3 ligases that provide an interface between the PQC system and the proteome.
Misprediction of structural disorder in extremophiles
Whereas the concept of intrinsic disorder derives from biophysical observations of the lack of structure of proteins under native conditions, many of our respective concepts rest on genome-scale bioinformatics predictions based on amino acid sequence. It is established that most predictors work reliably on proteins commonly encountered, however, little is known about their performance on proteins derived from microorganism that thrive in environments of extreme temperature, pH or salt concentration. To address the accuracy of disorder prediction in these extremophiles, we do draw general conclusions and formulate recommendations for how structural disorder in extremophiles can be more reliably addressed with current bioinformatics tools.
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| Project Home |
Vlaams Instituut voor Biotechnologie (VIB) |
| Supervisor | Peter Tompa |
| Starting Date | September 2011 |
| Publications |
Functional diversity and structural disorder in the human ubiquitination pathway paper is submitted in PLoS Computational Biology |
| Meetings |
FEBSub2012
Gordon Research Conferences - Intrinsically Disordered Proteins INGENUITY PATHWAYS ANALYSIS TRAINING Intensive Training Module – Marie Curie Training Network VIB Seminar 2012 Complementary Skills Training – Marie Curie Training Network Intensive Training Course – Marie Curie Training Network |
Scientific Posters:
Gordon Research Conferences - Intrinsically Disordered Proteins
West Dover, Vermont, USA
July 8-13, 2012