InstructFeaturing expert speakers from Instruct Centres across Europe, Instruct-ERIC Webinar Series: Structure Meets Function highlights some of the latest developments in structural biology, demonstrating how integrative methods are enabling scientists to decipher the mechanisms that underpin health and disease.
Watch the previous webinars in the series here.
The 13th webinar in the series will be hosted by Instruct Slovakia on 12 Oct 2021, 11:00 - 12:30 CEST
Agenda
Webinar moderator: Milos Hricovini, Institute of Chemistry Slovak Academy of Sciences
Talk 1:Interpreting Single-Molecule Force Spectroscopy Experiments with Normal Mode Analysis
Speaker: Jacob Bauer
Affiliation: Institute of Molecular Biology, Slovak Academy of Sciences
Abstract: Single-Molecule force spectroscopy is a technique for studying the folding and unfolding of protein molecules under the application of mechanical force. Steered molecular dynamics (MD) simulations are probably the most informative technique for analyzing the results, but they are computation-ally demanding and they often become the rate-limiting step for studies employing them. We have found that normal mode analysis (NMA) provides at least some of the insights given by MD simulation but with much less computational overhead. Here, we will briefly describe the ap-plication of NMA to a protein previously studied by single-molecule force spectroscopy and show that we can recover the main results provided by steered MD simulation.
Acknowledgements. This work was supported by VEGA research grant 2/0131/20 from the Slovak Grant Agency and by Interreg SK-AT StruBioMol ITMS: 305011X6662/0140/16.
Talk 2: Mass Spectrometry in Glycoproteomic Analyses
Speaker: Zuzana Pakanová
Affiliation: Institute of Chemistry Slovak Academy of Sciences
Abstract: Research at Laboratory of Glycomics and Proteomics, Institute of Chemistry, Slovak Academy of Sciences is dedicated to analysis of proteins with focus on their posttranslational/cotranslational modifications. Glycosylation is an essential factor determining activity, stability, folding, solubility and interactions of proteins. Thus, its analysis plays an important role in production of functional recombinant proteins, searching for new biomarkers, etc. Methods established in our laboratory, including the analysis of glycans (both N- and O-linked), glycopeptides, determination of glycosylation sites and their occupancy, analysis of peptides and proteins (intact mass), were successfully applied in diagnostics of rare diseases, analysis of recombinant proteins, immunoglobulins, mycobacterial oligosaccharide transporters, barley xyloglucan transferases, etc.
Talk 3: Development of single-molecule protein biophysics
Speaker: Gabriel Žoldák
Affiliation:UPJŠ Košice
Abstract: Center for interdisciplinary bioscience (CIB) was established at UPJS in 2016 by key researchers reintegrated during the implementation of the 7FP EU REGPOT grant CELIM. Nowadays, CIB is formed by eight independent research groups with individualized scientific topics. My research group is devoted to single-molecule protein research. The development of this research is a long-term process, which requires a step-by-step establishment of the critical technologies: protein expression and purification, protein/microparticle/nucleic acid modifications, biochemical/biophysical characterizations of proteins and nucleic acid conjugates and, last but not least, a specialized laboratory for custom-made laser setups. By setting up the laboratory of advanced laser technology this year, all core technologies and laboratory infrastructure are now finally established. In my presentation, I will talk about a recently published paper on a pathological variant of λ-light chain. Our study examined the relationship between stability and time-dependent solubility of the recombinant human antibody light chain, hLC, which was found to form renal tubular casts in the multiple myeloma patient. By the combination of experimental assays at different temperatures, different protein concentrations and kinetic modelling using ordinary differential equations, we were able to extrapolate time-dependent protein solubility to temperatures where both unfolding and aggregation processes are strongly kinetically coupled. Our study enables mechanism-based evaluation and interpretation of different physico-chemical factors contributing to the hLC unfolding and aggregation and their effect on the formation of extracellular protein deposits. In the future, we plan to extend our investigations by newly established single-molecule techniques.
Acknowledgements. My research is supported by VEGA 1/0175/19, KEGA 005UPJŠ-4/2021, APVV-18-0285, EU H2020 TWINNING program GA. No. 952333 - project CasProt, project OPENMED ITMS2014+:313011V455 and BioPickmol, ITMS2014+: 313011AUW6 supported by the Operational Programme Integrated Infrastructure, funded by the ERDF.
