Structural biology

The proposed “Structural biology” program follows the premise that physiological processes can be reproduced in vitro once we know all molecular components and understand their properties and interactions. Such understanding requires insight in the molecular mechanisms from the points of view of structural, molecular, and computational biology. It is the atomic 3-dimensional structures of macromolecules in particular that link the information from the sequences of biological polymers with the role of individual residues in biophysical and chemical mechanisms underlying physiological processes. The main biological theme of the proposed research is the process of adaptive immunity, where organism learns to discriminate between self and non-self proteins as a specific defense against invading microorganisms and their own misbehaved cells. This process begins with antigen presentation. Peptidyl candidates for antigenic presentation are generated by degradation of foreign proteins by endosomal proteases and other hydrolytic enzymes and continue with two level selection process, including binding to the MHC class II molecules and recognition of the formed complexes by the T-cells. The “Structural biology” program is a continuation of a decade of our research. Recently, we established a platform for high-throughput, parallelized, and semi-automated protein expression, purification, crystallization, and structure determination. This pipeline enables us to work simultaneously with groups of proteins, performing functional studies of experimental models with increasing complexity. In addition to continuing to study endosomal proteases, we will also study other endosomal enzymes, MHC class II molecules, their targets from the surface of bacterial pathogens Staphylococcus aureus, Clostridium difficile, and Enterococcus faecalis, and the selection process of antigen presentation. We aim to elucidate what makes a protein substrate of a cysteine cathepsin and to develop a method to predict this property. We expect that 3D structure of MHC class II molecules in complex with invariant chain will provide clues that will enable us to interpret in detail the complicated mechanism of invariant chain processing that occurs simultaneously with proteolytic degradation of antigenic proteins. We expect that continuation of our studies of proteins from pathogenic bacteria involved in the structure and remodeling of surface assemblies, such as S-layer, peptidoglycan cell wall, and biofilms, will help us to explore their potential as targets for novel anti-bacterial therapies. To pursue our goals, we will use biochemistry, molecular and cell biology, macromolecular crystallography, electron microscopy, small angle X-ray scattering, organic synthesis, proteomics, and computational biology. Such broad spectrum of technologies can only be applied within an extensive local and international network of collaborators.