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Biochemists Predict Properties of Fusion Proteins
March 14, 2006 15:18

Russian and American biologists supported by Russian Federal Innovation Agency and the united Stated Civilian Research and Development Foundation are going to use computer facilities for developing artificial proteins with tailor-made properties, and then start an experiment, proving their calculations. Such combination of mathematical calculations and biological experiments is expected to save much effort and money.
 

Recent biochemist considered chromatograph and electrophoresis unit to be his main facilities. But now computer replaces them. Bioinformatics professionals have developed special software for modeling biochemical processes and complex molecules’ behaviour. Research teams start experiments only when all dead ends are eliminated, and scientists see direct way to their goal. Such approach was used by international scientific team from Science and Research Institute of Biomedical Chemistry (Moscow, Russia) and Vanderbilt University (USA), while constructing artificial protein if cytochrome P450 family.
 

Proteins of cytochrome P450 family play an important role in living organisms: they are responsible for oxidizing alien chemical compounds, also known as xenobiotics, which can be harmful for cells. Oxidation process promotes excretion of xenobiotics from an organism, thus cleaning cells from chemical waste. P450 cytochromes have prime importance and can be found nearly in all existing organisms – bacteria, plants, fungi and animals. Keeping their unique general function, P450 cytochromes vary widely in their structure.
 

Biologists suggested regarding different structural elements of existing proteins as a design kit for creating artificial fusion proteins, which combine several structural components. Scientists expect these proteins to perform preprogrammed biological function. Why do they need it? The answer is simple: artificial proteins, designed on the basis of cytochrome P450 family, can be used for complex chemical synthesis of various drug prototypes, fertilizers, etc.
 

About three years ago Russian biochemists have come out with the hypothesis that the dominating role in P450 cytochrome structure and interactions with other chemical agents is played by motives, in other words, by special three-dimensional configurations of separate protein fragments, specific folds and turns of the molecule. Detecting these fragments is the first stage of the project. Then computer will start substituting motives and calculating three-dimensional configurations, which allows selecting fusion proteins with certain structure and functions, not just a simple chain of molecules. Then neurocomputer will step out.
 

"Neurocomputer" is a new fashionable bioinformatics term for software, looking like a virtual neural network – something like simplified brain model. Such network can learn and accumulate information. The network is expected to use various well-known reactions of P450 cytochromes with other chemical agents for learning how to select correct interactions. Then the network tries to find what chemical compounds would fusion protein, combined from natural fragments, select for interactions. The project will succeed after biologists prove their technique to make correct predictions of fusion proteins’ properties.
 

Modern genetic engineering allows easy creation of a transgenic (recombinant) organism, which will synthesize fusion protein, previously existed only as a computer model. American biologists will prepare all necessary reagents and send them to Russia. Russian project participants are going to clone microorganisms, purify proteins and measure their activity by means of American reagents. After that, protein samples will be sent back to Vanderbilt University, where they will be crystallized, and their structure will be studied for correct further computer modelling. One of the Russian students will take part in said experiments in the USA and will learn some methods of protein crystallography. Developed statistical model can be used for rational developing of new proteins with new or enhanced properties.
 


Tags: Russian Scientists     

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