A comparative study of integrase-binding domain of homologous HRP2 and LEDGF/p75 protein: from sequence to structural characterisation

Abstract

Human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) and hepatoma-derived growth factor related protein 2 (HRP2) are binding partners for human immunodeficiency virus type integrase protein in human cells. LEDGF/p75 and HRP2 share a similar domain organisation and have an apparent evolutionary and functional relationship. The integrase-binding domain (IBD) is located in the C-terminal region of both LEDGF/p75 and HRP2 protein. Unlike HRP2, the IBD of LEDGF/p75 is well explored and its NMR structure is available in Protein Data Bank (PDB) database. In this work, comparative sequence analysis and molecular modelling approaches were employed to characterise the IBD of human HRP2 protein. Sequence analysis of HRP2 IBD showed variability in C-terminal region while the other part remains conserved. The homologous sequence of the IBD in HRP2 was modelled by using NMR structure of LEDGF/p75 IBD as a template (PDB: 1Z9E). Secondary structure of variable region was initially predicted as an alpha helix using SAM-T06 server. The final model was subjected to molecular dynamics (MD) simulations up to 100 ns to find out the precise orientation of model structure. Root mean square deviation and B-factor analyses indicate stable IBD core region and loosely packed variable region during 100 ns MD simulation. The modelled IBD structure of HRP2 exhibits overall similar topology with LEDGF/p75 IBD and appears as a stable fold consisting of five compact alpha helices. However, the variable region (552–574 residues) shows unstable helix–loop–helix conformation. This comprehensive study of HRP2 IBD provides in-depth sequence and structural information that may be exploited in anti-retroviral drug design studies.