Publications by Elizabeth Claire Brunk

Genetic-Algorithm-Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO

Ursula Röthlisberger, Elizabeth Claire Brunk, Marta Andreia Da Silva Perez

Biomimicry is a strategy that makes practical use of evolution to find efficient and sustainable ways to produce chemical compounds or engineer products. Exploring the natural machinery of enzymes for the production of desired compounds is a highly profita ...

2016

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

Ursula Röthlisberger, Elizabeth Claire Brunk

The current state of the art of Quantum Mechanical/molecular mechanical (QM/MM) molecular dynamics approaches in ground and electronically excited states and their applications to biological problems is reviewed. For a complete description of quantum pheno ...

2015

Lessons from Nature: Computational Design of Biomimetic Compounds and Processes

Ursula Röthlisberger, Pablo Campomanes Ramos, Elizabeth Claire Brunk, Negar Ashari Astani, Esra Bozkurt, Marta Andreia Da Silva Perez, Nicholas John Browning

Through millions of years of evolution, Nature has accomplished the development of highly efficient and sustainable processes and the idea to understand and copy natural strategies is therefore very appealing. However, in spite of intense experimental and ...

2014

A Mechanochemical Switch to Control Radical Intermediates

Ursula Röthlisberger, Elizabeth Claire Brunk

B-12-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiri ...

2014

Computational, Structural, and Kinetic Evidence That Vibrio vulnificus FrsA Is Not a Cofactor-Independent Pyruvate Decarboxylase

Ursula Röthlisberger, Elizabeth Claire Brunk

The fermentation-respiration switch (FrsA) protein in Vibrio vulnificus was recently reported to catalyze the cofactor-independent decarboxylation of pyruvate. We now report quantum mechanical/molecular mechenical calculations that examine the energetics o ...

Amer Chemical Soc2013

Mechanism to Trigger Unfolding in O6--Alkylguanine-DNA Alkyltransferase

Ursula Röthlisberger, Birgit Mollwitz, Elizabeth Claire Brunk

O6-alkylguanine-DNA alkyltransferase (AGT) adopts a non-enzymatic suicide mechanism for the repair of methylated guanine bases by transferring the methyl adduct to itself, thereby initiating unfolding and fast degradation. Classical molecular dynamics simu ...

Wiley-Blackwell2013

Mechano-chemical switch to control reactive intermediates by negative enzyme catalysis

Ursula Röthlisberger, Elizabeth Claire Brunk

Amer Chemical Soc2013

Role of environment in the catalysis of the MutY DNA repair enzyme

Ursula Röthlisberger, Jeremy Samuel Arey, Elizabeth Claire Brunk

Amer Chemical Soc2013

Mechanism to trigger unfolding in alkylguanine alkyltransferase

Ursula Röthlisberger, Birgit Mollwitz, Elizabeth Claire Brunk

Amer Chemical Soc2013

Computational evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase

Ursula Röthlisberger, Elizabeth Claire Brunk

Amer Chemical Soc2013

Computational design of biomimetic strategies for the production of chemical compounds

Ursula Röthlisberger, Elizabeth Claire Brunk

Amer Chemical Soc2013

Understanding Evolutionary Strategies of Enzymes and Exploiting them for Biomimetic Purposes

Elizabeth Claire Brunk

EPFL2013

Role of Environment for Catalysis of the DNA Repair Enzyme MutY

Ursula Röthlisberger, Jeremy Samuel Arey, Elizabeth Claire Brunk

Control of the N-glycosylase reaction by the DNA repair enzyme, MutY, entails the organization of solvent molecules. Classical molecular dynamics and QM/MM simulations were used to investigate the solvent and environment effects contributing to catalysis. ...

2012

Integrating computational methods to retrofit enzymes to synthetic pathways

Ursula Röthlisberger, Ivano Tavernelli, Vassily Hatzimanikatis, Marilisa Neri, Elizabeth Claire Brunk

Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilize the full capacity of the microorganism to produce target ...

Wiley-Blackwell2012

Directed evolution of the suicide protein O⁶-alkylguanine-DNA alkyltransferase for increased reactivity results in an alkylated protein with exceptional stability

Kai Johnsson, Ursula Röthlisberger, Simone Schmitt, Florence Pojer, Birgit Mollwitz, Elizabeth Claire Brunk

Here we present a biophysical, structural, and computational analysis of the directed evolution of the human DNA repair protein O-6-alkylguanine-DNA alkyltransferase (hAGT) into SNAP-tag, a self-labeling protein tag. Evolution of hAGT led not only to incre ...

2012

Pushing the Frontiers of First-Principles Based Computer Simulations of Chemical and Biological Systems

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Marilisa Neri, Pablo Campomanes Ramos, Stefano Vanni, Elizabeth Claire Brunk, Manuel Dömer, Andrey Laktionov, Negar Ashari Astani, Polydefkis Diamantis, Thomas James Penfold, Giulia Palermo

The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these metho ...

2011