Characterization and Structural Analysis of the Human Papilloma Virus L1 Protein in Iran

Background: Human papillomavirus (HPV) is a small, non-enveloped DNA virus related to human cervical cancer. The genome is maintained within the basal epithelium where the primary infection is latent. During the late phase of infection, the capsid proteins (L1 and L2) are expressed to encapsidate the viral genome, generating the infectious virion particles required for HPV propagation. HPV genome encodes six proteins, namely E6 oncoprotein, E7 oncoprotein, E1 replication protein, E2 regulatory protein, L1 major capsid protein, and L2 minor capsid protein. L1 is the principal part of the current vaccines, and any changes in this region can decrease vaccine efficiency. The aim of this research was to conduct a comparative analysis among Iranian L1 protein sequences with reference sequences to determine the possible substation in this region and to find the physicochemical and structural properties of L1 by using bioinformatics tools to provide comprehensive comprehension of the HPV L1 protein. Methods: Thirteen Iranian PV sequences of the L1 protein and reference sequences were selected and obtained from the NCBI data bank. CLC Sequence Viewer software was used to translate the alignment. PrediSi and Phobius were employed to predict the signal peptide. The secondary and tertiary structures and structure validations of all sequences were analyzed by Qmean, (PS)2-v2, Phyre2server, Discovery Studio, and I-TASSER. Results: The findings showed that L1 is highly conserved, and only two mutations were found in this region. No signal peptide was described, and this region’s main part included a random coil. The tertiary structure was mapped using different software, and five distinct loops were found. Conclusion: This study is the first report that investigated the changes in the L1 protein of Iranian patients and provided helpful comprehension of the L1 properties vital for cloning and producing the new generation of virus-like particle (VLP) vaccines. Furthermore, the structural analysis showed several loops that had an indispensable role in antibody binding and the prevention of HPV infections.