A cure for HIV takes a step closer after supercomputers reveal how the virus moves

Grace Shallow July 18, 2017

A brief glimpse into how HIV travels through the body has been simulated for the first time on supercomputers in the US.

For two years, multiple supercomputers at the University of Illinois modelled the behaviour of 64 million atoms to capture 1.2 microseconds of the life of an HIV capsid, a protein cage that transports the HIV virus to the nucleus of a human cell. The capsid simulation was performed on the Department of Energy’s Titan supercomputer, while analysis was made using the Blue Waters supercomputer at the National Center for Supercomputing Applications at the university.

Described as “computational microscopy,” the method of studying large biological systems with molecular dynamics simulations was developed and led by Juan Perilla and the late Klaus Schulten.

It revealed several of the capsid’s characteristics, such as different parts of the protein that oscillate at different frequencies. This is likely how the capsid sends information to other parts, which allows it to navigate through its environment, Perilla said. The study also found that ions flow in and out of capsid pores and stick to it at different points: negative on the inside and positive on the outside. This keeps the capsid’s structure together.

By unlocking such secrets of the capsid’s structure, and exposing its vulnerabilities, the researchers claim the simulation will help scientists determine how to break this structure so that it bursts before infecting any human cell. This could eventually lead to a cure.

Along the same lines, the simulation showed researchers that stress is distributed through the capsid in patterns, allowing them to pinpoint more vulnerabilities that could be used to break the structure. The research is

published in the journal Nature Communications.

Today, HIV is not the life sentence it once was. Treatments have advanced that can significantly add years and even decades to the lives of patients and, while a full cure hasn’t been found, this capsid simulation is the latest in a line of research towards that goal.

In October, immunologists at five of the UK’s leading universities, along with the NHS, reported that the first patient being treated in a groundbreaking HIV study had shown “remarkable” results, with no sign of the virus after initial treatment.

The treatment combines antiretroviral drugs with a drug that reactivates dormant HIV alongside a vaccine that stimulates the immune system. This works to destroy the cells carrying the virus and ultimately eradicate it from the patient’s body.

Then, at the start of May, researchers at the Lewis Katz School of Medicine at Temple University (LKSOM) and the University of Pittsburgh found they could remove HIV DNA from genomes of living animals – in this case, mice – using gene-editing tool CRISPR.

Images: Juan Perilla

Caption: The genetic material of the HIV virus is encased in multiple structures that hide it from the host immune system. The capsid, in blue, protects the virus after it enters a cell and shuttles it to the nucleus, where it completes the process of infection.