Computing the connections between proteins

Searching for a soul mate, new friends, or just fresh contacts? Turns out that proteins have similar "goals." However, shaking off their single status generally doesn't come easy.

Biochemist, turned protein matchmaker, Dr. Gideon Schreiber of the Weizmann Institute of Science and doctoral student Tziki Seltzer, took their fate to heart. Working with colleagues at the Biological Chemistry Department, they developed a computer algorithm which calculates the rate at which two proteins associate, using it to fashion proteins with increased affinity - of a hundred times or more. Their achievement, recently appearing in Nature Structural Biology, holds much promise for the pharmaceutical and food industries, since protein complexes are fundamental to many life processes.

Protein affinity is defined by the rate at which two proteins associate with one another to form a complex, divided by the rate at which this complex dissociates. In order to improve protein affinity one can either intervene to reduce protein "break-up" statistics, or alternatively, increase protein association rates. Dr. Schreiber chose the latter.

Since association rates are influenced by the protein's (genetically determined) design, the scientists used this relationship as their guiding principle - developing an algorithm capable of determining the genetic changes necessary to boost association rates.

Dr. Schreiber: "A common approach to improving protein affinity is to create a large pool of mutations and discover the optimal complex through trial and error. However, the possibilities are often endless. Computer simulations are far more efficient in pinpointing potentially successful complexes."

Using the algorithm, the researchers significantly increased the production rate and strength of a specific protein complex. The new protein match-up system may lead to diverse medicinal applications based on increasing or inhibiting protein activity, as well as new diag

Contact: Jeffrey Sussman
American Committee for the Weizmann Institute of Science

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