Thursday, July 20, 2017

HIV breakthrough as researchers create incredible simulation that shows how the virus senses its environment and attacks cells


This structure, called the capsid (illustrated above), plays a critical role in the virus’s ability to infect human cells, but the freedom of its components to arrange asymmetrically makes it extremely difficult for scientists to study

A stunning 64-million-atom supercomputer simulation has revealed a look into the life of the ‘protein cage’ that carries HIV through the body.

This structure, called the capsid, plays a critical role in the virus’s ability to infect human cells, but the freedom of its components to arrange asymmetrically makes it extremely difficult for scientists to study.


The new simulation, and a subsequent analysis that required a second supercomputer, has now shed light on several properties that dictate how the virus senses its environment, and makes its way to the nucleus of a cell.

According to Juan R Perilla, a research scientist at the University of Illinois who led the study, this also uncovers potential vulnerabilities that could be exploited to develop more effective drugs.

‘We are learning the details of the HIV capsid system, not just the structure but also how it changes its environment and responds to its environment,’ Perilla said.

Perilla and his late co-author Klaus Shculten, a physics professor at the University of Illinois who died last year, used the Department of Energy’s Titan supercomputer to simulate more than 64 million atoms for an unprecedented look at the chemical-physical properties of an empty HIV-1 capsid.

An HIV capsid contains hundreds of identical proteins, which are arranged to form a network of six-sided and five-sided structures.

And, each of these structures has a tiny pore at the center.

Inside the capsid, the virus’s genetic material sits protected from any potential defense tactics by the host cell on its way to the nucleus.

Until now, however, the nature of this structure has largely stood in the way of scientists’ ability to better understand it.

The capsid is a large container, made of ~1,300 proteins with altogether 4 million atoms,’ the researchers explain in a paper published to Nature Communications.

‘Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers.


‘The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid.’

The Titan simulation took two years to complete, according to the researcher, and captures just 1.2 microseconds in the life of the HIV capsid.

The simulation showed negative ions build up on the positively charged interior, while the positive ions cling to the negatively charged outside. Pictured, the distribution of ions over the HIV-1 capsid can be seen. Yellow represents sodium, while blue shows chloride

The data were then analyzed on a second supercomputer, Blue Waters, at the university’s National Center for Supercomputing Applications,

These efforts revealed several new properties tied to the capsid’s behaviour.

The researchers found that different parts of the capsid oscillate at different frequencies – and, this movement likely transmits information from one part of the structure to another.

In addition, the simulation showed that ions flow into and out of the capsid pores, causing negative ions to build up on the positively charged interior, while the positive ions cling to the negatively charged outside.

This new insight could be used to develop drugs that target the capsid to defeat the virus, according to Perilla.

‘If you can break this electrostatic balance that the capsid is trying to keep together, you may be able to force it to burst prematurely,’ Perilla said.

The researchers found that different parts of the capsid oscillate at different frequencies – and, this movement likely transmits information from one part of the structure to another

The positively charged interior could play a role in the influx of DNA building blocks, which the virus needs from the host to convert its own RNA into DNA.

These building blocks are negatively charged, and small enough to fit through the capsid’s pores, the researcher explained.

The simulation also revealed that stress propagates through the capsid in patterns – and, these stresses align in regions that are now known to be most susceptible to bursting.

With this new understanding, the researchers say, ‘Our results may provide a new avenue for the development of therapeutic interventions that seek to alter the biophysical properties of the HIV-1 capsid towards the treatment of disease.’

Sources: Nature Communications

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