TY - BOOK
T1 - A Perspective on Bionanosensor Simulation & Computational Enzyme Engineering
AU - Hediger, Martin Robert
PY - 2013
Y1 - 2013
N2 - This essay describes the work of two projects. The first project, Bionanosensor Simulation, describes design and implementation
of a new web interface which allows to carry out simulations of a protein sensor conveniently and fast. Out of all biosensor simulation programs, our program is the rst which displays the proteins threedimensionally in a web browser. This can be applied to the study of how the orientation of a protein a affects the electric current which runs through the sensor. These changes in current allow to detect proteins of extremely low concentrations and our simulation program helps in optimizing such sensors. In the second project, Computational Enzyme Engineering, a method is developed which can be used to calculate the reaction barrier of a large number of enzyme mutants. First technical details are discussed, then we compare to experiments from Novozymes A/S and show how accurate the method is. Finally we use the method to calcualte the rate-limiting step in the reaction profile of around 400 mutants of an enzyme. This is the first time that the barrier of the rate-determining step is alculated in as set of mutants of this size, consisting of the full enzyme structure and with a
solvation model applied.
AB - This essay describes the work of two projects. The first project, Bionanosensor Simulation, describes design and implementation
of a new web interface which allows to carry out simulations of a protein sensor conveniently and fast. Out of all biosensor simulation programs, our program is the rst which displays the proteins threedimensionally in a web browser. This can be applied to the study of how the orientation of a protein a affects the electric current which runs through the sensor. These changes in current allow to detect proteins of extremely low concentrations and our simulation program helps in optimizing such sensors. In the second project, Computational Enzyme Engineering, a method is developed which can be used to calculate the reaction barrier of a large number of enzyme mutants. First technical details are discussed, then we compare to experiments from Novozymes A/S and show how accurate the method is. Finally we use the method to calcualte the rate-limiting step in the reaction profile of around 400 mutants of an enzyme. This is the first time that the barrier of the rate-determining step is alculated in as set of mutants of this size, consisting of the full enzyme structure and with a
solvation model applied.
UR - https://soeg.kb.dk/permalink/45KBDK_KGL/fbp0ps/alma99122153424305763
M3 - Ph.D. thesis
BT - A Perspective on Bionanosensor Simulation & Computational Enzyme Engineering
PB - Department of Chemistry, Faculty of Science, University of Copenhagen
ER -