Spring 2021 Seminar Series: Ana-Nicoleta Bondar
Freie Universität Berlin
Host: Kalina Hristova
Structural plasticity required for protein function is largely governed by dynamic hydrogen(H)-bonds and H-bond networks, and H-bond interactions are often central to formulating hypotheses about the reaction mechanism of the protein. G Protein Coupled Receptors (GPCRs) and the spike protein S of SARS-CoV-2 are prominent examples of proteins for which H-bonding plays a major role for the structural dynamics along the reaction path, including for interactions with other proteins.
To characterize the role of H-bonds and H-bond networks in GPCRs and spike protein, and in other large bio-systems, we have developed graph-based algorithms that allow us to derive two-dimensional representations of H-bond networks of the protein. Once computed, the two-dimensional H-bond graph can be queried to characterize the dynamics of the protein and protein-water H-bonding, and centrality measures enable groups of the protein to be ranked according to their relative importance for connectivity within the graph. From computations of conserved H-bond graphs we catalogue internal H-bond networks of sets of protein structures.
During my talk I will present the graph-based algorithms we developed, and applications from recent work on the conformational dynamics of GPCRs and of the SARS-CoV-2 protein S.
Research was supported in part by funding from the Excellence Initiative via the Freie Universität Berlin, the German Research Foundation (DFG) Collaborative Research Center SFB 1078 Project C4, and computing resources from the North German Supercomputing Center, HLRN.
Zoom Seminar Info:
Meeting ID: 982 0915 3548