<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div><font face="HelveticaNeue">Dear Soft Matter & Complex Systems Colleagues and Friends,</font></div><div><font face="HelveticaNeue"><br></font></div><div><div><font face="HelveticaNeue">On Friday 15 March 2024 at 9:30 AM at the UW Faculty of Physics (Pasteura 5, Warsaw; room 1.40) we are hosting a seminar during which </font></div><div><font face="HelveticaNeue"><br></font></div><div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;"><font face="HelveticaNeue"><b>Mateusz Sikora </b>(<span style="text-align: center;">Malopolska Centre of Biotechnology, Krakow, Poland</span><span style="text-align: center;"> & </span><span style="text-align: center;">Max Planck Institute of Biophysics, Frankfurt, Germany</span>)</font></div><div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;"><font face="HelveticaNeue"><br></font></div><div style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue">will give a talk</font></div><div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;"><span style="caret-color: rgb(68, 68, 68);"><font face="HelveticaNeue"><br></font></span></div><div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;"><div><h2 style="margin: 6px 0px 12px; padding: 0px; caret-color: rgb(68, 68, 68);"><font face="HelveticaNeue" style="font-size: 12px;"><span lang="EN-US" style="caret-color: rgb(0, 0, 0);">Integrative modeling of glycoproteins, lessons from the pandemic</span><span style="caret-color: rgb(0, 0, 0); font-weight: 400;"></span></font></h2></div><h2 style="margin: 6px 0px 12px; padding: 0px; caret-color: rgb(68, 68, 68);"><b><font face="HelveticaNeue" style="font-size: 12px;">Abstract</font></b></h2><div><p class="MsoNormal" style="margin: 0cm; text-align: justify;"><span lang="EN-US"><font face="HelveticaNeue">Glycans, complex sugars covalently attached to proteins, affect protein stability and function, participate in ‘self’ recognition, and modulate protein-protein interactions. The glycosylation machinery is frequently hijacked by pathogens, which hide their proteins behind a “glycan shield”, making them inaccessible to the immune system and complicating pharmacological interventions. Unlike many biomolecules, glycans do not typically form secondary structures and remain highly mobile, posing a challenge for traditional structural biology techniques. In our research, we combined molecular dynamics simulations with cryo-electron tomography and atomic force microscopy to understand how glycans affect viral fusion proteins, particularly the SARS-CoV-2 spike protein. We discovered a surprising flexibility of the spike protein [1,2] and predicted new antibody binding sites accessible through the dynamic glycan shield [3], which can aid in designing novel vaccines. Additionally, we developed a simplified, open-source method for rapidly predicting glycan shielding with minimal computing power. This method has been applied to refine existing cryo-EM maps of glycoproteins [4].</font></span></p><p class="MsoNormal" style="margin: 0cm; text-align: justify;"><span lang="EN-US"><font face="HelveticaNeue"> </font></span></p><p class="MsoNormal" style="margin: 0cm; text-align: justify;"><span lang="EN-US"><font face="HelveticaNeue"> </font></span></p><p class="MsoNormal" style="margin: 0cm; text-align: justify;"><font face="HelveticaNeue"><span lang="EN-US">1. B Turoňová, M Sikora, C Schürmann, WJH Hagen, S Welsch et al., In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. <br><b>Science</b>, 370(6513) 2020</span><span lang="EN-US"><o:p></o:p></span></font></p><p class="MsoNormal" style="margin: 0cm; text-align: justify;"><span lang="EN-US"><font face="HelveticaNeue"> </font></span></p><p class="MsoNormal" style="margin: 0cm; text-align: justify;"><font face="HelveticaNeue"><span lang="EN-US">2. R<span style="color: rgb(34, 34, 34);"> Zhu, D Canena, M Sikora, M Klausberger, H Seferovic, et al., <br></span>Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level; <b>Nat Comm</b>, 13(7926) 2022</span><span lang="EN-US"><o:p></o:p></span></font></p><p class="MsoNormal" style="margin: 0cm; text-align: justify;"><span lang="EN-US"><font face="HelveticaNeue"> </font></span></p><p class="MsoNormal" style="margin: 0cm; text-align: justify;"><font face="HelveticaNeue"><span lang="EN-US">3. M Sikora, S von Bülow, FEC Blanc, M Gecht, R Covino, G Hummer. <br>Computational epitope map of SARS-CoV-2 spike protein. <br><b>PLoS computational biology</b>, 17(4) 2021</span><span lang="EN-US"><o:p></o:p></span></font></p><p class="MsoNormal" style="margin: 0cm; text-align: justify;"><span lang="EN-US"><font face="HelveticaNeue"> </font></span></p><p class="MsoNormal" style="margin: 0cm; text-align: justify;"><font face="HelveticaNeue"><span lang="EN-US">4. Y-X Tsai, N-E Chang, K Reuter, H-T Chang, T-J Yang et al., Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries. <br><b>Biorxiv</b></span><span lang="EN-US"><o:p></o:p></span></font></p></div></div><div style="margin: 0px; font-stretch: normal; line-height: normal;"><div style="margin: 0px; font-stretch: normal; line-height: normal;"><div style="margin: 0px; font-stretch: normal; line-height: normal;"><div style="margin: 0px; font-stretch: normal; line-height: normal;"><div style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue"><br></font></div></div></div></div></div><div style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue">We warmly welcome everyone to attend the talk and the Soft Matter Coffee Break after the seminar, held in room 2.63 (2nd floor).</font></div></div><div><font face="HelveticaNeue"><br></font></div><div><div dir="auto" style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue">Maria Ekiel-Jeżewska</font></div><div style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue">Maciej Lisicki</font></div><div style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue">Piotr Szymczak</font></div><div style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue">Panagiotis Theodorakis</font></div><div style="margin: 0px; font-stretch: normal; line-height: normal;"><font face="HelveticaNeue">Marek Trippenbach</font></div></div></div></body></html>