Filamentous Bacteriophage Viruses: Preparation, Magic-Angle Spinning Solid-State NMR Experiments, and Structure Determination

Optimisation of GraPhage13 macro-dispersibility via understanding the pH-dependent ionisation during self-assembly: towards the manufacture of graphene-based nanodevices

GraPhage13 aerogels (GPAs) are micro-porous structures generated through the self-assembly of graphene oxide (GO) and M13 bacteriophage. As GPA fabrication involves the aggregation of GO and M13 in aqueous solution, we aim to understand its dispersibility across a wide pH range. Herein, a novel technique has been developed to relate the ionisation of functional groups to the surface charge, offering insights into the conditions required for GPA fabrication and the mechanism behind its self-assembly. The aggregation of GO and M13 was observed between pH 2-6 and exhibited dependence on the surface charge of the resulting aggregate with the M13 bacteriophage identified as the primary factor contributing to this, whilst originating from the ionisation of its functional groups. In contrast, GO exhibited a lesser impact on the surface charge due to the deprotonation of its carboxylic, enolic and phenolic functional groups at pH 6 and above, which falls outside the required pH range for aggregation. These results enhance our understanding of the GPA self-assembly mechanism, the conditions required for their fabrication and the optimal processability, laying the foundation towards its broad range of applications and the subsequent manufacture of graphene-based nanodevices.

Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR

RNA is a polymer with pivotal functions in many biological processes. RNA structure determination is thus a vital step toward understanding its function. The secondary structure of RNA is stabilized by hydrogen bonds formed between nucleotide basepairs, and it defines the positions and shapes of functional stem-loops, internal loops, bulges, and other functional and structural elements. In this work, we present a methodology for studying large intact RNA biomolecules using homonuclear ¹⁵N solid-state NMR spectroscopy. We show that proton-driven spin-diffusion experiments with long mixing times, up to 16 s, improved by the incorporation of multiple rotor-synchronous ¹H inversion pulses (termed radio-frequency dipolar recoupling pulses), reveal key hydrogen-bond contacts. In the full-length RNA isolated from MS2 phage, we observed strong and dominant contributions of guanine-cytosine Watson-Crick basepairs, and beyond these common interactions, we observe a significant contribution of the guanine-uracil wobble basepairs. Moreover, we can differentiate basepaired and non-basepaired nitrogen atoms. Using the improved technique facilitates characterization of hydrogen-bond types in intact large-scale RNA using solid-state NMR. It can be highly useful to guide secondary structure prediction techniques and possibly structure determination methods.

Nonuniformly sampled exclusively-13 C/15 N 4D solid-state NMR experiments: Assignment and characterization of IKe phage capsid

An important step in the process of protein research by NMR is the assignment of chemical shifts. In the coat protein of IKe bacteriophage, there are 53 residues making up a long helix resulting in relatively high spectral ambiguity. Assignment thus requires the collection of a set of three-dimensional (3D) experiments and the preparation of sparsely labeled samples. Increasing the dimensionality can facilitate fast and reliable assignment of IKe and of larger proteins. Recent progress in nonuniform sampling techniques made the application of multidimensional NMR solid-state experiments beyond 3D more practical. 4D ¹ H-detected experiments have been demonstrated in high-fields and at spinning speeds of 60 kHz and higher but are not practical at spinning speeds of 10-20 kHz for fully protonated proteins. Here, we demonstrate the applicability of a nonuniformly sampled 4D ¹³ C/¹⁵ N-only correlation experiment performed at a moderate field of 14.1 T, which can incorporate sufficiently long acquisition periods in all dimensions. We show how a single CANCOCX experiment, supported by several 2D carbon-based correlation experiments, is utilized for the assignment of heteronuclei in the coat protein of the IKe bacteriophage. One sparsely labeled sample was used to validate sidechain assignment of several hydrophobic-residue sidechains. A comparison to solution NMR studies of isolated IKe coat proteins embedded in micelles points to key residues involved in structural rearrangement of the capsid upon assembly of the virus. The benefits of 4D to a quicker assignment are discussed, and the method may prove useful for studying proteins at relatively low fields.

The Stabilizing Excipients in Dry State Therapeutic Phage Formulations

Phage therapy has gained prominence due to the increasing pathogenicity of "super bugs" and the rise of their multidrug resistance to conventional antibiotics. Dry state formulation of therapeutic phage is attractive to improve their "druggability" by increasing their shelf life, improving their ease of handling, and ultimately retaining their long-term potency. The use and selection of excipients are critical to stabilize phage in solid formulations and protect their viability from stresses encountered during the solidification process and long-term storage prior to use. Here, this review focuses on the current classes of excipients used to manufacture dry state phage formulations and their ability to stabilize and protect phage throughout the process, as discussed in the literature. We provide perspective of outstanding challenges involved in the formulation of dry state phage. We suggest strategies to improve excipient identification and selection, optimize the potential excipient combinations to improve phage viability during formulation, and evaluate new methodologies that can provide greater insight into phage-excipient interactions to improve design criteria to improve formulation of dry state phage therapeutics. Addressing these challenges opens up new opportunities to re-design and re-imagine phage formulations for improved efficacy as a pharmaceutical product.

Structural characterization of bacteriophage viruses by NMR

Magic-angle spinning (MAS) solid-state NMR has provided structural insights into various bacteriophage systems including filamentous, spherical, and tailed bacteriophage viruses. A variety of methodologies have been utilized including elementary two and three-dimensional assignment experiments, proton-detection techniques at fast spinning speeds, non-uniform sampling, structure determination protocols, conformational dynamics revealed by recoupling of anisotropic interactions, and enhancement by dynamic nuclear polarization. This review summarizes most of the studies performed during the last decade by MAS techniques and makes comparisons with prior knowledge obtained from static and solution NMR techniques. Chemical shifts for the capsids of the various systems are reported and analyzed, and DNA shifts are reported and discussed in the context of general high molecular-weight DNA molecules. Chemical shift and torsion angle prediction techniques are compared and applied to the various phage systems. The structures of the intact M13 filamentous bacteriophage and that of the Acinetobacter phage AP205 capsid, determined using MAS-based experimental data, are presented. Finally, filamentous phages, which are highly rigid systems, show interesting dynamics at the interface of the capsid and DNA, and their mutual electrostatic interactions are shown to be mediated by highly mobile positively charged residues. Novel results obtained from recoupling the chemical shift anisotropy of a single arginine in IKe phage, which is in contact with its DNA, further demonstrate this point. MAS NMR thus provides many new insights into phage structure, and on the other hand the richness, complexity and variety of bacteriophage systems provide opportunities for new NMR methodologies and technique developments.