Jos Onuchic has become an expert at connecting the dots, but finding connections merely implied by the dots well, that's quite a trick.
The Rice University biophysicist and his team have created a tool to do just that for proteins and, in the process, have advanced the art of predicting their form and function.
In this case, the dots are amino acid molecules known as residues that link together in chains to form proteins. Proteins are the workhorses that carry out the biological tasks essential to every living thing, but before they can go to work, they fold. Each protein has its own characteristic, folded shape, and various diseases, including cancer, have been linked to proteins that misfold or otherwise misbehave.
As computers grew more powerful over the past three decades, scientists have created many methods to predict how a particular chain of residues is likely to fold and the purpose the resulting protein serves.
Onuchic and colleagues at the Center for Theoretical Biological Physics have developed a tool, known as direct coupling analysis-fold (DCA-fold), that enhances existing methods. Details of their research appear today in the online version of the Proceedings of the National Academy of Sciences (PNAS). The center is currently based at the University of California at San Diego (UCSD) but is relocating to Rice's BioScience Research Collaborative.
While most protein-folding researchers look at the sequence of amino acids in a protein, either through X-ray crystallography of folded proteins or through computer simulations, Onuchic and his colleagues stepped back to look at the DNA sequences that serve as the blueprints for the proteins. By exploiting the increasingly large database of genomic sequence information, they're able to increase the accuracy of predicting the structures of folded proteins.
They start by finding points in the protein-encoding genome sequences that appear to
|Contact: David Ruth|