Background: Cancers of cervix, head and neck regions have been found to be associated
with Human Papilloma Virus (HPV) infection. E1 protein makes an important papillomavirus replication
factor. Among the ORFs of papillomaviruses, the most conserved sequence is that of the
E1 ORF. It is the viral helicase with being a member of class of ATPases associated with diverse
cellular activities (AAA+) helicases. The interactions of E1 with human DNA and proteins occurs
in the presence of short linear peptide motifs on E1 identical to those on human proteins.
Methods: Different Motifs were identified on HPV16 E1 by using ELMs. Elastic network models
were generated by using 3D structures of E1. Their dynamic fluctuations were analyzed on the basis
of B factors, correlation analysis and deformation energies.
Results: 3 motifs were identified on E1 which can interact with Cdk and Cyclin domains of human
proteins. 11 motifs identified on E1 have their CDs of Pkinase on human proteins. LIG_MYND_2
has been identified as involved in stabilizing interaction of E1 with Hsp40 and Hsp70. These motifs
and amino acids comprising these motifs play a major role in maintaining interactions with human
proteins, ultimately causing infections leading to cancers.
Conclusion: Our study identified various motifs on E1 which interact with specific counter domains
found in human proteins, already reported having the interactions with E1. We also validated
the involvement of these specific motifs containing regions of E1 by modeling elastic networks
of E1. These motif involving interactions could be used as drug targets.