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Computational Method for Detecting and Enhancing Protein Dynamics

ORNL researchers have developed a method that uses simulation and experimental data to detect, analyze, and manipulate protein activity. This approach enables enhancement of the chemical reaction rates of enzymes by many orders of magnitude. More efficient enzymes are widely sought for applications in the biochemical industry, pharmaceuticals, and protein engineering.

Theoretical and computational techniques are particularly useful in discovering and characterizing internal protein dynamics at picosecond to millisecond and longer time scales. The ORNL technology identifies the key vibration modes in a protein, analyzes them, and determines those factors that enable enzymes to achieve an enhanced rate of chemical reaction. This inexpensive, efficient method uses computer simulations alongside available experimental data to develop models that will expand understanding of enzyme function and allow rates of reaction to be increased or decreased, as desired.

The method enables identification of the protein motions that are present during a catalytic reaction. A protein vibration is then selected, based on how much overlap there is between a reaction coordinate in each of the motions and a reaction coordinate range for that reaction. The dynamically active residue of the protein molecule is then identified, based on the selected vibrations.

Computer Science and Mathematics Division
Oak Ridge National Laboratory
Technology Commercialization Manager, Building, Computational, and Transportation Sciences
Oak Ridge National Laboratory
Phone: 865. 241.3808
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