AIDS is a devastating disease that directly attacks and weakens the human immune system, making it vulnerable to a wide range of infections, and is responsible for the death and infection of millions of people around the world. AIDS is caused by the HIV virus. The action of a protein called ‘HIV protease’ is responsible for the initial step of the whole HIV virus maturation process, which is what enables the virus to become infectious. HIV protease acts like a pair of scissors, cutting the long chain of connected proteins that form HIV into individual proteins that will form the infectious structure of new virions.
The solution
Researchers at Bioinformaticians at IMIM (Instituto Hospital del Mar de Investigaciones Médicas) and UPF (Universidad Pompeu Fabra) in Barcelona used ACEMD, a GPU-accelerated molecular dynamics software, for the first time, to simulate the behaviour of the first crucial step in the HIV maturation process. This step revealed how the first HIV “scissors proteins” can cut themselves out from within the middle of these poly-protein chains, which initiates the whole HIV maturation process. They uncovered this major finding using GPUGRID.net, a voluntary distributed computing platform that provides the supercomputing power of thousands of NVIDIA GPUs – 10 times the computational performance of CPU-based systems. Using NVIDIA GPU accelerators, researchers were able to run several highly complex computer simulations, each for hundreds of nanoseconds (billionths of a second) for a total of almost a millisecond, giving them a very high-probability that their simulation accurately represented real-world behaviors. The researchers are of the opinion that simulations of this length and complexity would have been practically unfeasible to achieve using a computing system based on CPUs alone. By leveraging a distributed network of computers with affordable, high-performance NVIDIA GPU accelerators, researchers achieved the needed level computational power that previously was only available on dedicated, multi-million dollar supercomputers.
The outcome
This finding provides new visibility on the maturation of the HIV virons, specifically, how newly formed inert virus particles become infectious, which is essential in understanding how the virus replicates. By providing new visibility into how the HIV protease protein behaves, researchers can potentially design new antiretroviral drugs to halt the HIV maturation process and as a result, prevent it from becoming infectious. These findings have been published in the latest edition of Proceedings of the National Academy of Sciences of the United States of America (PNAS). Increased access to high-performance, affordable GPU-accelerated supercomputing, as was used in this research, promises to democratise computational science and potentially enable similar breakthroughs in other areas of science in the future.