The conformational feasibility for the formation of reaching dimer in ASV and HIV integrase: a molecular dynamics study

Abstract

Retroviral integrases are reported to form alternate dimer assemblies like the core–core dimer and reaching dimer. The core–core dimer is stabilized predominantly by an extensive interface between two catalytic core domains. The reaching dimer is stabilized by N-terminal domains that reach to form intermolecular interfaces with the other subunit’s core and C-terminal domains (CTD), as well as CTD–CTD interactions. In this study, molecular dynamics (MD), Brownian dynamics (BD) simulations, and free energy analyses, were performed to elucidate determinants for the stability of the reaching dimer forms of full-length Avian Sarcoma Virus (ASV) and Human Immunodeficiency Virus (HIV) IN, and to examine the role of the C-tails (the last ~16–18 residues at the C-termini) in their structural dynamics. The dynamics of an HIV reaching dimer derived from small angle X-ray scattering and protein crosslinking data, was compared with the dynamics of a core–core dimer model derived from combining the crystal structures of two-domain fragments. The results showed that the core domains in the ASV reaching dimer express free dynamics, whereas those in the HIV reaching dimer are highly stable. BD simulations suggest a higher rate of association for the HIV core–core dimer than the reaching dimer. The predicted stability of these dimers was therefore ranked in the following order: ASV reaching dimer < HIV reaching dimer < composite core–core dimer. Analyses of MD trajectories have suggested residues that are critical for intermolecular contacts in each reaching dimer. Tests of these predictions and insights gained from these analyses could reveal a potential pathway for the association and dissociation of full-length IN multimers.

Keywords:

• ASV
• HIV
• integrase
• reaching dimer
• core–core dimer

Abbreviations:

• DNA – deoxyribo nucleic acid
• IN – Integrase
• HIV – Human Immunodeficiency Virus
• NTD – N-terminal domain
• CCD – Catalytic Core domain
• CTD – C-terminal domain
• ASV – Avian Sarcoma Virus
• PFV – Prototype Foamy Virus
• MMTV – Mouse Mammary Tumor Virus
• RSV – Rous Sarcoma Virus
• SAXS – small angle X-ray scattering

Acknowledgments

One of the authors RA acknowledges the Science and Engineering Research Board, India and the University Grants Commission for providing computational facilities in the form of Research Projects. We thank Roland Dunbrack, Vivek Modi, and the Molecular Modeling facility of Fox Chase Cancer Center for helpful discussions. Research of MA is also supported in part by National Institutes of Health grants AI 040383, CA 71515 and CA 06927.