As scientists gain a better understanding of the role of human microbiome in the development of disease, they will be able to find and create better diagnoses and treatments.
“But to better understand the roles played by the various bacteria in the human microbiome, scientists need to study the proteins produced by these bacteria, which are encoded in their genomes,” said Dr. Rob Knight, a professor at the UC San Diego and founder of the American Gut Project, wherein scientists work with non-scientists in an effort to understand the life inside the gut and to figure out what characterizes healthy and sick guts.
“The first step is to determine the physical structures of the protein molecules coded by each bacteria’s genes. This is important because the physical structure of a protein determines its function. Once the protein functions are determined, scientists can explore how the bacterial proteins react with each other and determine which proteins play a role in any number of diseases. From these insights, scientists would be able to develop drugs to control those particular proteins and help treat diseases that originate in or are influenced by the human microbiome.”
The primary goal of the project is to generate a set of predicted protein structures of the entire human microbiome-containing some 3 million unique genes-to help scientists determine the role played by these bacteria.
In order to take on this monumental task and complete it in years instead of decades, scientists need massive supercomputing power to complete simulations and virtual experiments on behalf of scientists.
“In the past, researchers interested in individual proteins have solved the structures of those proteins either using computational techniques or in the laboratory. In this project, we are trying to do it for all proteins in the microbiome at once, which will provide a far more comprehensive view.”
Juan Hindo, IBM Corporate Citizenship Program manager and leader of World Community Grid explains the process: “The first step to understanding the role of the bacteria within the microbiome is to determine the structure of the protein molecule coded by each gene of the bacteria. The structure of a protein molecule determines its function. But the scale of this research is enormous. The microbiome is comprised of about 3 million unique bacterial genes. By comparison, the human body has about 20,000 genes. To study the proteins corresponding to each of these genes would be a monumental task that is nearly impossible in a laboratory setting.”