Novel technology solves the structure of the HIV capsid alone and in complex with host factors – archyde

A new technique using electron tomography and subtomogram averaging at Diamond’s Electron Bio-Imaging Center (eBIC) has elucidated the structure of the HIV capsid alone and in complex with host factors. This work also led to the construction of an atomistic model of the entire HIV capsid using information from electron tomography, which the team believes could serve as a blueprint for developing capsid-targeting antivirals.

The research paper on this important breakthrough is published today (November 19th) in Science Advances. Named, “High-resolution cryoET structures of native HIV-1 capsid in complex with IP6 and CypA;” The work was a collaboration between scientists from the University of Oxford, eBIC – the UK’s national cryo-electron microscopy facility within the Diamond Light Source, and the University of Delaware.

The team was led by Professor Peijun Zhang, Director of eBIC at Diamond and Professor of Structural Biology at Oxford University. The lead author Dr. Tao Ni, University of Oxford, explains the background to this important work. “Despite global efforts to fight HIV / AIDS and obtain antiviral treatments, there are still approximately 38 million people living with HIV / AIDS without a full cure.”

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

However, due to the metastable nature of the HIV-1 capsid, isolating fully intact native capsid in amounts and concentrations suitable for high-resolution structural analysis has been a challenge: the capsid undergoes artifact dissociation after the membrane is dissolved by a detergent, a traditional way for capsid cleaning.

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

Dr. Tao Ni, lead author, Oxford University

After the experimental approach was established, the authors examined the interactions between the authentic HIV capsid and a cellular factor cyclophilin A (CypA) and a low molecular weight 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 the HIV capsid alone and its complex with CypA and IP6 with a resolution of about 5.4. These structures confirm the double IP6 binding site in the mature HIV capsid and provide insight into the role of IP6 and CypA in regulating HIV capsid stability.

Prof. Zhang concludes; “Working with Prof. Juan Perilla’s group at the University of Delaware, we also created an atomistic model of the entire HIV capsid using information from electron tomography that could serve as a blueprint for the development of capsid-targeting antivirals . The perforation of the enveloped virus membrane also offers a novel approach to study host-virus interaction for other viral systems. “

Professor Peijun Zhang is an internationally respected scientist who conducts groundbreaking research on HIV and other infectious diseases. Over the past year, she and her team 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 for outstanding researchers across Europe. The awards are selected by the European Research Council (ERC) on the basis that research has the potential to change people’s lives and provide solutions to some of the world’s most pressing challenges by sparking breakthroughs and great scientific advances. Professor Zhang’s award is set to continue her work on chemotaxis over five years – specifically the molecular choreography and biological behavior of bacterial chemotaxis, which enables a cell or organism to move toward or away from chemicals. Modification of these microorganisms by pharmaceutical agents can reduce or inhibit infection or the spread of infectious diseases.

She has received many awards, including the Carnegie Science Emerging Female Scientist Award, the Senior Vice Chancellor’s Award, the On-the-Spot Award from the US Department of Health. Her research focuses on structural and functional studies of large molecular complexes and assemblies, viruses, and cellular machines using integrated structural, biochemical, and computational approaches to understanding biological complexity.

As Director of eBIC, Professor Zhang is building eBIC into a world-leading center for research, expertise and training in cryo-EM and a user facility that provides access to cutting-edge cryo-EM technologies. eBIC focuses on the use of the latest electron microscopic techniques for the high-resolution determination of the 3D structures of molecules, cells and tissues as well as on the development of new methods and technologies for the further development of 3D EM imaging.

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Journal reference:

Ni, T., et al. (2021) New technology solves HIV capsid structure and could be a blueprint for capsid-targeting antivirals. Scientific advances. doi.org/10.1126/sciadv.abj5715.

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