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KINARI-Mutagen : Using Rigidity Analysis to Infer Critical Regions in Mutant Proteins

When

02:00PM - 03:00PM, February 15, 2012

Where

S-3-143

Abstract

Proteins are dynamic molecules that bend and flex, and interact with other biomolecules. They are involved in virtually all biological functions; they metabolize the food that we eat, they help to ward off bacteria as part of our immune system, and they replicate our DNA to facilitate reproduction, growth, and cellular repair.

In order to understand the function of a protein, it is necessary to have detailed knowledge of its possible internal motions, and where it is flexible and rigid. Unfortunately proteins at the atomic level cannot be viewed by microscopes. However, data from X-ray crystallography experiments provide single snapshots of a protein's 3-dimensional structure, whose rigidity can be analyzed using an efficient graph-based algorithm. This pebble game algorithm, pioneered in the last 15 years, decomposes a protein into flexible and rigid regions, which can be used to infer where motion is feasible.

I will give a brief introduction to rigidity analysis and its use in the study of protein flexibility. I will motivate and demonstrate KINARI-Mutagen, a web tool for generating in silico mutants and analyzing their rigidities, to help infer which regions of a protein are mechanically critical. I will present recent computational results from KINARI-Mutagen, and discuss how they correlate with experimentally derived stability data for Crambin and Lysozyme from bacteriophage T4.

Speaker

Filip Jagodzinski

Speaker Bio

Filip Jagodzinski is completing his PhD in the Department of Computer Science at the University of Massachusetts Amherst (UMass). He is advised by Ileana Streinu, who directs the Linkage Laboratory. While at UMass he has also worked with Oliver Brock; he developed a method that leverages insights from kinematics and operational space control from robotics, to simulate the large scale motions of proteins. In 2003 he graduated with a masters degree in computer science from Villanova University, and in 1999 he earned a bachelors of science in biomedical engineering from Columbia University.