New computer simulations help scientists understand how—and why—viruses spread

June 18, 2013

It's not a hacker lab. At Brandeis University, sophisticated computational models and advances in graphical processing units are helping scientists understand the complex interplay between genomic data, virus structure and the formation of the virus' outer "shell"—critical for replication.

"We hope that some of what we are finding will help researchers alter virus assembly, leaving viruses unable to replicate," says post-doctoral fellow Jason Perlmutter, first author of the scientific paper describing the technique, published in the open access journal eLife.

Scientists know that many viruses are able to hijack the genetic machinery of host cells to produce copies of themselves and spread infection from cell to cell. For many virus families, a key part of this process is the formation of a protein "shell," called a capsid, around the during the assembly process.

The physics of this assembly process, which involves interactions between the negatively charged nucleic acid genome and the positively charged capsid protein, depends on a number of factors related to the structure of the virus genome.

"Changing all these critical genomic parameters in a live virus and looking at how capsid formation behaves is impossible given the speed of the process and our current imaging techniques," says associate professor of physics Michael Hagan, whose lab conducted the study.

That's why the team's modeling approach—the most realistic developed to date—is so important to scientists who are interested in how the virus capsid protein assembles around its genome in the cell. The Brandeis team used their modeling tool to calculate the optimal genome for a number of specific —which vary in size, shape and surface properties.

"If you take the model and apply it to biological viruses, we are able to predict within a narrow range key structural features of the and, by extension, how these parameters control whether the capsid assembles or misassembles and what misassembly looks like," says Perlmutter.

"Our tool should help scientists better understand the relationship between viral structure and packaging, making it easier to develop antiviral agents as well as aid the redesign of viruses for use in gene therapy and drug delivery."

Explore further: Scientists learn structure of enzyme in unusual virus

Related Stories

Do-it-yourself viruses: How viruses self assemble

December 16, 2012

A new model of the how the protein coat (capsid) of viruses assembles, published in BioMed Central's open access journal BMC Biophysics, shows that the construction of intermediate structures prior to final capsid production ...

Recommended for you

How bees naturally vaccinate their babies

July 31, 2015

When it comes to vaccinating their babies, bees don't have a choice—they naturally immunize their offspring against specific diseases found in their environments. And now for the first time, scientists have discovered how ...

New insights into the production of antibiotics by bacteria

July 31, 2015

Bacteria use antibiotics as a weapon and even produce more antibiotics if there are competing strains nearby. This is a fundamental insight that can help find new antibiotics. Leiden scientists Daniel Rozen and Gilles van ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.