07.09.2015 change 07.09.2015

Soap bubble mathematics helps describe proteins

Source:Fotolia Source:Fotolia

Some proteins - including the satiety hormone - are shaped like a lasso. They have been described by Polish scientists. Now, in a study of how these compounds are formed, they use mathematics and ... soap bubbles - told PAP mathematician Wanda Niemyska.

"In our work, we study the shape of proteins. Recently, we discovered that certain proteins resemble somewhat a lasso - they consist of a loops and tail, which is pulled through the loop, and sometimes wraps around it several times" - PhD student Wanda Niemyska spoke about the work of the team the Interdisciplinary Laboratory of Biological Systems Modelling, Centre of New Technologies of the University of Warsaw. Niemyska, PhD student in mathematics at the University of Silesia, is the winner of the program INTER of the Foundation for Polish Science. For her research on lasso proteins she received 100 thousand zlotys.

"For now, we have examined a group of two thousand proteins, which have loops. It turns out that among them approx. 18 percent - approx. 360 - has a lasso structure. Until recently, no one knew that proteins can have such form" - said Niemyska. One such lasso protein is leptin - the hormone responsible for satiety.

The mathematician explained, what determines the shape of protein. "Protein in the beginning is developed. It can be imagined as a thread with beads. Then, this compound folds, forming its proper shape" - said the researcher. She explained that it was only after appropriate orientation in space - adopting an active form - protein can perform its biological function. Scientists want to understand how proteins are arranged, what makes these compounds fold properly and how to prevent them from unfolding. If something goes wrong in the process of folding, protein ceases to fulfil its function well. Abnormal leptin could result in eating disorders and obesity.

"In our research, we wondered how to describe the geometric structure of proteins. We used soap bubble membranes that have a very interesting property: they are arranged in space in such a way as to minimize their field and energy" - said Niemyska. She explained that real membranes, which we know from soap bubbles, of course were not used. Researchers wrapped computer models of loops in virtual membranes. The mathematician explained that when the loop is short and has a regular shape similar to a circle, you can easily see with the naked eye, how many times and how the tail passes through it. But it is not always so easy.

"Loops are often long and bent. And in such case it is difficult to determine the relative position of the tail. Even after staring at the protein for a long time, to one person it may seem that the tail passes through the loop, and to another - that it does not pass. A more objective description is necessary"- explained the mathematician. She added that the stretching a virtual soap membrane between amino acids is a good way to define what it means that the tail passes through the loop. With the membrane it can be seem exactly how the loop is positioned relative to the tail and can be clearly observed how many times it passes through it.

Niemyska admitted that mathematics is rarely associated with applications. However, it turns out that chemists can benefit from cooperation with someone who knows topology, differential geometry and algorithmics. "As a mathematician, I wonder which mathematical theories and theorems can be useful in a given situation, and then I use them to make tools adapted to solve specific problems associated with proteins" - she explained.

PAP - Science and Scholarship in Poland, Ludwika Tomala

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