Hydrogen bonds and hydrogen-bond networks are of central interest for understanding protein structure, function, and dynamics. Recent developments in structural biology and computational methods enable access to the three-dimensional structures and dynamics of large proteins and protein complexes, but bring about the challenge of how to identify hydrogen-bond networks, study their dynamics, and rank hydrogen-bonding groups according to their importance in the network. To tackle these challenge, we developed highly efficient graph-based algorithms and graphical user interfaces, and apply these algorithms to study hydrogen-bond networks in proteins and lipid membrane interfaces. The HPC-Europe3 computing time allocation enabled prolonged computation of a pH-sensing ion channel described with different protonations relevant to physiology.
During my seminar I will present the applicability of the graph-based algorithms to analyses of dynamic hydrogen-bond networks of membrane transporters and receptors, including the pH-sensing ion channel studied with the HPC-Europe3 computing time allocation.
I am grateful to Prof Carmen Domene (University of Bath, UK) for her support with the application and for hosting my HPC-Europe3 application. I would like to thank Ms. Catherine Inglis and to Dr. William Lucas for the superb assistance during the HPC-Europe3 access.
This online session is open to all. It will use the Blackboard Collaborate platform.