Virus assembly, allostery and antivirals

Though the hepatitis B virus (HBV) core protein is an important participant in many aspects of the viral life cycle, its best-characterized activity is self-assembly into 240-monomer capsids. Small molecules that target core protein (core protein allosteric modulators [CpAMs]) represent a promising antiviral strategy. To better understand the structural basis of the CpAM mechanism, we determined the crystal structure of the HBV capsid in complex with HAP18. HAP18 accelerates assembly, increases protein-protein association more than 100-fold, and induces assembly of nonicosahedral macrostructures. In a preformed capsid, HAP18 is found at quasiequivalent subunit-subunit interfaces. In a detailed comparison to the two other extant CpAM structures, we find that the HAP18-capsid structure presents a paradox. Whereas the two other structures expanded the capsid diameter by up to 10 Å, HAP18 caused only minor changes in quaternary structure and actually decreased the capsid diameter by ϳ3 Å. These results indicate that CpAMs do not have a single allosteric effect on capsid structure. We suggest that HBV capsids present an ensemble of states that can be trapped by CpAMs, indicating a more complex basis for antiviral drug design. IMPORTANCEHepatitis B virus core protein has multiple roles in the viral life cycle-assembly, compartment for reverse transcription, intracellular trafficking, and nuclear functions-making it an attractive antiviral target. Core protein allosteric modulators (CpAMs) are an experimental class of antivirals that bind core protein. The most recognized CpAM activity is that they accelerate core protein assembly and strengthen interactions between subunits. In this study, we observe that the CpAM-binding pocket has multiple conformations. We compare structures of capsids cocrystallized with different CpAMs and find that they also affect quaternary structure in different ways. These results suggest that the capsid "breathes" and is trapped in different states by the drug and crystallization. Understanding that the capsid is a moving target will aid drug design and improve our understanding of HBV interaction with its environment. Hepatitis B virus (HBV) causes degenerative liver disease and is the leading cause of liver cancer, with 240 million chronically infected individuals (1, 2). Current antiviral therapies control the progression of the disease but fail to eliminate the virus (3, 4). There is a need for improved therapies to combat chronic infections. One approach is to target virus assembly (5-7).HBV is an enveloped, double-stranded DNA virus with an icosahedral nucleoprotein core. The HBV capsid is the protein shell of the core. Beyond genome protection, the capsid is involved in intracellular trafficking, interaction with nuclear import machinery, regulation of reverse transcription, signaling, completion of reverse transcription, RNA chaperoning, and envelope acquisition (8). Capsid assembly is central to HBV replication. In vivo HBV capsids assemble around an RNA copy of the viral g...

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“…There is a need for improved therapies to combat chronic infections. One approach is to target virus assembly (5)(6)(7).…”

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confidence: 99%

Hepatitis B Virus Capsids Have Diverse Structural Responses to Small-Molecule Ligands Bound to the Heteroaryldihydropyrimidine Pocket

Venkatakrishnan

Katen

Francis

et al. 2016

J Virol

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“…For example, Zlotnick and Mukhopadhyay (31) have shown the possibility of using compounds that increase the number of nuclei formed during assembly of spherical virus capsids, thus sequestering the available capsid protein in partially assembled capsids and preventing the formation of complete, biologically competent virus particles. The effect of different compounds on the number of nuclei (nps) originating 2D ''capsids'' (CA patches) could be readily determined by AFM (as shown here using different CA concentrations), leading to a direct visualization of this promising mechanism of antiviral action.…”

Section: Discussionmentioning

confidence: 99%

“…The use of in vitro assembly systems, together with theoretical models and simulations, has unveiled important principles on the thermodynamics and kinetics of self-assembly of cellular protein complexes (26,27), spherical viral capsids (28)(29)(30)(31)(32)(33)(34)(35) and artificial nanoassemblies (36). However, little is known on the thermodynamics and kinetics of self-assembly of extended 2D protein lattices (37,38).…”

