New 3D method improves the study of proteins – Look Professional

New method improves 3D study of proteins

BARCELONA, April 27: An international team of scientists developed a new computational method that favors 3D study of the structure of the folded globular proteins.

A joint investigation conducted by the Institute of Biotechnology and Biomedicine at the Autonomous University of Barcelona (IBB-UAB) and the University of Warsaw developed a computational method – called AGGRESCAN3D – allowing 3D studying the structure of the folded globular proteins and substantially improves the prediction of their propensity to form toxic protein aggregates. With the new algorithm, the proteins can also be modeled to study the pathogenic effects of aggregation or redesign therapeutic purposes.

The current understanding of the molecular basis of protein aggregation, causing many diseases, has generated a series of algorithms to identify regions prone to add protein. Among them, AGGRESCAN developed eight years ago by the same researchers from IBB, which was one of the first computational methods that were created for that purpose. But most of these algorithms analyze only the regions … <- onmouseout="this.style.overflow = 'hidden';" ! onmouseover="this.style.overflow = 'visible';" ->

which are in the linear sequence of the protein. This makes it difficult to predict the aggregation properties of globular proteins, where these sequences are often protected within their native spherical structure.

The AGGRESCAN3D (A3D), which is implemented as a web server free access to academia , overcomes these limitations with an approach based on the structure of proteins from folded conditions. According to the article in which the researchers have published in Nucleic Acids Research, the algorithm has a significantly higher accuracy than those based on linear sequences to predict the properties of aggregation of globular proteins and brings important new benefits, including is the possibility to easily model pathogenic mutations or redesigning proteins of therapeutic interest, including antibodies, with increased functionality.

“So far, the A3D is the algorithm faster available for predicting protein aggregation that can work in a dynamic mode, that is, taking into account the flexibility of the protein structure. This allows us to model aggregations attributable to natural fluctuations of the structure as well as those that are caused by destabilizing pathogenic mutations and predict their impact on the propensity to aggregation “says Salvador Ventura, researcher at IBB and Department of Biochemistry and Molecular Biology UAB, which has coordinated the creation of the new method.

The new algorithm can be applied to any protein from which the structure is known or can be generated by modeling. To validate the new method, researchers have used protein aggregation properly characterized as experimentally. In the static mode, you can study protein complexes of up to 20,000 atoms and individual proteins or protein 400 amino acids in the dynamic mode, as noted an JANO portal.