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PicoCB SIGNED

Exploring the Chemical Biology of Sequence Space via Picoliter Droplets

Total Cost €

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EC-Contrib. €

0

Partnership

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 PicoCB project word cloud

Explore the words cloud of the PicoCB project. It provides you a very rough idea of what is the project "PicoCB" about.

shown    microfluidic    functional    experiments    cheaper    screen    phenotype    proteins    biological    promiscuous    vivo    reactivity    metagenomic    encoding    enzyme    rare    plan    data    signalling    interpretation    promiscuity    capturing    investment    millions    cumbersome    reaction    compartments    mutations    oil    strategic    variants    mechanistic    facilities    hundred    directed    catalysis    protein    evolutionary    multiple    enormous    format    catalysts    fundamental    screening    group    microdroplets    catalytic    khz    water    members    unprecedented    chance    arguably    screened    lower    constitutes    costly    governing    emerged    library    collections    characterise    droplet    formats    environmental    vitro    lines    dollars    networks    led    throughput    successful    monodisperse    random    record    capacity    biocatalysis    landscapes    evolution    quantitative    gene    conventional    industrial    specificity    link    compartment    genotype    frequencies    individual    complement    engineering    conducting    libraries    enzymes    superfamilies    fitness    interconversion    made    function    indel    tens    guidelines   

Project "PicoCB" data sheet

The following table provides information about the project.

Coordinator
THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE 

Organization address
address: TRINITY LANE THE OLD SCHOOLS
city: CAMBRIDGE
postcode: CB2 1TN
website: www.cam.ac.uk

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country United Kingdom [UK]
 Total cost 2˙308˙221 €
 EC max contribution 2˙308˙221 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2015-AdG
 Funding Scheme ERC-ADG
 Starting year 2016
 Duration (year-month-day) from 2016-10-01   to  2021-09-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE UK (CAMBRIDGE) coordinator 2˙308˙221.00

Map

 Project objective

Directed evolution of functional proteins has arguably emerged as an approach to protein engineering that can complement or better design-led approaches to protein function. However, as a random process, enormous numbers of variants have to be screened and selected to have a chance to identify successful catalysts. This process is costly and cumbersome: Industrial screening facilities require investment of tens to hundred millions of dollars. My group has implemented key steps towards conducting quantitative biological experiments in a much cheaper format. Screening of individual library members in monodisperse oil-in-water compartments ('microdroplets’) that are generated at kHz frequencies in microfluidic devices has been shown to be possible. The droplet compartment constitutes a link between a given phenotype and its encoding genotype, by capturing reaction product, and thus providing a unique system to screen for catalysis.In this way quantitative fitness landscapes for interconversion of members of enzyme superfamilies along the lines of catalytic promiscuity, understanding the factors governing specificity and the mechanistic interpretation of the observed evolutionary pathways can be made. We now apply this screening system of unprecedented capacity for directed evolution and metagenomic screening of enzymes in in vivo and in vitro formats. We plan to apply this system to do experiments that would not be possible with conventional, lower throughput approaches: (i) screening of metagenomic libraries for rare and promiscuous activities that characterise environmental gene collections for their reactivity and potential for applied biocatalysis; (ii) developing a fundamental understanding of and strategic guidelines for enzyme evolution based on fitness landscapes that record data on multiple, promiscuous activities in response to Indel mutations; and (iii) evolution of gene networks to build up signalling networks in vitro.

