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Improving catalytic function by ProSAR-driven enzyme evolution

Richard J Fox, S Christopher Davis, Emily C Mundorff, Lisa M Newman, Vesna Gavrilovic, Steven K Ma, Loleta M Chung, Charlene Ching, Sarena Tam, Sheela Muley, John Grate, John Gruber (+3 others)
2007 Nature Biotechnology  
By formalizing the decision making processes about which mutations to include in combinatorial libraries, the ProSAR algorithm is an extension of traditional SAR-based approaches to molecular optimization  ...  It augments recombination-based directed evolution by incorporating a strategy for statistical analysis of protein sequence activity relationships (ProSAR).  ...  ; Malissa Jefferson and Susan Louie for additional assay support; Patricia Babbitt, Pim Stemmer, Lynne Gilson, Lori Giver, Birthe Borup, Anke Krebber, Stephen DelCardayre and Jonathan Blanding for careful  ... 
doi:10.1038/nbt1286 pmid:17322872 fatcat:kdevragibzegvbor3vtill7ezy

A web-based tool for rational screening of mutants libraries using ProSAR

M. Berland, B. Offmann, I. Andre, M. Remaud-Simeon, P. Charton
2014 Protein Engineering Design & Selection  
We propose a web-based tool that implements an established in silico method for the rational screening of mutant libraries. The method, known as ProSAR, attempts to link sequence data to activity.  ...  It drastically improves the search for leading mutants. The tool is freely available to noncommercial users at  ...  Technical assistance for web server setup was provided by Nicolas Fontaine from Peaccel SAS.  ... 
doi:10.1093/protein/gzu035 pmid:25169579 fatcat:pdktulrjrvfd3ja3vktnu7wf5u

Engineering of Biocatalysts: from Evolution to Creation

Maureen B. Quin, Claudia Schmidt-Dannert
2011 ACS Catalysis  
This review article aims to present some of the currently employed strategies for enzyme engineering and attempts to highlight the most recent advances in methodology.  ...  A number of enzyme engineering strategies are currently employed to modify biocatalysts, improving their suitability for large-scale industrial applications.  ...  Concluding remarks Advances in the methodology available to the enzyme engineer have allowed the development of new strategies to design biocatalysts.  ... 
doi:10.1021/cs200217t pmid:22125758 pmcid:PMC3224019 fatcat:e3lzfwud5bcdha5riewcx3pa3a

GeneORator: an effective strategy for navigating protein sequence space more efficiently through Boolean OR-type DNA libraries

Andrew Currin, Jane Kwok, Joanna Sadler, Elizabeth L. Bell, Neil Swainston, Maria Ababi, Philip J.R. Day, Nicholas J Turner, Douglas B Kell
2019 ACS Synthetic Biology  
We introduce GeneORator, a novel strategy for creating DNA libraries based on the Boolean logical OR operator.  ...  For DNA mutagenesis, conventional site-directed methods implicitly utilize the Boolean AND operator (creating all mutations simultaneously), producing a combinatorial explosion in the number of genetic  ...  Second, we created combinatorial OR-type libraries for a Combinatorial Active-Site Saturation Test (CASTing 40, 41 ) .  ... 
doi:10.1021/acssynbio.9b00063 pmid:31132850 pmcid:PMC7007284 fatcat:ddzkvu6mxjdnjpesuk2xhs4zju

Advances in laboratory evolution of enzymes

Shimon Bershtein, Dan S Tawfik
2008 Current Opinion in Chemical Biology  
We address recent developments in the area of laboratory, or directed evolution, with a focus on enzymes and on new methodologies of generic potential.  ...  We survey three main areas: (i) library making techniques, including the application of computational and rational methods for library design; (ii) screening and selection techniques, including recent  ...  A multi-purpose protocol for shuffling with synthetic oligos, which enables rational design inputs to be incorporated in a combinatorial manner.  ... 
doi:10.1016/j.cbpa.2008.01.027 pmid:18284924 fatcat:26hbhysjkndwxmc6utxk4d5h7a

Accurate computational evolution of proteins and its dependence on deep learning [article]

Prabha Sankara Narayanan, Ashish Runthala
2021 arXiv   pre-print
For ecologically safe production of numerous bioproducts including drugs and chemicals, we have been striving to design the industrially useful enzyme molecules with highly improved catalytic capability  ...  sites and the extent of rigorous screening of the mutant libraries.  ...  the construction of a smart mutation library for the desired enzyme.  ... 
arXiv:2106.01951v1 fatcat:wicc7bs7mbanlpuagdyrsj2yky

Complex systems in metabolic engineering

James D Winkler, Keesha Erickson, Alaksh Choudhury, Andrea L Halweg-Edwards, Ryan T Gill
2015 Current Opinion in Biotechnology  
designs.  ...  We conclude by predicting how metabolic engineering 12 practices may advance in light of an explicit consideration of design complexity. 13  ...  We also thank Gur Pines for helpful suggestions on the manuscript.  ... 
doi:10.1016/j.copbio.2015.08.002 pmid:26319897 fatcat:2itk7xdjznhnjopamj23iyw5ei

Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle

Pablo Carbonell, Andrew Currin, Adrian J. Jervis, Nicholas J. W. Rattray, Neil Swainston, Cunyu Yan, Eriko Takano, Rainer Breitling
2016 Natural product reports (Print)  
Bioinformatics tools facilitate and accelerate all steps along the Design–Build–Test cycle of synthetic biology, for the enhanced production of natural products in engineered microbes.  ...  Acknowledgements The authors acknowledge funding from the BBSRC under grant BB/M017702/1, "Centre for synthetic biology of ne and speciality chemicals".  ...  for their synthesis methodology.  ... 
doi:10.1039/c6np00018e pmid:27185383 pmcid:PMC5063057 fatcat:xhsvtgeborestosovil64hdx3u

Engineering the third wave of biocatalysis

U. T. Bornscheuer, G. W. Huisman, R. J. Kazlauskas, S. Lutz, J. C. Moore, K. Robins
2012 Nature  
Key advances in DNA sequencing and gene synthesis are at the base of tremendous progress in tailoring biocatalysts by protein engineering and design, and the ability to reorganize enzymes into new biosynthetic  ...  Over the past ten years, scientific and technological advances have established biocatalysis as a practical and environmentally friendly alternative to traditional metallo-and organocatalysis in chemical  ...  design of mutant libraries.  ... 
doi:10.1038/nature11117 pmid:22575958 fatcat:qzs6ni6osnb73by7coggogwizm

Recent Trends for Discovery and Enhancement of Enzyme Function: A Review

Abdelnasser Ibrahim, Ahmed I. El-Dewany
2018 Egyptian Journal of Microbiology  
R ECENTLY, there is a growing recognition of enzymes utilization as ecofriendly alternative for chemical catalysts in various industrial sectors.  ...  evolution, rational design, semi rational design and computational de novo enzyme design; in addition to the recently developed field, nanobiocatalysis.  ...  Figure 8 : 8 (A) Computational enzyme design methodology.  ... 
doi:10.21608/ejm.2018.2837.1047 fatcat:5reuscwlanajroekot37rybtpu

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

Andrew Currin, Neil Swainston, Philip J. Day, Douglas B. Kell
2015 Chemical Society Reviews  
This is a contribution from the Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM).  ...  Acknowledgements We thank Chris Knight, Rainer Breitling, Nigel Scrutton and Nick Turner for very useful comments on the manuscript, Colin Levy for some material for the figures, and the Biotechnology  ...  The integration of computational design and accurate gene synthesis methodology provide a strong platform that can be utilised for directed evolution.  ... 
doi:10.1039/c4cs00351a pmid:25503938 pmcid:PMC4349129 fatcat:4alcgtju6jfdrj7ditdnurs4qq

Directed polymerase evolution

Tingjian Chen, Floyd E. Romesberg
2013 FEBS Letters  
A variety of polymerases have been evolved, providing new or improved functionality, as well as interesting new insight into the factors governing activity.  ...  The availability of these enzymes for use at the bench has driven a revolution in biotechnology and medicinal research; however, polymerases did not evolve to function efficiently under the conditions  ...  Acknowledgment We thank the National Institutes of Health (GM097489) for supporting our work on the directed evolution of DNA polymerases.  ... 
doi:10.1016/j.febslet.2013.10.040 pmid:24211837 pmcid:PMC3982152 fatcat:f26ikkgs6rfgjpxvagz4gzliri

CADEE: Computer-Aided Directed Evolution of Enzymes

Beat Anton Amrein, Fabian Steffen-Munsberg, Ireneusz Szeler, Miha Purg, Yashraj Kulkarni, Shina Caroline Lynn Kamerlin
2017 IUCrJ  
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  ...  The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development.  ...  We would like to thank Professor John Richard for helpful discussion and Professor Johan Å qvist for access to the Q source code.  ... 
doi:10.1107/s2052252516018017 pmid:28250941 pmcid:PMC5331465 fatcat:7z6nurawmvc45cdf52esoqlc7a

Intelligent host engineering for metabolic flux optimisation in biotechnology

Lachlan J. Munro, Douglas B. Kell
2021 Biochemical Journal  
Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards  ...  However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering  ...  It is, of course, very well established in fields such as chemical or electronic engineering, where it would be inconceivable to design a process plant or a new chip without modelling it in parallel.  ... 
doi:10.1042/bcj20210535 pmid:34673920 pmcid:PMC8589332 fatcat:difpodhky5c3vcmmchymd6csl4

Biomolecular engineering for nanobio/bionanotechnology

Teruyuki Nagamune
2017 Nano Convergence  
Nanobiotechnology is used in relation to the ways in which nanotechnology is used to create materials, devices and systems for studying biological systems and developing new biological assay, diagnostic  ...  Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials.  ...  Currently, there are several methodologies for conjugating proteins with DNA [117] .  ... 
doi:10.1186/s40580-017-0103-4 pmid:28491487 pmcid:PMC5401866 fatcat:xa4yixjnd5d2fh6mzc6qub7ylu
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