Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate (IP₆)

Abstract

Inositol hexakisphosphates (IP 6 ) are cellular cofactors that promote the assembly of mature capsids of the human immunodeficiency virus (HIV). These negatively charged molecules coordinate an electropositive ring of arginines at the center of pores distributed throughout the capsid surface. Kinetic studies indicate that the binding of IP 6 increases the stable life times of the capsid by several orders of magnitude from minutes to hours. Using all-atom molecular dynamics simulations, we uncover the mechanisms that underlie the unusually high stability of mature capsids in complex with IP 6 . We find that capsid hexamers and pentamers have differential binding modes for IP 6 . Ligand density calculations show three sites of interaction with IP 6 including at a known capsid-inhibitor binding pocket. Free energy calculations demonstrate that IP 6 preferentially stabilizes pentamers over hexamers to enhance fullerene modes of assembly.These results elucidate the molecular role of IP 6 in stabilizing and assembling the retroviral capsid.Pittsburgh Supercomputing Center 17 . Similar to prior studies, IP 6 was initially added to the bulk solvent, approximately 10 Å away from any non-water molecules 18,19 . Four systems each for the CA hexamer and pentamer were prepared with IP 6 in randomized positions in bulk solvent, and selected for longer timescale simulations on Anton 2 (see: Materials and Methods for a complete description). In aggregate, the AA MD simulations totaled 32 µs for the hexamer and pentamer systems. In all cases, IP 6 was found to bind to the pore of the capsomere.

A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion

“…For example in HIV, CG simulations contributed to the understanding of the self-assembly of the capsid (62) and innate immune sensor recognition and block of viral activity (63), as well as its inhibition by drug molecules(64). Atomistic simulations of ligand binding have also revealed a variety of unexpected, drug-targetable protein-ligand interaction sites(65)(66)(67)(68)(69)(70)(71). It is likely that molecular probes into the processes the involving a holistic model of the SARS-CoV-2 virion can reveal new therapeutic strategies that exploit viral mechanisms involving large-scale behavior.…”

Strain and rupture of HIV-1 capsids during uncoating

“…1A) (16,17). IP6 polyanions were added to each CA hexamer or pentamer pore at the binding site, a location 2.7 Å above the R18 ring (5,7). In the absence of atomic resolution into the structure of the ribonucleoprotein complex (RNP), we constructed a model of two copies of the 9-kilobase pair RNA genome in complex with nucleocapsid proteins consistent with experimental secondary structure constraints from selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) analysis (18), in order to mimic the HIV-1 RNP.…”

“…As the core rigidifies further upon IP 6 binding, the dominant low frequency mode broadens, and the fluctuations are distributed to higher frequency modes, consistent with a stiffer capsid. Negatively charged IP 6 molecules bind tightly to an arginine ring in pores distributed throughout the capsid (4, 5, 7). RNP interactions with CA, on the other hand, could occur through interactions of positively charged residues on the flexible CTD tail of CA with the RNP (7).…”

“…Negatively charged IP 6 molecules bind tightly to an arginine ring in pores distributed throughout the capsid (4, 5, 7). RNP interactions with CA, on the other hand, could occur through interactions of positively charged residues on the flexible CTD tail of CA with the RNP (7). The cofactor interactions at the pore and CTD tail change the conformational flexibility of CA resulting in an increase in capsid rigidity that introduces strain on the underlying lattice.…”

“…Capsids play essential roles during replication, by transporting viral genetic material deep into the host cell (3). Pores in the capsid can bind or import small molecules, including inositol phosphates (IP6) and nucleotides (dNTPs) (4,5), and the binding of IP6 increases the stable lifetimes of the capsid and promotes the assembly of CA into fullerene structures (6,7). Cryo-electron tomography (cryo-ET) and other techniques have recently demonstrated that viral cores are imported with apparently intact capsids across the nuclear pore of infected cells (8)(9)(10)(11).…”