In Silico-Directed Evolution Using CADEE

2018 ◽  
pp. 381-415 ◽  
Author(s):  
Beat Anton Amrein ◽  
Ashish Runthala ◽  
Shina Caroline Lynn Kamerlin
Keyword(s):  
Directed Evolution ◽  
In Silico

In silico modelling of directed evolution: Implications for experimental design and stepwise evolution

2009 ◽  
Vol 257 (1) ◽  
pp. 131-141 ◽  
Author(s):  
David C. Wedge ◽  
William Rowe ◽  
Douglas B. Kell ◽  
Joshua Knowles
Keyword(s):  
Experimental Design ◽  
Directed Evolution ◽  
In Silico ◽  
In Silico Modelling ◽  
Stepwise Evolution

scholarly journals Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

2011 ◽  
Vol 407 (3) ◽  
pp. 391-412 ◽  
Author(s):  
Olga Khersonsky ◽  
Daniela Röthlisberger ◽  
Andrew M. Wollacott ◽  
Paul Murphy ◽  
Orly Dym ◽  
...  
Keyword(s):  
Directed Evolution ◽  
In Silico ◽  
Computational Design

scholarly journals CADEE: Computer-Aided Directed Evolution of Enzymes

IUCrJ ◽  
2017 ◽  
Vol 4 (1) ◽  
pp. 50-64 ◽  
Author(s):  
Beat Anton Amrein ◽  
Fabian Steffen-Munsberg ◽  
Ireneusz Szeler ◽  
Miha Purg ◽  
Yashraj Kulkarni ◽  
...  
Keyword(s):  
Directed Evolution ◽  
Biological System ◽  
In Silico ◽  
Enzyme Engineering ◽  
Drastic Reduction ◽  
Methodology Development ◽  
Computer Aided ◽  
New Framework

The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development. Here, a new framework for computer-aided directed evolution of enzymes (CADEE) is presented which allows a drastic reduction in the time necessary to prepare and analyzein silicosemi-automated directed evolution of enzymes. A pedagogical example of the application ofCADEEto a real biological system is also presented in order to illustrate theCADEEworkflow.

scholarly journals Panacea: a hyperpromiscuous antitoxin protein domain for the neutralisation of diverse toxin domains

2021 ◽  
Author(s):  
Tatsuaki Kurata ◽  
Chayan Kumar Saha ◽  
Jessica A Buttress ◽  
Toomas Mets ◽  
Tetiana Brodiazhenko ◽  
...  
Keyword(s):  
Directed Evolution ◽  
High Throughput ◽  
In Silico ◽  
Protein Domain ◽  
Type Ii ◽  
Computational Tool ◽  
Cellular Targets ◽  
High Throughput Detection ◽  
In Silico Analyses ◽  
Growth Of Bacteria

Toxin-Antitoxin (TA) gene pairs are ubiquitous in microbial chromosomal genomes and plasmids, as well as bacteriophages. They act as regulatory switches, with the toxin limiting the growth of bacteria and archaea by compromising diverse essential cellular targets, and the antitoxin counteracting the toxic effect. To uncover previously uncharted TA diversity across microbes and bacteriophages, we analysed the conservation of genomic neighbourhoods using our computational tool FlaGs (for Flanking Genes), which allows high-throughput detection of TA-like operons. Focussing on the widespread but poorly experimentally characterised antitoxin domain DUF4065, our in silico analyses indicated that DUF4065-containing proteins serve as broadly distributed antitoxin components in putative TA-like operons with dozens of different toxic domains with multiple different folds. Given the versatility of DUF4065, we have renamed the domain to Panacea (and proteins containing the domain, PanA) after the Greek goddess of universal remedy. We have experimentally validated nine PanA-neutralised TA pairs. While the majority of validated PanA-neutralised toxins act as translation inhibitors or membrane disruptors, a putative nucleotide cyclase toxin from a Burkholderia prophage compromises replication and translation, as well as inducing RelA-dependent accumulation of the nucleotide alarmone (p)ppGpp. We find that Panacea-containing antitoxins form a complex with their diverse cognate toxins, characteristic of the direct neutralisation mechanisms employed by Type II TA systems. Finally, through directed evolution we have selected PanA variants that can neutralise non-cognate TA toxins, thus experimentally demonstrating the evolutionary plasticity of this hyperpromiscuous antitoxin domain.

Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments

2016 ◽  
Vol 16 (3) ◽  
pp. 497-505 ◽  
Author(s):  
David Beneš ◽  
Alfonso Rodríguez-Patón ◽  
Petr Sosík
Keyword(s):  
Directed Evolution ◽  
In Silico ◽  
Conjugative Plasmids

scholarly journals Directed Evolution and In Silico Analysis of Reaction Centre Proteins Reveal Molecular Signatures of Photosynthesis Adaptation to Radiation Pressure

PLoS ONE ◽  
2011 ◽  
Vol 6 (1) ◽  
pp. e16216 ◽  
Author(s):  
Giuseppina Rea ◽  
Maya Lambreva ◽  
Fabio Polticelli ◽  
Ivo Bertalan ◽  
Amina Antonacci ◽  
...  
Keyword(s):  
Directed Evolution ◽  
Radiation Pressure ◽  
In Silico ◽  
In Silico Analysis ◽  
Reaction Centre ◽  
Molecular Signatures ◽  
Silico Analysis

Hydrophobic Repacking of the Dimer Interface of Triosephosphate Isomerase by in Silico Design and Directed Evolution†‡

Biochemistry ◽  
2008 ◽  
Vol 47 (20) ◽  
pp. 5556-5564 ◽  
Author(s):  
Mariana Peimbert ◽  
Lenin Domínguez-Ramírez ◽  
D. Alejandro Fernández-Velasco
Keyword(s):  
Directed Evolution ◽  
In Silico ◽  
Triosephosphate Isomerase ◽  
Dimer Interface ◽  
In Silico Design
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