Molecular Recognition of Ligands by Native Viruses and Virus-Like Particles as Studied by NMR Experiments

Abstract

Viral entry into host cells is a process that in the majority of cases is not understoodin its molecular details. The first step of viral entry is the recognition of cellular receptorson host cells by viruses, and although X-ray crystallography had yielded some spectacular resultsin individual cases, in general there is little data available to unravel the principles of virus-ligandrecognition at atomic resolution. Therefore, new techniques that uncover the molecular details ofthese recognition processes are needed. The investigation of virus-ligand interactions usingligand-based NMR techniques is an emerging field with the potential to substantially contribute toa deeper understanding of the molecular aspects of viral entry into host cells. Here, we givean overview that covers some of the systems studied so far. This comprises native viruses as wellas virus-like particles (VLPs). We will not address studies that have been performed with individualproteins that are not in a native environment. It turns out that STD NMR in particular has a greatpotential to shine light on the viral entry process as this technique requires only very moderateamounts of viruses or VLPs and corresponding ligands. As a further advantage, this approachis also applicable to ligands that bind to viruses with medium to low affinity. Therefore, STD NMRis extremely well suited for development of antiviral entry inhibitors utilizing fragment-based approacheswith low molecular weight compounds.

The αGal Epitope of the Histo-Blood Group Antigen Family Is a Ligand for Bovine Norovirus Newbury2 Expected to Prevent Cross-Species Transmission

“…All experiments were carried out on a Bruker Avance 500 MHz NMR spectrometer equipped with a TCI cryogenic probe. The temperature was set to 282 K. STD NMR experiments [31] were recorded with a 3-9-19 watergate sequence and an inter-scan delay of 25 s [60]. On- and off- resonance frequencies were set at −4 and 300 ppm, respectively [32].…”

Macromolecular NMR spectroscopy for the non‐spectroscopist: beyond macromolecular solution structure determination

“…Unlike most NMR approaches, interactions in which one of the binding partners is extremely large can be probed. The approach has been applied to integral membrane proteins [27] and even viral particles [28] and whole cells [29].…”

Spin ballet for sweet encounters: saturation-transfer difference NMR and X-ray crystallography complement each other in the elucidation of protein–glycan interactions

“…In both cases, STD-NMR can fill experimental gaps because the 'protein' part of the NMR sample can in fact be a complex, inhomogeneous, protein-containing entity that would itself resist high-resolution techniques. STD-NMR spectra have been recorded using intact viruses or virus-like particles with glycan receptors (Benie et al, 2003;Haselhorst et al, 2008;Rademacher & Peters, 2008). We made use of the technique to screen for potential oligosaccharide ligands in a multi-glycosylated 20-domain protein with 19 linkers of varying flexibility and took the results to two-domain constructs for crystallization (Blaum et al, 2015).…”