With the aim to characterise the structural dynamics of ligand-bound H-NOX domain at time scales ranging from picosecond to microseconds we have carried out all-atom molecular dynamics simulations of the H-NOX domain from cyanobacterium Nostoc sp. (Ns H‐NOX), both in its native (heme-bound) state and in complex with the known sGC activator, cinaciguat. The computational data in conjunction with the experimental investigation of Ns H-NOX structure and its dynamics over a large range of timescales using state-of-the-art Nuclear Magnetic Resonance (NMR) methods provide the first full characterisation of both structure and dynamics of the Ns-HNOX system in solution. Our results reveal that the binding of the activator has distinct effects on the backbone order parameters of H-NOX, and changes in order parameters upon activator binding are observed for residues that are connected via hydrogen bonds or sidechain interactions. Accumulating evidence from our experiments and calculations suggest that these different responses to binding of activator appear to involve dynamical modes that transmit through such interactions, and therefore this long-range communication via dynamics changes may transferred through sGC domains and activate the distal C-terminal catalytic guanylyl cyclase domain.
The results obtained have been disseminated to the scientific community through:
1) Open-access publication, “Backbone and side chain NMR assignments of the H-NOX domain from Nostoc sp. in complex with BAY58-2667 (cinaciguat)” published in the Biomolecular NMR Assignments (BNMR).
2) An oral presentation at the University of Edinburgh, School of Chemistry, 22 January 2019, Edinburgh, UK.
3) An oral presentation with the title “Solution NMR spectroscopy and enhanced conformational sampling computational approaches to study the H-NOX domain of soluble guanylate cyclase” at the Edinburgh Parallel Computing Centre, 28 February 2019, Edinburgh, UK.
4) Poster presentation with the title “NMR insights into the structural and functional properties of soluble guanylate cyclase (sGC)”, at the 3rd Symposium “Chemistry at the Interface of Biology and Medicine”, September 23-26, 2019, Department of Pharmacy, University of Patras, Greece.
