title: Denaturation of HIV-1 protease (PR) monomer by acetic acid: mechanistic and trajectory insights from molecular dynamics simulations and NMR.
abstract: Inside a living cell there can be a variety of interactions for any given protein, which serve to regulate denaturation and renaturation processes. Insights into some of them can be obtained by in vitro studies using various denaturing agents. In this study, all-atom MD simulations in explicit solvent and NMR relaxation studies were performed on HIV-1 Protease (PR) in 9 M acetic acid (AcOH) (the commonly used denaturant during PR preparation). Following previous reports that denaturation proceeds via dissociation of the dimer into monomers, unfolding of the monomer by acetic acid has been explicitly investigated here. Direct visualization of the denaturation process and evidence for the mechanism of denaturation have been presented. Our simulations reveal that the denaturation of the PR monomer is caused due to direct interaction between acetic acid molecules and PR. Autocorrelation of N-H vectors calculated from the simulations have revealed that the α-helix and the surrounding β-strands represent the sensitive regions of the PR that respond maximally to the change in the solvent environment around the PR and are prone to disruption by acetic acid. This disruption is caused due to increased penetration of the acetic acid molecules into the PR structure by formation of preferred tertiary contacts and hydrogen bonds between the PR and acetic acid molecules. Following the loss of these critical interactions, the PR follows a random and non-equilibrating path on the conformation landscape and cycles between  different denatured extended and compact states.
authors.affiliation: Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai-400005, India.
authors.forename: Aditi
authors.initials: A
authors.lastname: Borkar
authors.forename: Manoj Kumar
authors.initials: MK
authors.lastname: Rout
authors.forename: Ramakrishna V
authors.initials: RV
authors.lastname: Hosur
mesh_terms: D019342:Acetic Acid / Q000737:chemistry*; D016333:HIV Protease / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D011489:Protein Denaturation; D012997:Solvents / Q000737:chemistry
chemical_list: D012997:Solvents; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1; D019342:Acetic Acid