Dec 30, 2009
Center for Computational Engg, Coimbatore
The word E.coli brings up dreaded images of filth and disease. But actually, most strains of this bacterium are harmless. And some may even be useful, as a new study has shown. Research associates at Amrita’s Coimbatore campus have concluded that E.coli aquaporins can be effectively used to develop membranes for desalination of water.
It is said that if all of the world’s water were fit in a gallon jug, the fresh water available to mankind for use, would equal only about one tablespoon. 97% of the total amount of water on earth is stored in oceans. This water can be used by man, only if it is desalinated.
Desalination, currently, is not very cost-effective and the search is on for better technologies. Aquaporins or proteins embedded in cell membranes that regulate the flow of water in all living beings can be isolated to make membranes to do the job. Amrita’s study compared human and E.coli aquaporins and concluded that the latter were better.
The study’s results will be presented at the international conference Bioinformatica Indica 2010 during January 11-13, 2010 as a paper titled In-Silico Analysis (Structural and Sequence) of Aquaporins. The conference is organized by the DBT-BIF Center for Bioinformatics at the University of Kerala.
“In this research paper, we investigate the structural and sequence characterization of aquaporins that makes them behave as unique water channels of the body,” states the paper abstract. “Aquaporins being permeable only to water and a few other molecules like glycerol do not follow a normal size-based sieving mechanism.”
“… A comparative study was undertaken between human and E.coli aquaporins … Most of E.coli aquaporins were found to be hydrophilic in nature. From their instability index, it was confirmed that E.coli aquaporins are more stable as compared to human aquaporins. … E.coli aquaporins can be effectively used in developing a membrane for desalination of water.”*
M.Tech students at the Computational Chemistry Group of the Center for Computational Engineering and Networking also participated in the study. Alongside these students was an MSc student of Bioinformatics from the Amritapuri campus. “We wish to thank Dr. Bipin Nair, Dean of the Amrita School of Biotechnology and Dr. V. P. Mohandas, Chairman of the Department of ECE at Coimbatore, who guided us,” stated Krishnan Namboori P. K., who led the study.
* Varun Gopal K., Praveen Babu J., Radhagayathri K. U., Vasavi C. S., Premkumar P., Krishnan Namboori P. K., In-Silico Analysis (Structural and Sequence) of Aquaporins
Abstract
In this research paper, we investigate the structural and sequence characterization of aquaporins that makes them behave as unique water channels of the body. Aquaporins being permeable only to water and a few other molecules like glycerol do not follow a normal size-based sieving mechanism. This was proved by dimensionally analyzing the structures. Other properties like stability, hydrophobicity and aliphaticity were investigated based on the analysis of primary and secondary structures. A comparative study was undertaken between human and E.coli aquaporins. The thermodynamic behavior of these protein molecules was also studied and compared for the two species by means of computational modeling and simulation. From dimensionality analysis, it was concluded that the diameter of nanopores present in aquaporins was larger than the size of metal ions. Most of E.coli aquaporins were found to be hydrophilic in nature. From their instability index, it was confirmed that E.coli aquaporins are more stable as compared to human aquaporins. It was concluded that E.coli aquaporins can be effectively used in developing a membrane for desalination of water.
