Novel technique solves structure of the HIV capsid alone and in complex with host factors

A new technique using electron tomography and subtomogram averaging at Diamond's electron Bio-Imaging Centre (eBIC), has solved the structure of the HIV capsid alone and in complex with host factors. This work also led to the building of an atomistic model of the whole HIV capsid using information gained from electron tomography, which the team believe could serve as a blueprint for the development of capsid-targeting antivirals.

The research paper detailing this major breakthrough is published today (19 November) in Science Advances. Called, "High-resolution cryoET structures of native HIV-1 capsid in complex with IP6 and CypA;" the work was a collaboration between scientists at the University of Oxford, eBIC - the UK's national cryo-electron microscopy facility within Diamond Light Source and the University of Delaware.

The team was led by Professor Peijun Zhang, Director of the eBIC at Diamond and Professor of Structural Biology at the University of Oxford. Lead author Dr. Tao Ni, University of Oxford giving the background to this important work says; "Despite the global efforts to combat HIV/AIDS and the achievement of antiviral treatments, there are still approximately 38 million people with HIV/AIDS with no complete cure so far."

He explains that the human immunodeficiency virus (HIV) is a retrovirus which has its RNA genome encapsulated inside a conical-shaped capsid. During infection, HIV assembles and buds as immature virions with Gag polyprotein, which undergoes maturation process, a step involving proteolysis and conformational change, which converts from an immature spherical shape to mature conical capsid. The capsid plays multiple essential roles during the early stage of HIV-1 replication, including protecting the genome from cellular innate immune responses and fostering reverse transcription, as well as regulating intracellular transport and entry into the nucleus. Many of these functions are affected by its interactions with host cell factors and small molecules.

However, because of the metastable property of HIV-1 capsid, isolating fully intact native capsid in quantities and concentrations suitable for high-resolution structural analyses has been challenging: the capsid suffers artefactual dissociation after the membrane is dissolved by detergent, a traditional way for capsid purification.

To solve this problem, Peijun Zhang's team devised a novel approach. Instead of detergent extraction, we punctuate the membrane of HIV virus-like particles with a pore-forming toxin, which avoids the trauma associated with lysis of the virions and isolation of the cores, but also makes the capsid accessible to external cell factors and small molecules."

Dr. Tao Ni, Lead Author, University of Oxford

Having established the experimental approach, the authors investigated the interactions between the authentic HIV capsid and a cellular factor Cyclophilin A (CypA), and a small-molecule cofactor IP6 (inositol hexakisphosphate). The team then applied electron tomography and subtomogram averaging to these samples.

Using this new technique, the team solved the structures of HIV capsid alone, and its complex with CypA and IP6 at around 5.4 Å resolution. These structures confirm the double IP6 binding site in mature HIV capsid and provide insights into the role of IP6 and CypA in regulating HIV capsid stability.

Prof Zhang concludes; "In collaboration with Prof. Juan Perilla's group in the University of Delaware, using information derived from electron tomography, we also built an atomistic model of the whole HIV capsid which could serve as a blueprint for the development of capsid-targeting antivirals. The perforation of the enveloped virus membrane also provides a novel approach to study host-virus interaction for other viral systems."

Professor Peijun Zhang is an internationally respected scientist undertaking ground-breaking research into HIV and other infectious diseases. Over the past year she and her team have also made significant contributions to SARS-CoV-2 Covid-19 research for vaccines and antivirals.

Earlier this year, she and her team received one of only 209 ERC Advanced Grants given to outstanding researchers across Europe. The awards are selected by the European Research Council (ERC) on the basis that the research has the potential to make a difference in people's everyday life and deliver solutions to some of the world's most urgent challenges by triggering breakthroughs and major scientific advances. Professor Zhang's award, over five years, is to pursue her work into Chemotaxis – specifically the Molecular choreography and biological behaviour of bacterial chemotaxis which enable the movement of a cell or organism toward or away from chemicals. Modification of these microorganisms by pharmaceutical agents can decrease or inhibit infections or spreading of infectious diseases.

She has received many awards, including the Carnegie Science Emerging Female Scientist Award, Senior Vice Chancellor's Award, United States Department of Health and Human Services 'On-the-Spot' Award. Her research focuses on the structural and functional studies of large molecular complexes and assemblies, viruses and cellular machineries using integrated structural, biochemical and computational approaches to understand biological complexity.

As the Director of eBIC, Professor Zhang is establishing and leading eBIC to become a world-leading centre for research, expertise and training in cryo-EM and a user facility providing access to cutting-edge cryo-EM technologies. eBIC focuses on using state-of-the-art electron microscopic techniques to determine the 3D structures of molecules, cells and tissues at high resolution, as well as developing new methods and technologies to advance 3D EM imaging.