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Big Data for Life Sciences – Human Protein Coagulation Map Reveals New Protein Knowledge

Proteins are key molecules in living cells. They are responsible for almost every task of mobile life and are essential for maintaining the structure, function and regulation of tissues and organs in the human body.

The cells in the human body can form thousands of different types of proteins (the so-called proteiomes), which perform a variety of different functions, all key to cell viability and human health. Delivering the functions of the vast array of proteins present in our cells remains a challenging task in cell biology.

The scientists have now developed a coordinate map of the human proteome that was able to capture links between proteins that do not physically interact or co-localize. This will allow for the prediction and assignment of functions of uncharacterized human proteins. The co-regulation map can be explored at www.proteomeHD.net.

Many of the functions of human proteins are not yet known, but researchers from the Center for Cell Vegetation at Velcom, the University of Edinburgh and the Institute of Biotechnology, Technical University of Berlin have applied quantitative quantitative proteomics and machine learning data to machine learning. of the proteins of the human proteome. The database is the basis of a coordinate map that can be used to predict the potential function of undifferentiated human proteins.

"In this study, we took thousands of mass spectrometry experiments reported by other laboratories in recent years and reconstructed them in a way that was completely unrelated to what the original authors planned. We used machine learning algorithms to dig this huge data collection and we were able to assign biological function to hundreds of proteins that were previously uncharacterized. Berlin.

Map research has revealed unexpected co-regulatory partners, namely the peroxisomal membrane protein PEX11β with mitochondrial respiration factors. In collaboration with Professor Michael Schroeder and his team at Exeter University, this led to the identification of a new interaction between two key cellular organelles – mitochondria and peroxisomes.

"Peroxisomes and mitochondria in mammals are intimately related and cooperate in the breakdown of fatty acids and cellular energy balance. Using live cell imaging, we found that PEX11β mediates the formation of membrane protrusions, which arise from peroxisomes and interact with mitochondria. They probably function in metabolic co-operation and cross-linking between the two organelles and can facilitate the transfer of metabolites during the production of mitochondrial energy (ATP), "said Professor Michael Schroeder of Exeter University.

Scientists from the University of Edinburgh have created the website www.proteomeHD.net to allow users to search for protein of interest, showing their position in the co-regulation map along with all co-regulatory partners. The internet map is interactive and zooming in, making it easy to research the neighborhood of the search protein. It is designed to support researchers in researching multi-scale co-ordination data, validating existing hypotheses, or creating new ones.

"With the increasing amount of protein expression data available, protein expression analysis has the great potential to capture gene function. At a time when "big data" is becoming more relevant to life science, the key lessons we learned from this project are: never throw away your data – they can be re-targeted, recycled, and with the right tools there is a lot more information and knowledge what can be deduced from them, "said Dr. Georg Kustaster, of the University of Edinburgh.

The research was supported by Velovest Trust, Biotechnology and Biological Sciences Research Council and the EU, Marie Skodovska-Curie, Periko Innovative Training Network.

The paper, published in the journal Nature Biotechnology, is entitled "A Human Proteomic Coordination Map Enables Identification of Protein Functions."

The authors were Georg Kustacher, Piotr Grabowski, Tina A. Schroeder, Josiah B. Pasmore, Michael Schroeder and Yuri Rapsilber.

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