1/2011

Secrets of cells revealed

Protein and lipid

Cell membrane and embedded protein. Professor Ilpo Vattulainen's group investigates their properties using atomic-level computer simulations. The protein is one of many voltage-gated proteins, whose malfunction is associated with, among others, epilepsy.


Proteins and lipids play a key role in cells, the basic building blocks of life. Understanding cellular functions is one of the first steps toward developing new therapeutic drugs and treatments.

"Protein-lipid interaction is one of the primary functions of cells. We know that by controlling this interaction we can govern the functions of the entire cell," says Professor Ilpo Vattulainen from the Department of Physics at TUT.

Vattulainen is currently heading the Biological Physics and Soft Matter Group, which he was invited to set up at the University in 2006. The group is made up of 30 researchers who apply computational research methods to biological problems relevant to human health. The core activities of the group are fundamental research and collaboration with experimental research groups around the world.

"Eighty percent of our research is fundamental research. We have active ongoing collaboration with about 50 other research groups, 65 percent of which are based abroad."

Computational science is the field of study concerned with processing and modelling data with a computer.

"We construct an accurate, atomic-level model of the biological object under scrutiny. After perfecting and iterating the model, we use the model and computer simulation to analyse phenomena that cannot be experimentally investigated in sufficient detail," says Vattulainen.

Nature calls for a cross-disciplinary approach

The research group explores phenomena whose lifetime varies from nanoseconds to microseconds.

Biological processes are so complex that they cannot be studied without bringing together expertise across conventional disciplinary boundaries.

"We may be looking at, for example, how molecules bond to each other and how this affects protein functions. In other words, we produce basic, nanoscale data and attempt to discover the mechanisms involved in biological phenomena."

"Our results can help pharmaceutical companies initiate new lines of research, develop methods for delivering drugs to specific areas inside the body and improve diagnostics," explains Vattulainen.

In addition to fundamental research, the group fosters a cross-disciplinary approach.

"Biological processes are so complex that they cannot be studied without bringing together expertise across conventional disciplinary boundaries. We need to bridge the gap between medicine, physics, chemistry and engineering sciences to address these problems."

"The cornerstones of drug development are pre-clinical research and clinical testing, but computational modelling brings undisputed added value to the process. Our group has opted for collaboration with cell biologists and clinical research professionals."

At the forefront of modelling protein-lipid interactions

Vattulainen's group has been internationally recognized for excellence in modelling protein-lipid interactions needed to understand cellular phenomena. One of the group's current lines of research investigates cholesterol and is conducted together with the VTT Technical Research Centre of Finland and the National Institute for Health and Welfare. It is of great significance to Finns that have notoriously high levels of cholesterol.

Another line of research explores cell membrane functions and especially the characteristics of lipids that modulate cell behaviour. The results will shed light on the molecular effects of, for example, anaesthetics.

"We also take part in eye and lung membrane research. We still don't know how oxygen, carbon dioxide and different airborne particles penetrate into the lungs. It would be important to uncover the vital mechanisms underlying respiratory functions," says Vattulainen.

 

Text: Päivi Eskelinen
Photo: CSC - Tieteen tietotekniikan keskus


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