FUTDB – FUned Toxin Data Base: a database to store data for experiments of protein and toxin purification. Ricardo de Souza Ribeiro1, Danilo Mudado Teixeira2, Renato Almeida Soares1, Thais Melo Mendes1, Márcia Helena Borges2, Marta do Nascimento Cordeiro2, Michael Richardson2, Maurício de Alvarenga Mudado2, Bernardo Penna Resende de Carvalho1, Sanderson Vanucci Carvalho1. 1
Ottimah Tecnologia de Software Ltda. http://www.ottimah.com - Rua Padre Marinho, 37 / 13 – Santa Efigênia, Belo Horizonte – Minas Gerais – Brasil. Tel: (31) 3241-6295 2 FUNED – Fundação Ezequiel Dias. http://www.funed.mg.gov.br - Rua Conde Pereira Carneiro, 80 – Gameleira, Belo Horizonte – Minas Gerais – Brasil. Abstract Protein purification demands great lab effort and many rounds of experimentation. For more than 20 years, researchers from Fundação Ezequiel Dias - FUNED have been doing toxin and protein purification, especially from the venoms of the the spider Phoneutria nigriventer and the scorpion Tityus serrulatus. These experiments have generated great amounts of data, including diverse chromatography data, gel electrophoresis, molecular mass weight definitions and peptide sequencing. To store and make all this data available to FUNED researchers, we constructed a webtool that is a web interface connected to a relational database. This webtool, named FUTDB for FUned Toxin DataBase, and can store raw data from protein purification and characterization experiments. The web interface navigation is easy and simple and allows one to populate the database with chromatography data (chromatography images, column specifications, buffers, etc), cicle images and protein sequences from peptide sequencing, electrophoresis gel experiments (experimental data and images) and molecular weight mass determination data. The webtool was constructed using Apache/PHP/MySQL, HTML/CSS and is currently installed at FUNED’s intranet in a GNU/Linux server. Compared to other similar databases like BNDb [1], PEDRo[2] and 2DDB[3], the differential of this tool is that data is viewed in a form of an hierarchical tree, where children experiments are shown down in the same branch of its parent experiment. In this way it is possible to reconstruct the path from any experiment to the origin in an easy way. In order to help researchers in protein characterization, the peptides and protein sequences deposited can be used as input to homology searches with BLAST and public databases like nr, UniProt and four toxin databases: Tox-Prot [4], ATDB[5], Scorpion2 [6] and a non-redundant compilation of these three databases that we have constructed. FUTDB is still under construction and we intend to implement the storage of biological activity experiments and proteomic data, like two dimensional gel electrophoresis, as well as services for protein secondary structure prediction and toxin pattern searches. An alpha-version of the FUTDB webtool, with limited features, can be evaluated at the address: http://www.ottimah.com/funed. To access it, one can use the login “guest” and password “guest”. We have uploaded some data of the purification of TX1, a toxin from the venom of the spider Phoneutria nigriventer, for evaluation. The data consists of gel-filtration and reverse phase chromatographies, molecular mass calculations, gel electrophoresis and peptide sequencing.
Acknowledgements The authors would like to thank FAPEMIG for the support in the development of this work (process APQ-6751-4.01/07). References [1] Faria-Campos, A.C., Gomes, R.R., Moratelli, F.S., Rausch-Fernandes, H., Franco, G.R. and Campos, S.V.A. BNDb - Biomolecules Nucleus Database: an integrated proteomics and transcriptomics database. Genet. Mol. Res. 2007, 6 (4): 937-945. [2] Garwood, K., McLaughlin, T., Garwood, C., Joens, S., et al. PEDRo: a database for storing, searching and disseminating experimental proteomics data. BMC Genomics 2004, 5: 68. [3] Malmström, L., Marko-Varga, G., Westergren-Thorsson, G., Laurell, T., et al. 2DDB - A bioinformatics solution for analysis of quantitative proteomics data. BMC Bioinformatics 2006, 7: 158. [4] Jungo, F. and Bairoch, A. Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase. Toxicon 2005, 45:293-301. [5] Tan, P. T. J., Veeramani, A., Srinivasan, K. N., Ranganathan, S., Brusic, V. Scorpion2: A database for structure-function analysis of scorpion toxins. Toxicon 2006, 46:356-363. [6] He, Q. Y., He, Q. Z., Deng, X. C., Yao, L., Meng, E., Liu, Z. H., Liang, S. P. ATDB: a uni-database platform for animal toxins. Nucleic Acids Research. 2007, 1–5.
