Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein

Abstract

Oligomerization of Pr55Gag is a critical step of the late stage of the HIV life cycle. It has been known that the binding of IP6, an abundant endogenous cyclitol molecule at the MA domain, has been linked to the oligomerization of Pr55Gag. However, the exact binding site of IP6 on MA remains unknown and the structural details of this interaction are missing. Here, we present three high-resolution crystal structures of the MA domain in complex with IP6 molecules to reveal its binding mode. Additionally, extensive Differential Scanning Fluorimetry analysis combined with cryo- and ambient-temperature X-ray crystallography and GNM-based transfer entropy calculations identify the key residues that participate in IP6 binding. Our data provide novel insights about the multilayered HIV-1 virion assembly process that involves the interplay of IP6 with PIP2, a phosphoinositide essential for the binding of Pr55Gag to membrane. IP6 and PIP2 have neighboring alternate binding sites within the same highly basic region (residues 18–33). This indicates that IP6 and PIP2 bindings are not mutually exclusive and may play a key role in coordinating virion particles’ membrane localization. Based on our three different IP6-MA complex crystal structures, we propose a new model that involves IP6 coordination of the oligomerization of outer MA and inner CA domain’s 2D layers during assembly and budding.

Identification of New L-Heptanoylphosphatidyl Inositol Pentakisphosphate Derivatives Targeting the Interaction with HIV-1 Gag by Molecular Modelling Studies

“…Then, in our recently published paper, we performed both synchrotron cryo X-ray crystallography and ambient-temperature serial femtosecond X-ray crystallography (SFX) with an XFEL to obtain MA-IP6 co-crystal structures. We reported three crystal forms and the resulting X-ray structures of MA in complex with the IP6 molecule (PDB IDs: 7E1I, 7E1J, and 7E1K) ( Figure 2 ) [ 44 ].…”

“…The validated molecular docking protocol, with docking scores and binding interactions comparable to the co-crystallized ligands, was applied for eight new L-HIPPO derivatives to explore their binding affinities using three templates, which were recently solved by our group (PDB IDs: 7E1I, 7E1J, and 7E1K) [ 44 ].…”

“…Our first report of XFEL study for the determination of MA and IP6 interaction revealed that SFX is suitable for the diffraction of microcrystal forms of the MA-IP6 complex, which were diffracted to beyond 3.5 Å resolution [ 45 ]. Our recently published study clarified the MA structures in complex with IP6 (PDB IDs: 7E1I, 7E1J, and 7E1K) and the interactions between them were orchestrated by hydrogen bonding with basic residues Lys and Arg together [ 44 ].…”

“…The crystal structures of MA with its inhibitor IP6 were retrieved from the RSCB database (PDB IDs: 7E1I, 7E1J, and 7E1K) [ 44 ]. The raw file was prepared for the docking assessment by the PrepWizard module of Maestro.…”

“…In the current work, initially, we rationally designed eight new L-HIPPO derivatives related to four new design strategies. After that, we performed molecular docking for new phosphoinositides via Schrödinger software, using three high-resolution crystal structures of the MA in complex with IP6 that our research group had previously identified [ 44 ]. The most promising docking scores and interactions were obtained with benzene-inserted compounds.…”