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Computational Method for Detecting and Enhancing Protein Dynamics

Oak Ridge National Laboratory

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Technology Marketing SummaryORNL 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.DescriptionThe 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.Benefits• A more efficient, less expensive approach for enhanced chemical reaction rates of enzymes
• A more efficient means of identifying surface or distal regions in the protein that can be targeted for creation of new small molecules and enzymes
• A unique method to identify key protein vibration modes and dynamic regions that can be used to control enzyme function and the rate of protein-mediated reactions
Applications and Industries• Pharmaceutical industry for novel drug design
• Biotechnology, chemical, and biochemical industry, for protein engineering
Patents and Patent Applications
ID Number
Title and Abstract
Primary Lab
Date
Patent 8,417,461
Patent
8,417,461
Identification and modification of dynamical regions in proteins for alteration of enzyme catalytic effect
A method for analysis, control, and manipulation for improvement of the chemical reaction rate of a protein-mediated reaction is provided. Enzymes, which typically comprise protein molecules, are very efficient catalysts that enhance chemical reaction rates by many orders of magnitude. Enzymes are widely used for a number of functions in chemical, biochemical, pharmaceutical, and other purposes. The method identifies key protein vibration modes that control the chemical reaction rate of the protein-mediated reaction, providing identification of the factors that enable the enzymes to achieve the high rate of reaction enhancement. By controlling these factors, the function of enzymes may be modulated, i.e., the activity can either be increased for faster enzyme reaction or it can be decreased when a slower enzyme is desired. This method provides an inexpensive and efficient solution by utilizing computer simulations, in combination with available experimental data, to build suitable models and investigate the enzyme activity.
Oak Ridge National Laboratory 04/09/2013
Issued
Technology Status
Technology IDDevelopment StageAvailabilityPublishedLast Updated
UT-B ID 200601716DevelopmentAvailable10/04/201110/04/2011

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To: David L. Sims<simsdl@ornl.gov>