Department of Chemistry
University of Copenhagen
H. C. Ørsted Institute
2100 Copenhagen Ø
Phone : (+ 45) 35 32 02 50
Fax : (+ 45) 35 32 02 59
Mail : firstname.lastname@example.org
Homepage : http://theochem.ki.ku.dk/~tl/
Theoretical studies of peptidase and esterase reactions catalyzed by Serine Proteases.
We are aiming at studying the dynamics of the enzyme catalyzed cleavage of peptide bonds and ester bonds. For Serine Proteases, the reaction mechanism is well established, and calculating the associated potential energy surfaces we will study the reaction using a reaction path description for the active site plus substrate, whereas we approximate the remainder of the enzyme by a dielectric phonon medium approach.
The current state of the project is the construction of appropriate potential energy surfaces, on which to do the dynamics. This involves 1 or 2 dimensional potential energy surface scans in appropriate internal coordinates. The calculations are performed using Gaussian 94 from Gaussian Inc. and we are using Unichem 20 from Cray Inc. for visualization. Due to the large molecular reacting system we are restricted to using semi empirical PM3 calculations, but as soon as the reaction pathway has been determined we will replace the semi empirical PM3 method with a modest ab initio method.
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