New method reveals changes in protein structure more efficiently and accurately than ever before

Important processes take place among the subunits of the molecules that make up our cells. Defects in these processes or distortions in the subunits can lead to serious illness. In order to better understand this microscopic world, researchers from Hungary and Germany jointly developed a method that reveals changes in the structure of proteins more efficiently and precisely than before. The study is published in one of the leading journals in chemistry, Angewandte Chemie.

Amino acids are the building blocks of protein in our body. The amino acid sequence determines the properties of proteins and the processes in which they are involved. In recent years, there has been increasing interest in intrinsically disordered proteins (IDPs), which lack a stable structure, are mobile and can be described as a set of conformational sets.

Research has shown that IDPs, or intrinsically disordered regions (IDRs) play an important regulatory role in various biochemical processes and contribute to the development of many diseases. They have been linked to Parkinson’s and Alzheimer’s disease, various cancers, and type 2 diabetes.

An IDP is rich in amino acids having hydrophilic and charged side chains. In addition, the presence of proline, which has “structural disruption” properties, is also common. Proline is difficult to study due to its unique structure, but it is also involved in important biochemical regulatory processes, which makes its full characterization of great importance.

NMR spectroscopy: the measurement method

Researchers from Eötvös Loránd University, Hungary, KIT University Karlsruhe, Germany, and the Bruker company jointly developed a new NMR (Nuclear Magnetic Resonance) spectroscopic method based on specific manipulations of quantum states , which can be used to map the function of an IDP easier, faster and more accurate.

The methodological breakthrough will make it possible to characterize biochemical processes hitherto unexplored and difficult to study.

The results will shed light on the mechanisms of the processes involved and will greatly contribute to our understanding of the pathogenesis of certain diseases.

Proline: the “structuring” amino acid

One of the unique properties of proline is that, unlike other natural amino acids, it is more likely to be present in different forms, called cis / trans isomers. While the usual position in proteins is generally trans, in displaced people, both forms of proline may appear in varying amounts. The two forms create different structures in the environment of proline: trans-proline forms a more elongated shape, while cis-proline forms a turn. These different geometric states of IDPs affect interactions with their binding partners, thus influencing how biochemical processes occur.

“It is understood that the determination of the isomeric forms of proline and the quantification of specific isomers is an important problem. Previously, expensive, synthetic, and expensive procedures were used to map the influence of proline. These are artificial interventions, which lead to a disturbance of the cis-trans balance of proline, skewing results.

The appropriate solution can be obtained by measuring the actual equilibrium which should be based on a sufficiently sensitive and widely applicable technique – therefore a new approach had to be established. “

Andrea Bodor, Associate Professor, Institute of Chemistry, Eötvös Loránd University

NMR spectroscopy is a suitable technique for characterizing IDPs at the atomic level, since characterization of mobile molecules is not possible with X-ray crystallography and currently popular electron cryo-microscopy methods. “In view of this, we had to develop a technique that would allow the detection of small amounts of proline isomers in a relatively short measurement time with excellent resolution. The advantage of the new method is that the measurements can be performed in any bioRMN laboratory. , without the need for special instrumentation ”, underlined Andrea Bodor, responsible for this research project.

The New Method and the Future of Understanding Protein Function

The effectiveness of the new method has been demonstrated on a disordered fragment of the biologically important tumor suppressor protein p53, showing that the changes (in this case phosphorylation) that occur in the body can affect the cis-trans balances proline, thereby directing the function of the protein. In general, it is possible to detect equilibrium isomers for any given protein, especially if it is an IDP, under in vitro conditions without long and complex procedures. In addition, the involvement of a given isomeric form in other post-translational modifications can also be traced, thus leading to information about the function of the protein.

On broader aspects, the new method will help to follow the process of protein dysfunction and to understand the development of the disease.

“The results presented are based on successful collaborations,” added Andrea Bodor. “We have a long history of collaboration with László Nyitray’s group at the Department of Biochemistry at Eötvös Loránd University, Hungary, Burkhard Luy’s group at KIT Karlsruhe and Wolfgang Bermel de Bruker. “The scientific article accepted for publication has been classified as” very important article “by the editor of Angewandte Chemie.