Small compounds targeted to subunit interfaces arrest maturation in a nonenveloped, icosahedral animal virus

Confessions of an icosahedral virus crystallographer

This is a personal history of my structural studies of icosahedral viruses that evolved from crystallographic studies, to hybrid methods with electron cryo-microscopy and image reconstruction (cryoEM) and then developed further by incorporating a variety of physical methods to augment the high resolution crystallographic studies. It is not meant to be comprehensive, even for my own work, but hopefully provides some perspective on the growth of our understanding of these remarkable biologic assemblies. The goal is to provide a historical perspective for those new to the field and to emphasize the limitations of any one method, even those that provide atomic resolution information about viruses.

Rationally designed interfacial peptides are efficient in vitro inhibitors of HIV-1 capsid assembly with antiviral activity

Virus capsid assembly constitutes an attractive target for the development of antiviral therapies; a few experimental inhibitors of this process for HIV-1 and other viruses have been identified by screening compounds or by selection from chemical libraries. As a different, novel approach we have undertaken the rational design of peptides that could act as competitive assembly inhibitors by mimicking capsid structural elements involved in intersubunit interfaces. Several discrete interfaces involved in formation of the mature HIV-1 capsid through polymerization of the capsid protein CA were targeted. We had previously designed a peptide, CAC1, that represents CA helix 9 (a major part of the dimerization interface) and binds the CA C-terminal domain in solution. Here we have mapped the binding site of CAC1, and shown that it substantially overlaps with the CA dimerization interface. We have also rationally modified CAC1 to increase its solubility and CA-binding affinity, and designed four additional peptides that represent CA helical segments involved in other CA interfaces. We found that peptides CAC1, its derivative CAC1M, and H8 (representing CA helix 8) were able to efficiently inhibit the in vitro assembly of the mature HIV-1 capsid. Cocktails of several peptides, including CAC1 or CAC1M plus H8 or CAI (a previously discovered inhibitor of CA polymerization), or CAC1M+H8+CAI, also abolished capsid assembly, even when every peptide was used at lower, sub-inhibitory doses. To provide a preliminary proof that these designed capsid assembly inhibitors could eventually serve as lead compounds for development of anti-HIV-1 agents, they were transported into cultured cells using a cell-penetrating peptide, and tested for antiviral activity. Peptide cocktails that drastically inhibited capsid assembly in vitro were also able to efficiently inhibit HIV-1 infection ex vivo. This study validates a novel, entirely rational approach for the design of capsid assembly interfacial inhibitors that show antiviral activity.

Dynamics and stability in maturation of a T=4 virus

Nudaurelia capensis omega virus is a T=4, icosahedral virus with a bipartite, positive-sense RNA genome. Expression of the coat protein gene in a baculovirus system was previously shown to result in the formation of procapsids when purified at pH 7.6. Procapsids are round, porous particles (480 A diameter) and have T=4 quasi-symmetry. Reduction of pH from 7.6 to 5.0 resulted in virus-like particles (VLP(5.0)) that are morphologically identical with authentic virions, with an icosahedral-shaped capsid and a maximum dimension of 410 A. VLP(5.0) undergoes a maturation cleavage between residues N570 and F571, creating the covalently independent gamma peptide (residues 571-641) that remains associated with the particle. This cleavage also occurs in authentic virions, and in each case, it renders the morphological change irreversible (i.e., capsids do not expand when the pH is raised back to 7.6). However, a non-cleavable mutant, N570T, undergoes the transition reversibly (NT(7.6)<-->NT(5.0)). We used electron cryo-microscopy and three-dimensional image reconstruction to study the icosahedral structures of NT(7.6), NT(5.0), and VLP(5.0) at about 8, 6, and 6 A resolution, respectively. We employed the 2. 8-A X-ray model of the mature virus, determined at pH 7.0 (XR(7.0)), to establish (1) how and why procapsid and capsid structures differ, (2) why lowering pH drives the transition, and (3) why the non-cleaving NT(5.0) is reversible. We show that procapsid assembly minimizes the differences in quaternary interactions in the particle. The two classes of 2-fold contacts in the T=4 surface lattice are virtually identical, both mediated by similarly positioned but dynamic gamma peptides. Furthermore, quasi and icosahedral 3-fold interactions are indistinguishable. Maturation results from neutralizing the repulsive negative charge at subunit interfaces with significant differentiation of quaternary interactions (one 2-fold becomes flat, mediated by a gamma peptide, while the other is bent with the gamma peptide disordered) and dramatic stabilization of the particle. The gamma peptide at the flat contact remains dynamic when cleavage cannot occur (NT(5.0)) but becomes totally immobilized by noncovalent interactions after cleavage (VLP(5.0)).

Surface display of an internal His-tag on virus-like particles of Nudaurelia capensis ω virus (NωV) produced in a baculovirus expression system

Nudaurelia capensis omega virus (NomegaV) is a member of the Tetraviridae, a family of small, icosahedral, non-enveloped, (+) sense single-stranded RNA insect viruses with T = 4 symmetry. NomegaV virus-like particles (VLPs), which are morphologically indistinguishable from native virions and capable of packaging heterologous RNA, may be produced in the baculovirus expression system. As a first step towards manipulating the tropism of tetraviral nanoparticles (Capsivectors), a (His)6-tag was inserted into the GH loop (between Ala 378 and Gly 379) of the surface-exposed Ig-like domain of NomegaV capsid protein (p70). His-tagged p70 produced in a baculovirus expression system self-assembled into omegaHis VLPs that exhibited similar morphological and RNA encapsidation properties as wild-type NomegaV VLPs produced in the same system. Two assays using paramagnetic pre-charged nickel beads confirmed that multiple affinity tags were present on the surface of omegaHis VLPs and were capable of binding. These results indicate that the GH loop is a suitable site for the retargeting of NomegaV particles for potential biotechnological applications.

Maturation of a tetravirus capsid alters the dynamic properties and creates a metastable complex

The assembly of monomeric protein subunits into a viral capsid is a finely tuned molecular process. In response to subtle changes in environmental conditions, this supramolecular complex can dramatically reorganize. Defining the forces that control this structure and the cooperative action of subunits has implications for biology and nanotechnology. The small icosahedral RNA tetravirus family members Nudaurelia omega capensis (NomegaV) and Helicoverpa armigera stunt virus (HaSV) can be purified as provirions, and maturation to capsids can be induced by a drop in pH. In this study, a comparison of capsid secondary structure using FT-IR revealed that the procapsid has more alpha-helical content than the capsid, supporting the proposal that helix to coil transition may be important for maturation. The dynamic properties of the two states were probed using limited proteolysis and peptide mass mapping to identify regions of significant flexibility. Interestingly, the initial sites of protease cleavage were the N and C terminal domains that are internal in high-resolution models, and to inter-subunit surfaces. Further comparison of the two particle forms using FT-IR revealed that in response to thermal stress, the provirion disassembles and unfolds in a cooperative manner over a narrow temperature range (approximately 5 degrees C). Paradoxically, the capsid form, which is stable in a wide range of pH and ionic conditions and is more resistant to proteolysis, responds to thermal stress at a lower temperature than the procapsid form. This suggests that a metastable state is the end product of assembly.