Secondary structure prediction of the hemagglutinin-neuraminidase from a porcine rubulavirus

Abstract

The Hemagglutinin-Neuraminidase (HN) from 'La Piedad, Michoacan' porcine rubulavirus (LPMV) interacts specifically with NeuAc alpha 2,3 lactose residues on the target cell. In this work we report the secondary structure of this protein, determined with five different theoretical algorithms. Results indicate that the HN protein is organized in: an intracellular region (from amino acid 1 to 25); in a beta-strand transmembrane region (residue 26 to 47), typically hydrophobic, rigid and solvent inaccessible; and extracellular region (48 to 576), which possesses hemagglutinating and neuraminidase activity. The secondary structure in this region is organized in a beta-loop-beta alternated with few alpha-helices. Regions with structural and functional implications were determined by pattern search and multiple alignment of the HN from LPM with 12 rubulaviruses and paramyxoviruses HN sequences. The low diversity observed among the HN sequences evaluated indicates that in general the structural organization of the protein, and in particular its sugar binding domain, is closely related among both genera, thus suggesting that the sugar binding domain is well preserved through evolution.

Data_Sheet_3.PDF

“…When H protein sequences were subjected for the analysis of secondary structure prediction by PsiPred and SOPMA, our results showed that H proteins of different members of morbilliviruses are rich in beta sheets followed by alpha helices. Similar studies were done wherein it had been reported that Porcine Rubulavirus hemagglutinin protein is rich is beta sheets suggesting that hemagglutinin proteins of genus Morbillivirus are beta sheets enriched structures (Zenteno-Cuevas et al, 1998). Besides that, supramolecular assembly of MeV and CDV clearly depicts the presence of high ratio of beta sheets in their structures (Hashiguchi et al, 2011;Kalbermatter et al, 2023).…”

Identification of Potential B Cell Epitope Determinants by Computer Techniques, in Hemagglutinin–Neuraminidase from the Porcine Rubulavirus La Piedad Michoacan

“…In conclusion, antibodies from mice immunized with live E. coli UH302-pST13-OMPC-HN-B were able to inhibit viral hemagglutination, suggesting that the saccharidic recognition site of the cellular receptor could be located near amino acids 533-544 in the HN sequence (38). We are currently evaluating the capacity of HN-A and HN-B antibodies to neutralize the infectious process of RvpLPM in vivo, and the feasibility of using HN-A and HN-B as a diagnostic tool for RvpLPM.…”

“…Analysis of the amino acid sequence of HN from RvpLPM, using the Hoop and Woods (14), Parker et al (27), and Welling et al (37) algorithms in combination with physicochemical and structural information (38), allowed for the identification of 18 potential antigenic B cell epitopes (Table 1). Of these peptides, only three were analyzed further; the two peptides with the highest antigen and physicochemical scores and best structural properties, and the one with the lowest antigenic score: (1) an 18-amino acid peptide, spanning residues 251 to 267, and YVATRSETDYYAGNSPPQ sequence (HN-A); (2) a 12-amino acid peptide, spanning residues 533 to 544, and the sequence TTTCFRDTDTGK (termed HN-B), and (3) a 12-amino acid peptide, with the lowest antigenic score (HN-R), spanning residues 313 to 324, and FPAYG-GMQQILA sequence, which was selected just for the purpose of comparison.…”

“…S77541/AAB21049), three programs included in the ANTHEPROT suite of programs version 2.0 (11) were used to predict B cell epitopes, in accordance with the authors' instructions: antigenicity from Parker and co-workers (27), antigenicity from Welling and coworkers (37), and hydrophilicity from Hoop and Woods (14). The procedure for epitope mapping was as follows: only peptides defined by all the algorithms were considered; the final antigenic value was calculated on the basis of the average of the antigenicity scores obtained with each program; final peptide length was established when at least two of the programs detected two consecutive amino acids with zero values; and, finally, we included the previously calculated percent residues with a looplike secondary structure and the average of solvent accessibility (38). Using this procedure, 18 peptides were identified and defined as potential antigens (Table 1).…”

“…These receptors have been found in the epididymal and lung tissues of adult pigs, but their highest concentration has been detected in the central nervous system of newborn pigs, explaining in part the behavior of this disease (8). The HN gene is composed of 1906 nucleotides that encode a 63.3-kDa protein with 576 amino acids (33), one hydrophobic N terminus with a cleavage membrane domain (19), and one secondary structural organization of the ␤ strand-loop-␤ strand type that is disrupted occasionally by ␣-helix structures; the protein has four potential N-glycosylation sites (38).…”