title: Functional dynamics of hexameric helicase probed by hydrogen exchange and simulation.
abstract: The biological function of large macromolecular assemblies depends on their structure and their dynamics over a broad range of timescales; for this reason, it is a significant challenge to investigate these assemblies using conventional experimental techniques. One of the most promising experimental techniques is hydrogen-deuterium exchange detected by mass spectrometry. Here, we describe to our knowledge a new computational method for quantitative interpretation of deuterium exchange kinetics and apply it to a hexameric viral helicase P4 that unwinds and translocates RNA into a virus capsid at the expense of ATP hydrolysis. Room-temperature dynamics probed by a hundred nanoseconds of all-atom molecular dynamics simulations is sufficient to predict the exchange kinetics of most sequence fragments and provide a residue-level interpretation of the low-resolution experimental results. The strategy presented here is also a valuable tool to validate experimental data, e.g., assignments, and to probe mechanisms that cannot be observed by x-ray crystallography, or that occur over timescales longer than those that can be realistically simulated, such as the opening of the hexameric ring.
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.
authors.forename: Gaël
authors.initials: G
authors.lastname: Radou
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.
authors.forename: Frauke N
authors.initials: FN
authors.lastname: Dreyer
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom. Electronic address: r.tuma@leeds.ac.uk.
authors.forename: Roman
authors.initials: R
authors.lastname: Tuma
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom. Electronic address: e.paci@leeds.ac.uk.
authors.forename: Emanuele
authors.initials: E
authors.lastname: Paci
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D017910:Cystoviridae; D003903:Deuterium / Q000737:chemistry*; D041961:Deuterium Exchange Measurement; D006859:Hydrogen / Q000737:chemistry*; D007700:Kinetics; D013058:Mass Spectrometry; D056004:Molecular Dynamics Simulation; D020365:RNA Helicases / Q000737:chemistry*; D013696:Temperature; D014764:Viral Proteins / Q000737:chemistry*
chemical_list: D014764:Viral Proteins; D006859:Hydrogen; D003903:Deuterium; D020365:RNA Helicases