XXVIII-th International Conference “Mathematics. A computer. Education "(January 25 - 30, 2021)

On January 25-30, 2021 the International Conference “Mathematics. A computer. Education ”in the online format, within which Alexey Shaitan, Researcher of the International Laboratory of Bioinformatics, presented a report on the article“ Modeling and Molecular Design of Protein and Nucleic Acid Complexes.

Nucleic acids DNA and RNA are carriers of information in living nature. The key to understanding how the interpretation, modification, copying of genetic information occurs is based on our knowledge of  the interaction between  nucleic acids and proteins. A similar understanding is required in many problems of bioengineering related to the recognition of nucleic acid sequences, their modification, editing, and regulation of gene expression. For a logical understanding of processes, it plays the role of cells with nucleic acids. Approaches to modeling nucleic acid complexes can be divided into several groups: methods of atomistic molecular dynamics, methods of coarse modeling, and methods of integrative modeling. Molecular dynamics methods make it possible to study the conformational mobility of systems with limited resolution, however, they have serious limitations  associated with the possible calculation times and the accuracy of force fields. Due to the charged nature of nucleic acids, their parameters in classical force fields are more complex than the parameters of proteins. Methods for rough modeling of nucleotide acids are possible both on the basis of a coarse-grained representation, and on the basis of the representation of DNA in the dinucleotide approximation with setting the parameters of the deviation of nucleotide pairs along the DNA chain. Integrative modeling methods allow for the construction of models experimental data of various nature, including data from various biophysical and biochemical experiments. In this context, the application of various molecular modeling approaches to study complexes of nucleic acids based on DNA proteins is discussed. The latter problem is an example of the application of modeling methods for the molecular design of functional complexes of nucleic acids and proteins. The problem comes down to determining the optimal planting of two proteins on DNA so that the functional devices attached to them are at an optimal interaction distance. Reporter proteins can be a pair of fluorescent proteins that interact according to the mechanisms of Foerster resonance energy transfer, or a pair of split domains of an enzyme (for example, beta-lactamase or luciferase), which, when interacting, form a functional enzyme. The research was carried out with the financial support of the Russian Foundation for Basic Research in the research project 19-34-51053.