AlloPathFinder User Profile: Jung-Chi Liao

Columbia’s Jung-Chi Liao seeks pathways within proteins using AlloPathFinder, a Simbios tool he co-developed while at Stanford.

from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips

 

As a Simbios post-doc, Jung-Chi Liao, PhD, sought to understand how a conformational change in one part of the myosin protein (at the ATP binding site) triggers a change in the other part (the functional site), allowing movement. Understanding this “allosteric pathway” can help researchers understand why certain mutations alter the protein’s function. So Liao developed AlloPathFinder with Susan Tang, a Simbios Masters student, Russ Altman, and Jeanette Schmidt, executive director of Simbios. The tool was developed for and tested on myosin proteins, Liao says, “But we aimed to apply it to other proteins.”

 

Now an assistant professor of mechanical engineering at Columbia University, Liao is applying AlloPathFinder to another family of proteins: helicases, which unwind the DNA helix. Like myosin, they use the breakdown of ATP to do mechanical work: ATP binding to one part of the helicase triggers it to move one base pair along the DNA. Liao is trying to identify the specific amino acids that bridge ATP binding to changes at the DNA binding site. Knowing which amino acids are important will help researchers generate testable hypotheses for mutational experiments.

 

Aside from the Simbios tools he continues to use, Liao says he valued being part of Simbios because the team nurtured a spirit of collaboration. “Scott and Russ gave me a lot of opportunities to lead projects, talk to many people, and to generate ideas with collaboration in mind.”



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