Molecular cloning, biophysical and in silico studies of Human papillomavirus 33 E2 DNA binding domain

Abstract

Human papillomavirus 33, a high-risk HPV strain, is mainly responsible for HPV infection and cervical cancer in Asian countries. The E2 protein of HPV 33 is a DNA-binding protein that plays a crucial role in viral replication and transcription. We have cloned, overexpressed, and purified the DNA binding domain of the E2 protein. Size exclusion chromatography results suggested that the protein exists in a homodimeric state in the native form. Circular dichroism data showed that the protein has a higher content of β-sheet. The melting temperature obtained from differential scanning calorimetry is 52.59 °C, and the protein is stable at pH 8 and is in a dimeric form at basic pH. The protein is monomeric or unfolded at a very low pH. Chemical denaturation studies suggested that the protein denatured and dissociated simultaneously. The DNA binding activity of the protein was also confirmed and it showed binding affinity in the order of 10⁶ M⁻¹. The protein structure was modeled using homology modeling and other bioinformatic tools. The virtual screening and molecular dynamic simulation studies were performed to find compounds that can act as potent inhibitors against E2 DBD. This study expands the understanding of the conserved structural and binding properties of HPV33 E2 DBD and provides the first report on the characterization of the viral protein.

Communicated by Ramaswamy H. Sarma

Keywords:

• Human papillomavirus
• size exclusion chromatography
• DNA binding domain
• fluorescence
• circular dichroism
• homology modeling
• molecular dynamic simulations

Acknowledgments

The authors are thankful to the International Human Papillomavirus (HPV) Reference Center, Karolinska Institute, Stockholm, for providing the HPV 33 E2 gene. The authors are grateful to Dr. Rakesh Kumar, Scientist, Central Institute for Cotton Research (CICR), Nagpur for providing cloning and expression vectors, helpful discussions, and suggestions during the work. Bharti gratefully acknowledges the Council of Scientific and Industrial Research (CSIR), India, for a student research fellowship. This work was supported by a grant to MSN from the Council of Scientific and Industrial Research (CSIR), India (37/1732/19-EMR II). Authors also thank the Ashok Soota Molecular Medicine Facility for different experimental facility and Prof. K. M. Poluri, Department of Biosciences and Bioengineering for early stage discussions.

Author contributions

MSN conceived the work. MSN and Bharti designed the experiments. Bharti performed the experiments. Data analysis and writing were done by Bharti and MSN.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was funded by Council of Scientific and Industrial Research, India.