PageRank Helps Form Breakthroughs in Biology.
In class, we have recently analyzed the PageRank algorithm, rooted at the heart of the almighty Google search engine. Each page or node in the network is initially assigned a weight of 1/n, with n representing the total number of nodes in the network, which all sum to a total of one. After repeated steps, a hierarchy of importance is established. It is this very process that is used for the millions to billions of searches on the internet each day. Researchers at Yale University have applied the same logic to a surprising field, biology. In an effort to better understand the complexity of enzyme structures, they have used PageRank to analyze underlying chemical reactions that correspond to information flow in enzymes.
Enzyme reactions are split between two subsets; the active site, where chemical reactions take place, and the allosteric site, where the binding of molecules regulate the speed of said reactions. This extremely complex field of study has lead to only minor advancements in understanding how information is transferred between the two sites. This is primarily due to the ‘great structural flexibility’ of enzymes and the sheer number of atoms that comprise them. The research remarked that the issue of information flow between the active and allosteric sites was similar to the network analysis of the internet that birthed the PageRank algorithm. “By finding out how the information flows through each atom changes with the binding of an allosteric activator to the enzyme, it is possible to find the information channels that are being activated,” said Uriel Morzan, a co-first author of the study. By applying the computational approach of the PageRank algorithm to the study of enzymes, the researchers were able to identify crucial amino acids for the allosteric process, a major breakthrough in this particular area of study for decades.
Graph illustrating the allosteric process, showing activator triggered decrease (blue) or increase (red) or of information flow in the enzyme.
Link to article: https://news.yale.edu/2018/12/11/yale-chemists-find-new-tool-understanding-enzymes-google