 Publications

year authors and title journal last update
List of publications.
2019 Tomas Buryska, Michal Vasina, Fabrice Gielen, Pavel Vanacek, Liisa van Vliet, Jan Jezek, Zdenek Pilat, Pavel Zemanek, Jiří Damborský, Florian Hollfelder, Zbyněk Prokop
Controlled oil/water partitioning of hydrophobic substrates extends the bioanalytical applications of droplet-based microfluidics
published pages: , ISSN: 0003-2700, DOI: 10.1021/acs.analchem.9b01839
Analytical Chemistry 2020-01-22
2019 Hans Kleine‐Brüggeney, Liisa D. van Vliet, Carla Mulas, Fabrice Gielen, Chibeza C. Agley, José C. R. Silva, Austin Smith, Kevin Chalut, Florian Hollfelder
Long‐Term Perfusion Culture of Monoclonal Embryonic Stem Cells in 3D Hydrogel Beads for Continuous Optical Analysis of Differentiation
published pages: 1804576, ISSN: 1613-6810, DOI: 10.1002/smll.201804576
Small 15/5 2020-01-22
2018 Bert van Loo, Christopher D. Bayer, Gerhard Fischer, Stefanie Jonas, Eugene Valkov, Mark F. Mohamed, Anastassia Vorobieva, Celine Dutruel, Marko Hyvönen, Florian Hollfelder
Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily
published pages: 370-387, ISSN: 0002-7863, DOI: 10.1021/jacs.8b10290
Journal of the American Chemical Society 141/1 2020-01-22
2019 Bert van Loo, Ryan Berry, Usa Boonyuen, Mark F. Mohamed, Marko Golicnik, Alvan C. Hengge, Florian Hollfelder
Transition-State Interactions in a Promiscuous Enzyme: Sulfate and Phosphate Monoester Hydrolysis by Pseudomonas aeruginosa Arylsulfatase
published pages: 1363-1378, ISSN: 0006-2960, DOI: 10.1021/acs.biochem.8b00996
Biochemistry 58/10 2020-01-22
2016 Fabrice Gielen, Raphaelle Hours, Stephane Emond, Martin Fischlechner, Ursula Schell, Florian Hollfelder
Ultrahigh-throughput–directed enzyme evolution by absorbance-activated droplet sorting (AADS)
published pages: E7383-E7389, ISSN: 0027-8424, DOI: 10.1073/pnas.1606927113
Proceedings of the National Academy of Sciences 113/47 2020-01-22
2017 Tze Han Sum, Tze Jing Sum, Súil Collins, Warren R. J. D. Galloway, David G. Twigg, Florian Hollfelder, David R. Spring
Divergent synthesis of biflavonoids yields novel inhibitors of the aggregation of amyloid β (1–42)
published pages: 4554-4570, ISSN: 1477-0520, DOI: 10.1039/C7OB00804J
Organic & Biomolecular Chemistry 15/21 2020-01-22
2016 Fabrice Gielen, Maren Butz, Eric J. Rees, Miklos Erdelyi, Tommaso Moschetti, Marko Hyvönen, Joshua B. Edel, Clemens F. Kaminski, Florian Hollfelder
Quantitative Affinity Determination by Fluorescence Anisotropy Measurements of Individual Nanoliter Droplets
published pages: 1092-1101, ISSN: 0003-2700, DOI: 10.1021/acs.analchem.6b02528
Analytical Chemistry 89/2 2020-01-22
2016 Miriam Kaltenbach, Stephane Emond, Florian Hollfelder, Nobuhiko Tokuriki
Functional Trade-Offs in Promiscuous Enzymes Cannot Be Explained by Intrinsic Mutational Robustness of the Native Activity
published pages: e1006305, ISSN: 1553-7404, DOI: 10.1371/journal.pgen.1006305
PLOS Genetics 12/10 2020-01-22
2018 Bert van Loo, Markus Schober, Eugene Valkov, Magdalena Heberlein, Erich Bornberg-Bauer, Kurt Faber, Marko Hyvönen, Florian Hollfelder
Structural and Mechanistic Analysis of the Choline Sulfatase from Sinorhizobium melliloti : A Class I Sulfatase Specific for an Alkyl Sulfate Ester
published pages: 1004-1023, ISSN: 0022-2836, DOI: 10.1016/j.jmb.2018.02.010
Journal of Molecular Biology 430/7 2020-01-22
2018 Charlotte M. Miton, Stefanie Jonas, Gerhard Fischer, Fernanda Duarte, Mark F. Mohamed, Bert van Loo, Bálint Kintses, Shina C. L. Kamerlin, Nobuhiko Tokuriki, Marko Hyvönen, Florian Hollfelder
Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset
published pages: E7293-E7302, ISSN: 0027-8424, DOI: 10.1073/pnas.1607817115
Proceedings of the National Academy of Sciences 115/31 2020-01-22
2017 Christopher D. Bayer, Bert van Loo, Florian Hollfelder
Specificity Effects of Amino Acid Substitutions in Promiscuous Hydrolases: Context-Dependence of Catalytic Residue Contributions to Local Fitness Landscapes in Nearby Sequence Space
published pages: 1001-1015, ISSN: 1439-4227, DOI: 10.1002/cbic.201600657
ChemBioChem 18/11 2020-01-22

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