Critical mechanistic features of HIV-1 viral capsid assembly

Abstract

The maturation of HIV-1 capsid protein (CA) into a cone-shaped lattice capsid is critical for viral infectivity. CA can self-assemble into a range of capsid morphologies made of ~175 to 250 hexamers and 12 pentamers. The cellular polyanion inositol hexakisphosphate (IP6) has recently been demonstrated to facilitate conical capsid formation by coordinating a ring of arginine residues within the central cavity of capsid hexamers and pentamers. However, the kinetic interplay of events during IP6 and CA coassembly is unclear. In this work, we use coarse-grained molecular dynamics simulations to elucidate the molecular mechanism of capsid formation, including the role played by IP6. We show that IP6, in small quantities at first, promotes curvature generation by trapping pentameric defects in the growing lattice and shifts assembly behavior toward kinetically favored outcomes. Our analysis also suggests that IP6 can stabilize metastable capsid intermediates and can induce structural pleomorphism in mature capsids.

Understanding Virus Structure and Dynamics through Molecular Simulations

“…17 However, in vitro assembly experiments in the absence of IP6 generated mature tubes, 17 while the CG simulations showed relatively flatter lattices, meaning there are still some limitations in this simplified model. Gupta et al 84 also discovered that IP6 facilitates conical capsid formation by stabilizing metastable assembly intermediates and thus showed the potential of viral inhibition by targeting IP6 binding sites.…”

K-Means Clustering Coarse-Graining (KMC-CG): A Next Generation Methodology for Determining Optimal Coarse-Grained Mappings of Large Biomolecules

“…Highly coarse-grained systems have proven very useful for modeling complex biomolecular processes, such as the polymerization and conversion of actin filaments 63,64 and the HIV-1 viral capsid assembly. 4 Key biological processes involve the participation of a great number of large biomolecules and occur on long length and time scales. A simple but physically accurate CG model can, therefore, greatly enhance the efficiency of computer simulations of such processes while preserving the critical physical behavior of the constituent biomolecules.…”

“…With the ongoing growth in computational power, particularly with the deployment of GPU-powered molecular dynamics (MD) engines, all-atom (AA) MD has become an extensively used tool for studying large biomolecular systems. , Nevertheless, as the time and length scales of the systems of interest continue to increase, many critical biological and even cellular processes, such as the polymerization dynamics of actin filaments and the self-assembly of viral capsids, , are beyond the capability of AA MD simulations. Therefore, further development of coarse-grained (CG) MD is necessary to reduce the complexity and to study these systems on coarse scale .…”

Sub-stoichiometric Modulation of Viral Targets─Potent Antiviral Agents That Exploit Target Vulnerability

“…Structural studies with 3 that have emerged only recently have revealed that the compound binds to the core of the assembled 6-helix bundle (6-HB) form of CA-SP-1 and stabilizes the complex in a fashion that interferes with the exposure of the site of protease-mediated cleavage, which lies between Leu 363 and Ala 364 . − The most contemporary structural analysis studied microcrystalline assemblies of the C-terminal domain of CA-SP-1 complexed with 3 using magic-angle-spinning NMR and demonstrated that the compound bound to the 6-HB in conjunction with inositol hexakis­phosphate (IP 6 ), which has been identified as an assembly cofactor that is critical to virus replication (Figure ). ,− The equatorial phosphates of IP 6 coordinate with the basic side chains of Lys 290 that are located close to the junction between the base of the goblet shape created by CA and the top of the goblet stem, which is mostly defined by SP-1 residues, and which project in a ring-like arrangement around the central core of the bundle. The immature 6-HB assembly is convened by the Lys 290 residues engaging IP 6 , a phenomenon that extends to other retroviruses, while the axial phosphate associates with Lys 359 , which is proximal to the cleavage site between Leu 363 and Ala 364 . − ,− In the absence of IP 6 , inositol pentakis­phosphate (IP 5 ) is an effective substitute, while a Thr 371 Ile mutation in the SP-1 protein that appears in response to the passaging of viruses incorporating a Lys 359 Ala mutation, which compromises IP 6 binding, is able to rescue infectivity. − , In WT virus, the Thr 371 Ile mutation mimics the effects of 3 by suspending CA-SP-1 processing, while, interestingly, 3 itself was found to be capable of rescuing a mutant virus defective in IP 6 binding by acting as a functional surrogate .…”

“… ,− The equatorial phosphates of IP 6 coordinate with the basic side chains of Lys 290 that are located close to the junction between the base of the goblet shape created by CA and the top of the goblet stem, which is mostly defined by SP-1 residues, and which project in a ring-like arrangement around the central core of the bundle. The immature 6-HB assembly is convened by the Lys 290 residues engaging IP 6 , a phenomenon that extends to other retroviruses, while the axial phosphate associates with Lys 359 , which is proximal to the cleavage site between Leu 363 and Ala 364 . − ,− In the absence of IP 6 , inositol pentakis­phosphate (IP 5 ) is an effective substitute, while a Thr 371 Ile mutation in the SP-1 protein that appears in response to the passaging of viruses incorporating a Lys 359 Ala mutation, which compromises IP 6 binding, is able to rescue infectivity. − , In WT virus, the Thr 371 Ile mutation mimics the effects of 3 by suspending CA-SP-1 processing, while, interestingly, 3 itself was found to be capable of rescuing a mutant virus defective in IP 6 binding by acting as a functional surrogate . After cleavage of the CA-SP-1 junction, IP 6 stabilizes the mature lattice by engaging with the circle of side chains presented by Arg 18 in the goblet element of the 6-HB structure.…”