In our group we aslo implement novel structural proteomics approaches.
native MS
protein covalent labelling
protein crosslinking
hydrogen-deuterium exchange MS
These complementary methods allow to study protein structures and characterize not only protein-protein interactions but also interactions of proteins with other biological molecules.
Ion mobility spectrometry (IMS) of amyloid beta peptide (1-42). Individual chrge states of monomers and oligomers are labeled.
Phosphorylase B labeled by D2O in two time points (20 seconds and 2 hours). Obtained data were shown in phosphorylase B structure where the relative deuteration uptake of identified regions was expressed in a color scale.
Projects
Our group is involved in numerous projects where the MS-based proteomic approaches is required. These projects deal with, for example, the research of Hepatitis B viral infection or analysis of rhomboid dependent proteome changes, etc.
analysis of lipoproteins/lipopeptides and membrane proteins
Separation and identification of lipoproteins/lipopeptides is rather challenging due to the limited solubility of lipo-modified segments in water-based solutions, whose are exclusively used within standard proteomic workflows. Therefore, we focus on the implementation of new workflows to the increase the yield of lipo-modified and hydrophobic segments of the proteins.
The fragmentation spectrum of the myristoylated peptide GVSGSK obtained by CID and HCD fragmentation technique. In the case of HCD both indicator fragments of myristoylation b0 (m/z 211.205) and b1 (m/z 268.227) were detected.
Application of the methods of structural proteomics on the field of retroviral life cycle studies
Although the life cycle of retroviruses is intensively studied worldwide, some of the mechanism used by retroviruses in host cells are still not elucidated. This refers to the interaction of newly formed virus particles with cell membrane before they are released from the host cell. To clarify the mechanism that retroviruses use in this step, we apply structural proteomics methods, mainly protein cross-linking and the hydrogen-deuterium exchange method.