ALBUQUERQUE, N.M. — Researchers working on the Sandia National Laboratories Interfacial Bioscience (IBIG) project have learned a lot over the past two years about the role membrane proteins play in causing healthy cellular processes to go awry during illness or injury.
When a pathogen exploits the presence of a protein on a cell membrane to infect the cell, or a toxin specifically docks against a surface protein like an interlocking puzzle piece, the cell often spews out short-lived messenger compounds. This is much like the way signals are relayed after a switchboard operator patches a caller through to a phone extension.
A goal of IBIG is to better understand such signal pathways — the series of molecules that relay information between and within cells, something like a “bucket brigade” lining up to quench a fire. Also the researchers want to discern the course of cell poisoning so the outcome might be prevented.
The IBIG team is trying to develop computer simulations and models of toxin and signal-molecule interactions with cell membranes. They are investigating the structure of the proteins themselves (coiled into shapes something like knotted skeins of wool), their interactions, and dynamics of membranes.
“We think there’s room for some cross-cutting efforts that are going to be valuable in this area,” says Joe Schoeniger, the Sandia IBIG principal investigator.
For instance, biology has been benefiting from a high-throughput approach in which many permutations of structures and interactions are screened using computer science.
“We’re trying to develop new experimental and computational tools and take steps to integrate them,” Schoeniger says.
Although membrane proteins are important, they are difficult to study with most techniques because they are not water-soluble. Nor are they as abundant as the proteins that exist within the watery interior of the cell. To amass sufficient quantities of protein in question, team members have raised membrane proteins in bacterial culture.
To investigate binding, complexes of membrane proteins attached to an agent are chemically linked, trimmed, then analyzed with mass spectrometry — which Schoeniger calls a new kind of “microscope” to probe structural interactions.
Molecular dynamic simulations are being studied with the world’s most sophisticated massively parallel code, and data analysis has been automated for researching the structural twists and turns of a model protein system, the light-sensitive visual protein rhodopsin, which is closely related to proteins that viruses interact with when they attack your immune system.
Using an atomic force microscope (AFM) in Albuquerque, the group was able to take images of single, isolated pores formed by cholera toxin molecules bound to the membrane. This result shows that it is feasible to use the AFM to study the interactions of toxins with membranes at the single-molecule level.
Schoeniger says the results were accomplished surprisingly fast, and “we were really happy.”
Sandians are collaborating with leading universities to look at the role of membrane proteins in normal neurotransmitter function and after exposure to nerve agents (such as botulism, a toxin that shuts down the firing of neurons to cause paralysis).