Proteins are a basis of life -- malfunctions may lead to Alzheimer's disease -- repair requires the protein structure to be known -- experimental method is cumbersome
Nothing works without proteins in the body, they are the molecular all-rounders in our cells. If they do not work properly, severe diseases, such as Alzheimer's, may result. To develop methods to repair malfunctioning proteins, their structure has to be known. Using a big data approach, researchers of Karlsruhe Institute of Technology (KIT) have now developed a method to predict protein structures.
Homodimers are identical pairs of protein chains (proteins, green and blue) that bind to each other. Statistical analysis of protein sequences looks for mutations reflecting spatial proximity of protein segments both within the same protein (orange) and with a partner protein (red). This information can be used to predict the protein structure of the homodimer.
In the Proceedings of the National Academy of Sciences of the United States of America (PNAS), the researchers report that they succeeded in predicting even most complicated protein structures by statistical analyses irrespective of the experiment. Experimental determination of protein structures is quite cumbersome, success is not guaranteed. Proteins are the basis of life. As structural proteins, they are involved in the growth of tissue, such as nails or hairs. Other proteins work as muscles, control metabolism and immune response, or transport oxygen in the red blood cells.
The basic structure of proteins with certain functions is similar in different organisms. "No matter whether human being, mouse, whale or bacterium, nature does not constantly invent proteins for various living organisms anew, but varies them by evolutionary mutation and selection," Alexander Schug of the Steinbuch Centre for Computing (SCC) says. Such mutations can be identified easily when reading out the genetic information making up the proteins. If mutations occur in pairs, the protein sections involved mostly are located close to each other. With the help of a computer, the data of many spatially adjacent sections can be composed to an exact prediction of the three-dimensional structure similar to a big puzzle. "To understand the function of a protein in detail and to influence it, if possible, the place of every individual atom has to be known," Schug says.
For his work, the physicist uses an interdisciplinary approach based on methods and resources of computer science and biochemistry. Using supercomputers, he searched the freely available genetic information of thousands of organisms, ranging from bacteria to the human being, for correlated mutations. "By combining latest technology and a true treasure of datasets, we studied nearly two thousand different proteins. This is a completely new dimension compared to previous studies," Schug adds. He emphasizes that this shows the high performance of the method that promises to be of high potential for applications ranging from molecular biology to medicine. Although present work is fundamental research according to Schug, the results may well be incorporated in new treatment methods of diseases in the future.
Karlsruhe Institute of Technology (KIT) pools its three core tasks of research, higher education, and innovation in a mission. With about 9,300 employees and 25,000 students, KIT is one of the big institutions of research and higher education in natural sciences and engineering in Europe.
KIT - The Research University in the Helmholtz Association
Monika Landgraf | EurekAlert!
Barium ruthenate: A high-yield, easy-to-handle perovskite catalyst for the oxidation of sulfides
16.07.2018 | Tokyo Institute of Technology
The secret sulfate code that lets the bad Tau in
16.07.2018 | American Society for Biochemistry and Molecular Biology
For the first time ever, scientists have determined the cosmic origin of highest-energy neutrinos. A research group led by IceCube scientist Elisa Resconi, spokesperson of the Collaborative Research Center SFB1258 at the Technical University of Munich (TUM), provides an important piece of evidence that the particles detected by the IceCube neutrino telescope at the South Pole originate from a galaxy four billion light-years away from Earth.
To rule out other origins with certainty, the team led by neutrino physicist Elisa Resconi from the Technical University of Munich and multi-wavelength...
For the first time a team of researchers have discovered two different phases of magnetic skyrmions in a single material. Physicists of the Technical Universities of Munich and Dresden and the University of Cologne can now better study and understand the properties of these magnetic structures, which are important for both basic research and applications.
Whirlpools are an everyday experience in a bath tub: When the water is drained a circular vortex is formed. Typically, such whirls are rather stable. Similar...
Physicists working with Roland Wester at the University of Innsbruck have investigated if and how chemical reactions can be influenced by targeted vibrational excitation of the reactants. They were able to demonstrate that excitation with a laser beam does not affect the efficiency of a chemical exchange reaction and that the excited molecular group acts only as a spectator in the reaction.
A frequently used reaction in organic chemistry is nucleophilic substitution. It plays, for example, an important role in in the synthesis of new chemical...
Optical spectroscopy allows investigating the energy structure and dynamic properties of complex quantum systems. Researchers from the University of Würzburg present two new approaches of coherent two-dimensional spectroscopy.
"Put an excitation into the system and observe how it evolves." According to physicist Professor Tobias Brixner, this is the credo of optical spectroscopy....
Ultra-short, high-intensity X-ray flashes open the door to the foundations of chemical reactions. Free-electron lasers generate these kinds of pulses, but there is a catch: the pulses vary in duration and energy. An international research team has now presented a solution: Using a ring of 16 detectors and a circularly polarized laser beam, they can determine both factors with attosecond accuracy.
Free-electron lasers (FELs) generate extremely short and intense X-ray flashes. Researchers can use these flashes to resolve structures with diameters on the...
13.07.2018 | Event News
12.07.2018 | Event News
03.07.2018 | Event News
16.07.2018 | Physics and Astronomy
16.07.2018 | Life Sciences
16.07.2018 | Earth Sciences