Conformational dynamics of bovine serum albumin: molecular metadynamics combined with spectroscopy.
I.A. Reshetnik, P.M. Ilicheva, N.A. Burmistrova; Saratov State University, Saratov, Russia
Abstract
Molecular recognition, as a fundamental mechanism of nature, encourages many researchers to create synthetic systems based on the same biophysical processes as their natural originals. To date, imprinted proteins (IPs) have proven themselves in various biological fields due to their simple and relatively cheap production. Today, the number of works using IPs as a recognition element in various types of immunoassay is increasing. Most studies use the classical technique, while the imprinting efficiency differed significantly when varying the target molecules. Therefore, most of the developed systems remained at the stage of a laboratory prototype. To solve this problem, the use of molecular modeling methods to predict the efficiency of imprinting seems promising.
Conformational mobility of the protein plays an important role in obtaining IPs. Changes in the acidiс conditions the production process are accompanied by changes in the conformational structure of the biomolecule. Intuitive selection of synthesis parameters was applied to different systems, however, with this approach, problems with the formation of the ligand-protein complex remain, which leads to low imprinting efficiency. Since the ligand may require a specific pattern of protonated states among residues, it becomes important to determine the structure of the protein molecule before introducing template molecules into the reaction mixture. Molecular dynamics methods are used to model the conformational mobility of the protein. In particular, the molecular metadynamics method allows one to establish the most favorable conformation when assessing the free energy of a complex of molecular systems. In this work, the mobility of BSA, as the most common protein matrix for imprinting, was studied using the molecular dynamics method, and collective variables were selected for subsequent study of the system using the metadynamics method. Fluorescence spectroscopy and circular dichroism spectroscopy were used to assess the structural changes in BSA and confirm the modeling results.
Speaker
Reshetnik Ivan
Saratov State University, Saratov, Russia
Russia
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