Section: Introductionmentioning

confidence: 99%

Kinetics of Surface-Driven Self-Assembly and Fatigue-Induced Disassembly of a Virus-Based Nanocoating

Valbuena

Mateu

2017

Biophysical Journal

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Self-assembling protein layers provide a ''bottom-up'' approach for precisely organizing functional elements at the nanoscale over a large solid surface area. The design of protein sheets with architecture and physical properties suitable for nanotechnological applications may be greatly facilitated by a thorough understanding of the principles that underlie their self-assembly and disassembly. In a previous study, the hexagonal lattice formed by the capsid protein (CA) of human immunodeficiency virus (HIV) was self-assembled as a monomolecular layer directly onto a solid substrate, and its mechanical properties and dynamics at equilibrium were analyzed by atomic force microscopy. Here, we use atomic force microscopy to analyze the kinetics of self-assembly of the planar CA lattice on a substrate and of its disassembly, either spontaneous or induced by materials fatigue. Both selfassembly and disassembly of the CA layer are cooperative reactions that proceed until a phase equilibrium is reached. Self-assembly requires a critical protein concentration and is initiated by formation of nucleation points on the substrate, followed by lattice growth and eventual merging of CA patches into a continuous monolayer. Disassembly of the CA layer showed hysteresis and appears to proceed only after large enough defects (nucleation points) are formed in the lattice, whose number is largely increased by inducing materials fatigue that depends on mechanical load and its frequency. Implications of the kinetic results obtained for a better understanding of self-assembly and disassembly of the HIV capsid and protein-based two-dimensional nanomaterials and the design of anti-HIV drugs targeting (dis)assembly and biocompatible nanocoatings are discussed.

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“…1 Due to their useful characteristics, such as a uniform nanoscale size, 2 symmetric structure, 3 easy fabrication, 4 and easy modification, 5 viral capsids have been used as nanoplatforms. 6 Various types of virus-based nanoparticles (VNPs) have been developed.…”

Section: Introductionmentioning

confidence: 99%

Quantum dot-induced viral capsid assembling in dissociation buffer

Gao¹,

Zhang²,

Li³

et al. 2013

IJN

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Viruses encapsulating inorganic nanoparticles are a novel type of nanostructure with applications in biomedicine and biosensors. However, the encapsulation and assembly mechanisms of these hybridized virus-based nanoparticles (VNPs) are still unknown. In this article, it was found that quantum dots (QDs) can induce simian virus 40 (SV40) capsid assembly in dissociation buffer, where viral capsids should be disassembled. The analysis of the transmission electron microscope, dynamic light scattering, sucrose density gradient centrifugation, and cryo-electron microscopy single particle reconstruction experimental results showed that the SV40 major capsid protein 1 (VP1) can be assembled into ≈25 nm capsids in the dissociation buffer when QDs are present and that the QDs are encapsulated in the SV40 capsids. Moreover, it was determined that there is a strong affinity between QDs and the SV40 VP1 proteins (K D = 2.19E-10 M), which should play an important role in QD encapsulation in the SV40 viral capsids. This study provides a new understanding of the assembly mechanism of SV40 virus-based nanoparticles with QDs, which may help in the design and construction of other similar virus-based nanoparticles.

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Virus assembly, allostery and antivirals

Cited by 130 publications

References 101 publications

Hepatitis B Virus Capsids Have Diverse Structural Responses to Small-Molecule Ligands Bound to the Heteroaryldihydropyrimidine Pocket

Hepatitis B Virus Capsids Have Diverse Structural Responses to Small-Molecule Ligands Bound to the Heteroaryldihydropyrimidine Pocket

Kinetics of Surface-Driven Self-Assembly and Fatigue-Induced Disassembly of a Virus-Based Nanocoating

Quantum dot-induced viral capsid assembling in dissociation buffer

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