Identification and stability analysis of potential ADP-ribose modification sites on vascular endothelial growth factor (VEGF) through molecular dynamics simulation

Abstract

Post-translational modifications (PTMs) are crucial covalent processes that alter protein properties, achieved through proteolytic cleavage or addition of modifying groups like acetyl, phosphoryl, glycosyl, or methyl to amino acids. ADP-ribosylation is a reversible post-translational modification, where ADP-ribose units are covalently attached to target protein side chains. Vascular endothelial growth factor (VEGF) is a potent angiogenic factor that plays a key role in physiological and pathological conditions. Studies have reported that ADP-ribosylation affects VEGF's ability to bind to VEGF receptors, impacting angiogenesis signalling. However, the specific amino acid undergoing ADP-ribosylation on VEGF remained unknown. To understand the mechanism of ADP-ribose addition to VEGF, an in silico study was designed. The study initially checked for the presence of any conserved motif where ADP-ribosylation could potentially occur and identified the presence of the EIE motif in VEGF, a probable site for ADP-ribosylation for many proteins. Subsequently, the amino acids near this motif were selected and their structural properties were analyzed. Surface-exposed amino acids were chosen, and ADP-ribose was then added to their side chains. The results revealed that the amino acids ASP (67) and GLU (70) underwent glycosidic linkage with ADP-ribose, indicating that they are the most probable modification sites. Subsequently, Molecular dynamic simulation analysis such as RMSD, RMSF, Rg, PCA, and FEL, along with MM-PBSA binding free energy calculations were performed to understand the stability of the VEGF-ADP-ribose complexes. The analysis revealed that amino acid at position 67 (ASP67) is the most probable site for ADP-ribosylation in VEGF.

Communicated by Ramaswamy H. Sarma

Keywords:

• Post translational modification
• ADP-ribosylation
• vascular endothelial growth factor
• molecular dynamics
• binding free energy

Acknowledgments

The authors acknowledge the Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University) for providing the necessary facilities to carry out this study.

Author’s contributions

CSA designed the study. KS, KNH and CSA performed the experiments. Data analyzed by CSA and PRS. Manuscript written by KS, KNH and CSA and edited by RR, TSKP, SR and PRS. All authors have read and agreed to the published version of the manuscript.

Disclosure statement

The authors declare no conflict of interest.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.