Engineering enzymes with non-canonical active site functionality

The combination of computational enzyme design and laboratory evolution provides an attractive platform for the creation of protein catalysts with new function. To date, designed mechanisms have relied upon Nature’s alphabet of 20 genetically encoded amino acids, which greatly restricts the range of functionality which can be installed into enzyme active sites. Here, we have exploited engineered components of the cellular translation machinery to create a protein catalyst which operates via a non-canonical catalytic nucleophile. We have subsequently shown that powerful laboratory evolution protocols can be readily adapted to allow optimization of enzymes containing non-canonical active site functionality. Crystal structures obtained along the evolutionary trajectory highlight the origins of improved activity. Thus our approach merges beneficial features of organo- and biocatalysis, by combining the intrinsic reactivities and greater versatility of small molecule catalysts with the rate enhancements, reaction selectivities and evolvability of proteins. Please click Additional Files below to see the full abstract

Selection of bacterium for mass production of {Phasmarhabditis} spp. and its effect on mortality and feeding activity of slugs

Bacteria was collected from dead slugs and the nematode species Phasmarhabditis apuliae. From the isolated bacteria nine times one bacterium was selected to produce monoxenic nematode/bacteria cultures which then were tested on growth in liquid and solid growth medium and two monoxenic culture were tested on the effectiveness to kill Deroceras species

Microscopic Laval Nozzle: Molecular Dynamics Study of the Sonic Horizon.

A Laval nozzle with its typical convergent and then divergent shape has the interesting thermodynamic properties of accelerating expanding gas above supersonic velocities and of cooling the gas in the process. This work gives a theoretical approach to the thermody- namics in a macroscopic Laval nozzle and studies the expansion of the gas in a microscopic Laval nozzle by means of non-equilibrium molecular dynamics simulations. A scheme for simulating such a non-equilibrium system is introduced for the nozzle with grand canon- ical Monte-Carlo exchange of particles to provide a stationary flow. The simulation is realized for a mono-atomic gas simulated with a Lennard-Jones-potential and for a nozzle with perfectly smooth walls. We investigate the thermodynamic state variables pressure, density, and temperature as well as the Knudsen number, Mach number and velocity of the gas for nozzles of different size. For the temperature we will have a closer look how well macroscopic assumptions are still fulfilled during the expansion in the nozzle. This investigation will also motivate a closer look at the velocity distribution inside the nozzle as well as a investigation of the velocity auto-correlation and pair-correlation function. Another focus of this work is on the speed of sound inside the nozzle and with this the position of the sonic horizon and if there is even a well defined sonic horizon on a micro- scopic scale. This work tries to answer this by studying density fluctuation correlation in the nozzle which provide information about the dispersion and attenuation of small per- turbations of the density which are naturally occurring in molecular dynamic simulations.submitted by Helmut OrtmayerUniversität Linz, Masterarbeit, 2018(VLID)258189