Team members*
* in order of percentage of time on the project
Dr. Zoran Štefanić
project leader
Dr. Zoran Štefanić senior research associate and Head of the Laboratory for Chemical and Biological Crystallography at the Ruđer Bošković Institute. His main areas of expertise include: chemical crystallography of small organic molecules and hydrogen bonded networks, macromolecular crystallography, strong background in physics and mathematics, development of computer algorithms mainly in Python programming language, database design and web development. As the principal investigator of the proposed project, he will be responsible for the overall coordination of the research and managing all activities between team members, organizational and financial matters, as well as for the publication of results, annual scientific and financial reports to the Croatian Science Foundation. More specifically in this project his tasks will be data collection and 3D structure determination of new enzyme structures, development of central relational database, programming of algorithms for data extraction, development of web server, and co-mentorship of PhD student.
Dr. Ivana Leščić Ašler
Research associate in the Laboratory for Chemical and Biological Crystallography at the Ruđer Bošković Institute. She is experienced in various biochemical methods and techniques, such as chromatographic separation methods (including FPLC), various electrophoretic methods spectrophotometric and titrimetric methods for determination of protein activity, as well as molecular biology methods for protein cloning and expression. She will use her expertise for enzyme purification and characterization (enzyme kinetics w/o inhibitors, small molecule binding studies). Specifically, she will be in charge of purification and kinetic characterization of PNP from H. pylori with inhibitors. Also, she will work AdSS from H. pylori in cooperation with Ante Bubić – purification, kinetic characterization with potential activator and binding studies of this enzyme with small molecules (substrates/inhibitors/activator). Thanks to her experience in micro crystallization of biological macromolecules (hanging drop technique, crystallization of proteins in gel), she will be included in crystallization of PNP and AdSS as well. Finally, she will work on preparation and characterization of mutants of studied enzymes, using the above-mentioned techniques.
Boris Gomaz
PhD student Boris Gomaz was employed in February 2021. As part of the project he will enrol to Doctoral study programme at the Faculty of Science, Chemistry department. He will be under direct mentorship of dr. Zoran Štefanić and co-mentorship of prof. Bojana Dalbelo Bašić. His PhD thesis will be in centered under developing special relational database of PNP structures and machine learning algorhythms for extracting information about the allosteric pathways from MD that database (under the guidance of prof. Dalbelo Bašić who has great expertise in this field). The visit to dr. Pandini's lab is also planned.
Ante Bubić
Is a PhD student and a member of the Laboratory for Chemical and Biological Crystallography at the Ruđer Bošković Institute. His main areas of expertise include biochemistry and enzyme kinetics, molecular dynamics with strong background in biochemistry and molecular biology. As collaborator on the proposed project he will be responsible for crystallization trials and further biophysical characterization of AdSS protein, and MD simulations part of the project.
Dr. Aleksandra Maršavelski
Assistant professor at the Department of Chemistry, the Faculty of Science, the University of Zagreb. Her areas of expertise include: molecular dynamics simulations of proteins, lipids, membrane proteins, glycoproteins and carbohydrates as well as modelling of DNA/RNA nucleic acids in complexes with small compounds and/or proteins. Her areas of expertise also include modelling of enzymatically catalysed reactions by quantum-mechanical cluster approach and by EVB (empirical valence bond) simulations. In the proposed project, she will be responsible for the molecular dynamics simulations of model proteins.
Dr. Alessandro Pandini
Lecturer in computer science at the Brunel University in London. His expertises include: computational chemistry methods (molecular simulations, molecular docking, molecular visualisation), machine learning methods (cluster analysis, PCA, neural networks, random forests), sructural bioinformatics methods (residue coevolution prediction, protein structure prediction), software development (C, Python) and collaborative tools (Eclipse, GitHub), statistics and data analysis (R, Python) and system administration (Linux). He developed the structural alphabet (SA), a method for encoding structural changes in molecular dynamic simulations of enzymes, and also a programme called GSATools for the analysis of those changes. Both the SA and the GSATools will be used throughout the project.
Prof. Bojana Dalbelo Bašić
Full professor at Faculty of Electrical Engineering and Computing, University of Zagreb. Her research interests involve artificial intelligence, machine learning, multivariate statistics and visualisation, text analysis and information retrieval. She is one of the pioneers who introduced the discipline of machine learning in Croatian scientific community. In the proposed project her main role will be to choose the most appropriate set of machine learning techniques to apply to the data in the central relational database and their application to extract allosteric communication pathways. This will also involve mentoring of the PhD student in her/his thesis work on this subject.
Prof. Maria Agnieszka Bzowska
Professor at the Division of Biophysics, the Faculty of Physics, the University of Warsaw. Her areas of expertise include various methods of molecular biophysics and biochemistry, like spectroscopy, analytical ultracentrifugation, protein-ligand binding methods, kinetic studies. For many years she has been studying homooligomeric enzymes belonging to the PNP family, with the aim to understand the role of the allosteric communication in their molecular mechanism of catalysis. Her role in the project will be carrying out experiments characterizing wild type and mutated enzymes, PNP and AdSS from H. pylori, in solution, using analytical ultracentrifugation, kinetic measurements and enzyme-ligand binding studies involving spectroscopic, calorimetric and thermophoretic methods.