The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations

• Published in: Biophysical chemistry 2014-12, Vol.195, p.32-42
• Main Authors: Caldarini, M., Sonar, P., Valpapuram, I., Tavella, D., Volonté, C., Pandini, V., Vanoni, M.A., Aliverti, A., Broglia, R.A., Tiana, G., Cecconi, C.
• Format: Article
• Language: English
• Subjects: HIV Protease - chemistry; HIV Protease - genetics; HIV Protease - metabolism; HIV-1 - enzymology; HIV-1-protease; Humans; Intermediate states; Molecular Dynamics Simulation; Molecular dynamics simulations; Optical Tweezers; Protein Denaturation; Protein folding; Protein Refolding; Protein Structure, Secondary; Recombinant Proteins - biosynthesis; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Single-molecule studies
• ISSN: 0301-4622; 1873-4200
• DOI: 10.1016/j.bpc.2014.08.001

We have used optical tweezers and molecular dynamics simulations to investigate the unfolding and refolding process of a stable monomeric form of HIV-1-protease (PR). We have characterized the behavior under tension of the native state (N), and that of the ensemble of partially folded (PF) conformations the protein visits en route to N, which collectively act as a long-lived state controlling the slow kinetic phase of the folding process. Our results reveal a rich network of unfolding events, where the native state unfolds either in a two-state manner or by populating an intermediate state I, while the PF state unravels through a multitude of pathways, underscoring its structural heterogeneity. Refolding of mechanically denatured HIV-1-PR monomers is also a multiple-pathway process. Molecular dynamics simulations allowed us to gain insight into possible conformations the protein adopts along the unfolding pathways, and provide information regarding possible structural features of the PF state. [Display omitted] •HIV-1-PR plays a key role in the life cycle of the human immunodeficiency virus.•Complex (un)folding behavior was revealed by single-molecule and MD studies.•HIV-1-PR unfolds either in a two-state manner or by populating an intermediate state.•Folding of denaturated HIV-1-PR monomer is a multi-pathway process.•Folding information can guide rational design of HIV-1-PR folding inhibitors.