The National Institute for Computational Sciences

Little Particles, Big Effect

Research into Nanoparticles Reveals Potential First Step in Impeding HIV

© Imredesiuk | Dreamstime.comFullerenes—New Opportunities Photo

Since the time the human immunodeficiency virus (HIV) first swept into America’s social consciousness in 1982, HIV has been misunderstood.

But research conducted with the support of supercomputer allocations from the eXtreme Science and Engineering Discovery Environment (XSEDE) and grants from the National Science Foundation (NSF) reveals a potential breakthrough in the way scientists pursue treatment—it’s all about the nanoparticles.

A nanoparticle is microscopic and so small it exhibits size-related qualities. Most definitions specify that, to be considered nano, the particle must measure between 1 nanometer and 100 nanometers (for reference: a human hair is about 60,000 nanometers wide).

Scientists are particularly interested in the properties and function of carbon-based nanoparticles called fullerenes, and researcher Jerzy Leszcznski and colleagues at Jackson State University through their XSEDE–NSF project titled “Multiscale Research in Nanotoxicity” have discovered that fullerenes block a key function of HIV. In September 2013, an article containing the details of their finding was featured on the cover of Organic & Biomolecular Chemistry, and by 2014 the research team had seven published papers, 13 invited talks, and five poster presentations on the effect of fullerenes on HIV.

HIV works like all viruses do—it reproduces itself by taking over cells in the body of its host. In HIV’s particular case, however, the virus attacks T-cells, or the white blood cells normally responsible for defending the body against infection and disease. HIV uses these T-cells to replicate itself before destroying the cell, creating a life cycle that strengthens the virus by weakening the body’s immune system. Eventually, the virus enters its last stage of acquired immunodeficiency syndrome (AIDS), a complex illness with a wide range of complications and symptoms.

By applying a synergistic combination of several different computational approaches, the research team discovered that the structural features of fullerenes are what make them inhibit HIV-1 PR, a key biological molecule in the HIV maturation process.

“Due to the large sizes of the considered species, the quantum mechanical calculations were only possible on large supercomputers—without this component the study would not be reliable,” Leszczynski says.

Their study also revealed additional features of fullerenes, such as its 3D molecular geometry and the specific landscape of the molecule. This research may assist future scientists in further research into the applications of fullerenes within electrochemical, photophysical, and biological situations. And though HIV remains a mystery, research shows that its capsid, or viral casing, is best described by a fullerene core model.

Leszczynski says he believes findings from the project will make the creation and analyses of such models easier and gives much credit to the XSEDE-managed machines that made his work possible.

“Inclusion of large numbers of fullerenes and a huge group of proteins was possible only because of the access to supercomputers,” Leszczynski says.

R. J. Vogt, science writer, NICS, JICS

Article posting date: 17 May 2015

About JICS and NICS:The Joint Institute for Computational Sciences (JICS) was established by the University of Tennessee and Oak Ridge National Laboratory (ORNL) to advance scientific discovery and leading-edge engineering, and to further knowledge of computational modeling and simulation. JICS realizes its vision by taking full advantage of petascale-and-beyond computers housed at ORNL and by educating a new generation of scientists and engineers well-versed in the application of computational modeling and simulation for solving the most challenging scientific and engineering problems. JICS operates the National Institute for Computational Sciences (NICS), which had the distinction of deploying and managing the Kraken supercomputer. NICS is a leading academic supercomputing center and a major partner in the National Science Foundation's eXtreme Science and Engineering Discovery Environment (XSEDE). In November 2012, JICS sited the Beacon system, which set a record for power efficiency and captured the number one position on the Green500 list of the most energy-efficient computers.