Scientists of St. Petersburg University and The University of Montpellier has developed the first program to search for pairs of amyloid proteins capable of coagulation, that is, binding to each other. Studies have shown an accuracy of more than 94%.
Amyloids are protein aggregates that cause a number of severe and often incurable diseases, such as Alzheimer's, Parkinson's, Huntington's, and others. But not all such substances are pathogenic, many of them perform important functions in cells. According to scientists, the formation of amyloids is primarily associated with a change in the structure of protein in the body. However, recently in science there are more and more cases when several different elements are included in the composition of aggregates at once.
The team of geneticists and biotechnologists of St. Petersburg University in collaboration with researchers from For the first time in the world, the University of Montpellier (France) has proposed a bioinformatic approach called AmyloComp, which allows searching for pairs of proteins capable of coagulation — binding to each other. The method is implemented in the Python programming language and is available as an online application.
"Amyloids resemble filaments in shape. They form a kind of "stack" of many molecules located across the fiber. When only one protein is present in the aggregate, the layers are completely identical in structure. We are trying to find such sequences in different proteins that could form similar "stacks", but at the same time differed in sequence," said one of the authors of the study, associate professor at St. Petersburg State University (Department of Genetics and Biotechnology) Stanislav Bondarev.
According to him, the AmyloComp program developed by University scientists demonstrates an accuracy of more than 94% on a model dataset, and also reliably classifies known positive and negative examples of protein coagulation. Thus, protein coagulation can play various biological roles in the body.
On the one hand, the hypothesis of the "amyloid cascade" has been proposed for quite a long time, according to which pathological amyloid aggregates can provoke the aggregation of other proteins. On the other hand, some important biological processes require the formation of aggregates from different proteins. One striking example is a pair of human proteins, RIPK1 and RIPK3. Their coagulation is part of the signaling cascade when the antiviral response is triggered. The AmyloComp program allows you to search for similar examples at the proteome scale.
The uniqueness of the program created by St. Petersburg State University researchers lies in the fact that other approaches existing in modern bioinformatics do not allow modeling the coagulation of two amyloid proteins. The method of St. Petersburg State University researchers is based on comparing the amino acid sequence of two proteins and at the same time takes into account the possibility of their spatial arrangement as part of a single aggregate. This approach allows you to search for different sequences that form a single structure.
The team of scientists from the Department of Genetics and Biotechnology of St. Petersburg State University is one of the leading amyloid researchers in the world. The study of amyloids at St. Petersburg State University under the leadership of academician Sergei Inge-Vechtomov began back in the 90s of the XX century: then a number of world-class breakthrough works on infectious yeast amyloids (prions) were published. Later in the The University has a laboratory of amyloid biology, the head of which is Alexander Rubel, a graduate of the department.
In 2021, Anton Nizhnikov, a professor at St. Petersburg State University (Department of Genetics and Biotechnology), and Kirill Antonets, a leading researcher at St. Petersburg State University (Department of Cytology and Histology), became laureates of the prize of the President of the Russian Federation in the field of science and innovation for young scientists. The universants were awarded for the discovery of amyloid proteins in plants and symbiotic bacteria. At the same time, under the guidance of Professor Alexey Galkin, a number of functional amyloids in various animals were described.
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