The Three-Fold Axis of the HIV-1 Capsid Lattice Is the Species-Specific Binding Interface for TRIM5α

Abstract

Rhesus TRIM5α (rhTRIM5α) potently restricts replication of human immunodeficiency virus type 1 (HIV-1). Restriction is mediated through direct binding of the C-terminal B30.2 domain of TRIM5α to the assembled HIV-1 capsid core. This host-pathogen interaction involves multiple capsid molecules within the hexagonal HIV-1 capsid lattice. However, the molecular details of this interaction and the precise site at which the B30.2 domain binds remain largely unknown. The human orthologue of TRIM5α (hsTRIM5α) fails to block infection by HIV-1 both in vivo and in vitro. This is thought to be due to differences in binding to the capsid lattice. To map the species-specific binding surface on the HIV-1 capsid lattice, we used microscale thermophoresis and dual-focus fluorescence correlation spectroscopy to measure binding affinity of rhesus and human TRIM5α B30.2 domains to a series of HIV-1 capsid variants that mimic distinct capsid arrangements at each of the symmetry axes of the HIV-1 capsid lattice. These surrogates include previously characterized capsid oligomers, as well as a novel chemically cross-linked capsid trimer that contains cysteine substitutions near the 3-fold axis of symmetry. The results demonstrate that TRIM5α binding involves multiple capsid molecules along the 2-fold and 3-fold interfaces between hexamers and indicate that the binding interface at the 3-fold axis contributes to the well-established differences in restriction potency between TRIM5α orthologues.IMPORTANCE TRIM5α is a cellular protein that fends off infection by retroviruses through binding to the viruses' protein shell surrounding its genetic material. This shell is composed of several hundred capsid proteins arranged in a honeycomb-like hexagonal pattern that is conserved across retroviruses. By binding to the complex lattice formed by multiple capsid proteins, rather than to a single capsid monomer, TRIM5α restriction activity persists despite the high mutation rate in retroviruses such as HIV-1. In rhesus monkeys, but not in humans, TRIM5α confers resistance to HIV-1. By measuring the binding of human and rhesus TRIM5α to a series of engineered HIV-1 capsid mimics of distinct capsid lattice interfaces, we reveal the HIV-1 capsid surface critical for species-specific binding by TRIM5α.

Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations

“…TRIM5α binding also affects residues in critical assembly interfaces, including the NTD-NTD and NTD-CTD intrahexameric interfaces and the CTD-CTD interhexameric dimer interface, in accordance with the observation that TRIM5α does not bind appreciably to CA monomers (51). Indeed, the mechanisms of capsid recognition by TRIM5α involve higher-order capsid assembly (48,26). While emerging evidence suggests that dynamics may play a role in capsid function (2,(15)(16)(17)(18), in-depth atomic-level investigations of the relevant timescales are needed to understand how dynamic allostery may fine-tune infectivity.…”

“…The presence of the β-hairpin has been proposed to be an important feature in the assembly of the mature viral core (45,46) and may be exploited by TRIM5α as a molecular recognition motif (47), although this hypothesis is currently debated. A recent study suggested that the TRIM5α B30.2 domain recognizes the capsid through the capsid's trimeric interface, conferring species-specific HIV-1 restriction activity (48).…”

TRIM5α self-assembly and compartmentalization of the HIV-1 viral capsid

“…Attractive interactions between B-box domain residues were added to promote the formation of the crystallographically resolved trimer-of-dimer structures. Attractive interactions were added between SPRY and CA domain residues that demonstrated decreased or abolished TRIM5α binding in experimental mutagenesis studies 21,29 . (For a complete description on the models, see also Materials & Methods).…”

“…CypA has a much higher affinity for the CA protein (K D~1 0 μM) [38][39][40] , and the high-resolution crystallographic structure of CypA in complex with CA reveals that it binds to a flexible loop region that connects helices 4 and 5 (resid 80-100) 41 . Given the weak affinity between the SPRY and CA domains and the lack of available structural data, several studies have attempted to model the SPRY binding interface either using computational methods 42,43 or experimental mutagenesis 29,44 . Our CG simulations provide an alternative approach.…”

Delayed disease progression in HIV-2: the importance of TRIM5α and the retroviral capsid

“…Increasing viral load level has a strong association with decreasing survival probability [12]. and is associated with high-affinity binding and determines species-specific restriction of TRIM5α orthologues [19].…”