Computational methods are being used to design new anti-flu virus proteins that are not found in nature. One goal of antiviral protein design is to block molecular mechanisms involved in cell invasion and virus reproduction.
Computationally designed, surface targeting, antiviral proteins might also have diagnostic and therapeutic potential in identifying and fighting viral infections.
In their report, Sarel J. Fleishman and Timothy Whitehead of the University of Washington (UW) Department of Biochemistry, and Damian C. Ekiert from the Department of Molecular Biology described their general computational methods for designing new, tiny protein molecules that could bind to a certain spot on large protein molecules.
They took apart some protein structures and watched how these disembodied sections interacted with a target surface. They analyzed particular high-affinity interactions, and used this information to further refine computer-generated designs for interfaces.
"Protein surfaces are never flat, but have many crevices and bulges at the atomic scale," lead author Sarel Fleishman explained.
"The challenge is to identify amino acid side chains that would fit perfectly into these surfaces. The fit must be precise both in shape and in other chemical properties such as electrostatic charge.
This geometrical and biophysical problem can be computationally solved, but requires large computational resources," he added.
The study was recently published in the journal Science.