4.9  S1-NCD motif FFSNVTWFHAIHV
In this stage of the study the predicted regions of the SARS-CoV spike protein were examined in more detail. While as discussed above tryptophan can be involved in the fundamental structure of a sialic acid binding domain, an exposed tryptophan like that binding a sialic acid glycan in Fig. 2 would be particularly persuasive. The first predicted sialic acid binding motif is segment FFSNVTWFHAIHV 58–70 with SABR-P score ranging from 101 for valine (V) to 113 for tryptophan (W) and for phenylalanine (F) is visible in PDB entry 6VVX (spike closed state) and 6VYB (spike open state).
As shown in Fig. 6 , the tryptophan sidechain in FFSNVTWFHAIHV as residues 58–70 of the sars-cov-3 spike glycoprotein is exposed in a site that has all the appearance of a sialic acid glycan binding site, comparable with the influenza virus B neuraminidase (PDB entry 2BAT) tryptophan site known to have interaction with and sialic acid, that was shown in Fig. 2.
Fig. 6 The Tryptophan sidechain in FFSNVTWFHAIHV 58–70 of Spike Glycoprotein is Exposed in a Site that Has all the Appearance of a Sialic Acid Glycan binding site.
It is useful to see how recurrent a potential more universal motif may be, to give insight, to avoid cross reactions of vaccine in human and veterinary patients as hosts, to detect an underlying common function that one might not wish to inhibit in the host with an anti-viral therapeutic, and so on. A BLAST search on non-viruses picks this subsequence up as FFSNVTNIAWIHAI of Parasteatoda tepidariorum, the common house spider, and related sequences, a zinc figure domain because it contains FYVE the zinc finger motif, but more abundantly it picks up sugar-binding proteins such as glycosyl transferases such as FFSPVWARTPNVTWFH-HV of actinobacteria, Ribulose-phosphate 3-epimerase of animals, a-amylase of the Chitinophagia (“chitin eating”) bacteria, C-type lectin 37Db-like of Drosophila hydei, and related sugar binding proteins, all varying around 100% cover and 55% match, 92% cover 71% match, 76% cover 70% match, and so on.