Naturally occurring capsid protein variants L1 of human papillomavirus genotype 16 in Morocco

Abstract

HPV L1 protein is a corner stone in HPV structure, it's involved in the formation of the viral capsid; widely used as a systematic material and considered as the main component in vaccines development and production. The present study aims to characterize genetic variation of L1 gene of HPV 16 specimens and to evaluate in silico the impact of major variants on the epitope change affecting its conformational structure. A fragment of L1 gene from 35 HPV 16 confirmed specimens were amplified by PCR and sequenced. Overall, five amino acids residues changes were reported: T390P in 16 specimens, M425I and M431I in 2 cases, insertion of Serine at 460 and aspartic acid deletion at position 477 in all analyzed cases. The 3D generated model showed that T389P amino acid substitution is located in the H-I loop; the two substitutions M424I and M430I are both located in the H2 helice. The Serine insertion and aspartic acid deletion are located in the H4 helice and B-C loop, respectively. Superimposition of sequences' structures showed that they share a very similar conformation highlighting that the reported amino acids variations don't affect the structure of the L1 protein. However T389P, located in the H-I loop identified as an immunogenetic region of L1 capsid, was reported in 51.4% of cases could interact with vaccines induced monoclonal antibodies suggesting a potential impact on the efficacy of available anti-HPV vaccines.

Keywords: HPV 16; L1 protein; genetic variation; in silico prediction; vaccine.

Figure 1

Phylogenetic tree of the Moroccan HPV16 variants. Phylogenetic study was constructed based on the partial L1 nucleotide sequence alignment of thirty-five sequences, which were constructed by the Maximum likelihood method and the Kimura 2-Parameter model by MEGA 6 package. Bootstrap proportions were calculated with 1000 replicates. Our study sequences are shown in Arabic numbers; others are shown with abbreviations, African lineage (Af), European prototype (Ep). European variant (E), Asia lineage (As), Asian American lineage (AA) and the prototype (K02718.1).

Figure 2

Variability of amino acid residues using SeqLogo. The twenty-three sequences have been used to estimate amino acids residue variation using SeqLogo. Sequence conservation is represented by the height of residue logos “indicated in bits”, and the arrow indicates the change in amino acids residues.

Figure 3

Carton structure of the major capsid protein (L1) of HPV16. (K02718.1). K: Lisyne, L: Leucine, Helix in green, Sheets in red, Loops in black), Ct: C-terminal amino acid, Nt: N-terminal amino acid.

Figure 4

3D structure of L1 HPV16 protein showing the positions of the non-synonymous amino acids variation. Threonine changed to Proline, located in the H1 loop. Methionine in the position 424 was changed to Isoleucine and Methionine in position 430 was changed to Isoleucine are both located in the H2 helice. The serine insertion and aspartic acid deletion are located in the H4 helice and B-C loop, respectively.

Figure 5

3D carton structure of HPV16 L1 homology models generated and visualized by PyMol. A: 3D sequence representation of the L1 fragments containing the insertion of Serine (460) and deletion of aspartic acid (477). B: 3D sequence representation of the L1 fragments containing the insertion of Serine (460), deletion of aspartic acid (477) and Thr/Pro substitution (390). C: 3D sequence representation of the L1 fragments containing the insertion of Serine (460), deletion of aspartic acid (477), Thr/Pro (390), Met/Iso (425) and Met/Iso (431) substitutions. D: Superimposition of both 3D structures with the prototype model showing that the structures share a very similar conformation.