Integrative Modeling of Glycoproteins
December 17, 2024 @ 15:15 – 16:15 CET
Spotlight Seminar series welcomes Dr. Mateusz Sikora, Head of the Dioscuri Centre for Modelling of Posttranslational Modifications, Jagiellonian University, Krakow, Poland
& Max Planck Institute of Biophysics in Germany
Biography
Dr. Mateusz Sikora is an expert in biophysics and computational biology. He currently leads the Dioscuri Centre for Modelling of Posttranslational Modifications at Jagiellonian University, Kraków, Poland, co-affiliated at the Max Planck Institute of Biophysics in Frankfurt, Germany. His research focuses on the role of posttranslational modifications (PTMs) in protein-protein interactions, using molecular dynamics simulations to study inherently flexible biological systems.
Dr. Sikora obtained his Ph.D. in Biophysics from the Institute of Physics, Polish Academy of Sciences* in 2012, graduating summa cum laude, with Prof Marek Cieplak as a supervisor. His doctoral work on biomolecular dynamics and coarse-grained modeling laid the foundation for his future research into protein flexibility and interaction. He also holds an M.S. in Biophysics from Jagiellonian University.
His postdoctoral career includes notable fellowships, including the FWF Schrödinger Fellowship (2018–2020) at the Max Planck Institute of Biophysics in Frankfurt am Main and University of Vienna, where he worked with Gerhard Hummer and Christoph Dellago unraveling dynamic behaviour of large protein complexes, and the EMBO Fellowship (2012–2017) at the Institute of Science and Technology (IST) in Austria with Carl Philipp Heisenberg, where he applied cell and molecular biology experiments to understand cell-cell contact formation in zebrafish.
Dr. Sikora’s work is at the intersection of computational biophysics, structural biology, and systems biology, with a particular emphasis on understanding how posttranslational modifications affect the structure and function of proteins.
He has authored over 30 peer-reviewed publications (including 1st author Science, and corresponding author Cell) and made significant contributions to the study of SARS-CoV-2, including computational models of viral spike proteins and their interactions with host cells, as well as new methods to study the effects of glycans on proteins. His work has been widely recognized, with his research featured in prominent media outlets such as Science, The New York Times, and National Geographic.
Dr. Sikora has received numerous grants and awards, including the joint Max Planck and Polish National Science Centre Dioscuri grant. He is also involved in translational research, with patents related to posttranslational modifications for vaccine development and medical applications.
With an h-index of 17 and over 1,700 citations, Dr. Sikora is recognized as a leading researcher in his field, combining advanced computational methods with experimental biology to explore critical biological processes at the molecular level.
Abstract
Glycans, complex sugars covalently attached to proteins, play crucial roles in protein stability and function, participate in “self” recognition, and modulate protein-protein interactions. Unlike proteins, glycans typically do not form secondary structures and remain highly mobile, posing challenges for traditional structural biology techniques. This high mobility, coupled with glycan heterogeneity, complicates the elucidation of complete glycoprotein structures and hinders research on the role of glycans in protein function. Although computer simulations can help address these challenges, they often require millions of hours on specialized supercomputers, highlighting the need for approximate methods that can be integrated into protein-solving pipelines.
To overcome these obstacles, we developed a simplified, open-source method for rapidly predicting the span and shape of glycans with minimal computing power. Using this approach, we can accurately predict SARS-CoV-2 spike protein epitopes that are not shielded by glycans, as well as assess the impact of glycans on protein flexibility. We also demonstrate that this method can be integrated with structural biology methods and glycoproteomics pipelines, offering a comprehensive tool for glycoprotein analysis.
Host: Piotr Draczkowski piotr.draczkowski@scilifelab.se
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