To surmount the computational cost associated with simulations at an atomic level of detail, we developed a CG model for TRIM5α self-assembly on viral capsids, using methods established in prior studies 25, 26, 27, 28. At least two hundred TRIM5α monomers are required to form an encaging hexagonal lattice around the core of the virus that blocks HIV infection in a slow dynamical process that takes place on the order of minutes 24 and is currently not amenable to analysis by all-atom molecular dynamics simulations. Mature HIV-1 capsid structures are large protein assemblies consisting of ~1500 individual CA domains arranged in a fullerene cone around the viral RNA, reverse transcriptase, and other enzymes that facilitate the replication of the virus. In this work, we investigate the self-assembly mechanisms of TRIM5α on the HIV-1 retroviral capsid, using a combined coarse-grained (CG) molecular simulation, cryo-electron tomography (cryo-ET) imaging, and computational analysis approach. Given the low affinity of individual TRIM5α monomers for the capsid, how does TRIM5α effectively encage the viral capsid? Dimerization enhances TRIM5α binding in vitro, and several studies, including ours, have suggested that the weak interactions are amplified by avidity effects resulting from higher-ordered oligomerization, which positions the SPRY domains to interact with repeating structural elements on the capsid surface 22, 23 although none have explored the dynamics of how this might occur. In addition, TRIM5α contains a C-terminal SPRY domain, connected to the center of the coiled-coil domain by the L1 helix and a flexible linker region, that has a very weak affinity for the capsid protein (CA) (estimated K D > 1 mM) 13, 19, 20, 21. B-box domains interact with the B-box domains of other TRIM5α dimers in a layered fashion with electrostatic interactions sandwiching a hydrophobic core to produce a three-fold symmetric trimer-of-dimers structure 18. The B-box domain caps the N-terminal end of each α-helix and mediates interactions between TRIM5α dimers. At low concentrations in solution, TRIM5α proteins primarily form dimeric complexes, mediated by interactions between two antiparallel α-helices that comprise the coiled-coil domain. Like all tripartite motif containing proteins, TRIM5α consists of three distinct domains – a RING domain, B-box domain, and coiled-coil domain (i.e., RBCC or tripartite motif). Higher-ordered oligomers of TRIM5α spontaneously assemble into hexagonally patterned structures on the surface of the capsid, which are detectable under negative-stained electron microscopy 16, 17. TRIM5α proteins are cytoplasmic proteins that bind to the retroviral capsid of HIV-1 and promote signaling pathways that alert the innate immune system to invasion 11, 12, causing the premature dissociation of the capsid and inhibiting reverse transcription 13, 14, 15. TRIM5α and TRIMCyp, in particular, have been found to be responsible for the species-specific resistance to infection by the human immunodeficiency virus type 1 (HIV-1) in rhesus macaques 9 and owl monkeys 10, respectively. Several TRIM proteins directly restrict viral activity by interfering with distinct steps in the viral life cycle, while others regulate signal transduction pathways induced by innate immune sensors. TRIMs have been implicated in diverse biological processes, including autophagy, cell differentiation, apoptosis, and intracellular signaling 5, 6, 7, 8. Tripartite motif containing proteins (TRIMs) are a large family of proteins that play central roles in host cellular responses to viral infection 1, 2, 3, 4. These simulations elucidate the molecular-scale mechanisms of viral capsid cellular compartmentalization by TRIM5α. Statistical analysis localizes the TRIM5α binding interface at or near the CypA binding loop of CA. Constrained diffusion allows the lattice to reorganize, whereas defects form on highly curved capsid surfaces to alleviate strain and lattice symmetry mismatches. Using a combination of computational simulations and electron cryo-tomography imaging, we reveal the dynamical mechanisms by which these lattices self-assemble. Several studies suggest TRIM5α oligomerizes into a lattice with a symmetry and spacing that matches the underlying capsid, to compensate for the weak affinity, yet little is known about how these lattices form. Higher-ordered oligomerization of this protein forms hexagonally patterned structures that wrap around the viral capsid, despite an anomalously low affinity for the capsid protein (CA). The tripartite-motif protein, TRIM5α, is an innate immune sensor that potently restricts retrovirus infection by binding to human immunodeficiency virus capsids.
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