Computational Studies of Protein-Protein Interactions

Benoit Roux, University of Chicago

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Benoit Roux, Jing Li, Rong Shen, Prithviraj Nandigrami, Ziwei He, Christopher Boughter, Donghyuk Suh, Jonathan Thirman

One of the most basic questions about the protein molecules in the living cell is the manner by which they interact with one another. How proteins recognize and bind (stick) to the correct partner(s) is one of the ways information is communicated within and between the cells. This is how cells process information and make decisions at the molecular level. Atomic-level information is essential to explain the specific interactions between proteins in terms of structure and dynamics.

The research project consists in developing and improving the computer-based approach of "molecular dynamics" to calculate and predict accurately how proteins bind to one another. Molecular dynamics (MD) consists of using Newton's classical equation, force = mass x acceleration, to simulate the motions of all the atoms as a function of time. The MD simulation, although an approximation to the real world, provides detailed information about the time course of the atomic motions that cannot be accessed experimentally.

The approach based on atomic models and MD simulations is advantageous because it does not rely on any particular assumption about protein binding. Being able to predict the possible binding partners of a protein from computations will open the door to a much better understanding of living cells.