Conformational Control of Fast Asparagine Deamidation in a Norovirus Capsid Protein

Abstract

Accelerated spontaneous deamidation of asparagine 373 and subsequent conversion into an isoaspartate has been shown to attenuate the binding of histo blood group antigens (HBGAs) to the protruding domain (P-domain) of the capsid protein of a prevalent norovirus strain (GII.4). Here, we link an unusual backbone conformation of asparagine 373 to its fast site-specific deamidation. NMR spectroscopy and ion exchange chromatography have been used to monitor the deamidation reaction of P-domains of two closely related GII.4 norovirus strains, specific point mutants, and control peptides. MD simulations over several microseconds have been instrumental to rationalize the experimental findings. While conventional descriptors such as available surface area, root-mean-square fluctuations, or nucleophilic attack distance fail as explanations, the population of a rare syn-backbone conformation distinguishes asparagine 373 from all other asparagine residues. We suggest that stabilization of this unusual conformation enhances the nucleophilicity of the backbone nitrogen of aspartate 374, in turn accelerating the deamidation of asparagine 373. This finding should be relevant to the development of reliable prediction algorithms for sites of rapid asparagine deamidation in proteins.

NMR Reveals the Synergistic Roles of Bivalent Metal Ions in Norovirus Infections

“…We had previously studied the P-dimers of the GII.4 Saga strain in detail by NMR [14, 16, 20-21, 38, 44-46] . An important finding was that N373 in wild-type GII.4 Saga P-dimers undergoes spontaneous and fast deamidation [14,44] . Therefore, here we used the stable N373D mutant [38] instead of the wild type P-dimers for all NMR binding experiments.…”