Abstract
Protein plasticity and dynamics are important aspects of their function. Here we use solid-state NMR to experimentally characterize the dynamics of the 3.5 MDa hepatitis B virus (HBV) capsid, assembled from 240 copies of the Cp149 core protein. We measure both T 1 and T 1ρ relaxation times, which we use to establish detectors on the nanosecond and microsecond timescale. We compare our results to those from a 1 microsecond all-atom Molecular Dynamics (MD) simulation trajectory for the capsid. We show that, for the constituent residues, nanosecond dynamics are faithfully captured by the MD simulation. The calculated values can be used in good approximation for the NMR-non-detected residues, as well as to extrapolate into the range between the nanosecond and microsecond dynamics, where NMR has a blind spot at the current state of technology. Slower motions on the microsecond timescale are difficult to characterize by all-atom MD simulations owing to computational expense, but are readily accessed by NMR. The two methods are, thus, complementary, and a combination thereof can reliably characterize motions covering correlation times up to a few microseconds.
Highlights
Characterizing the dynamics of proteins and their assemblies is often key to understanding their function, and NMR has proven to be suitable to study dynamical behavior at the atomic level
We show that results of the two methods coincide, demonstrating the validity of using Molecular Dynamics (MD) simulation data to extrapolate correlation functions for atoms and dynamic timescales which are not observable by NMR
A first overview over dynamic and rigid regions of the capsids is provided by the random coil index (RCI) (Berjanskii and Wishart, 2005, 2008; Fowler et al, 2020), an empirical quantity calculated from the NMR chemical shifts
Summary
Characterizing the dynamics of proteins and their assemblies is often key to understanding their function, and NMR has proven to be suitable to study dynamical behavior at the atomic level. For large systems with a limited monomer size, such as oligomeric proteins and multimeric assemblies like fibrils and sub-viral particles, solid-state NMR is the method of choice, since it allows evaluation of dynamical properties on a per-residue basis The latter is achieved by measuring NMR relaxation parameters, in particular the 15N spin-lattice relaxation T1 that addresses fast motions (correlation times around 1 ns), as well as the rotating frame relaxation, T1ρ, which probes hundredsof-nanosecond to millisecond motions (Krushelnitsky et al, 2010; Schanda et al, 2010; Quinn and McDermott, 2012; Tollinger et al, 2012; Lamley et al, 2015; Schanda and Ernst, 2016; Rovó et al, 2019; Shi et al, 2019). While they can be accessed in NMR by rotating-frame relaxation measurements, they are difficult to measure by most other techniques
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