THE BOERSMA LAB
Welcome to the website of the Arnold Boersma Lab. We are embedded within the DWI-Leibniz Institute for Interactive Materials, in Aachen, Germany.
The Boersma group works in the area of chemical biology, synthetic biochemistry, synthetic chemistry and biochemistry. We engineer new proteins, small molecules, oligonucleotides, as well as larger cell-like systems for fundamental biological understanding but also with specific applications in mind. Applications range from medical tools (diagnosis, screening and/or treating the disease) to materials and devices. The group has especially a strong record of accomplishment on the design of FRET-based protein probes for macromolecular crowding in diverse living and nonliving systems and for ionic strength measurements. Current interests lie in the development of novel probes and cell-like systems to detect novel parameters in fields that range from biology to material science.
RESEARCH
DESIGNING NEW FRET SENSORS TO UNDERSTAND THE INTRACELLULAR ENVIRONMENT
The interior of the cells is obviously not like dilute buffer. Yet, traditionally most biochemistry experiments have been performed in dilute buffer. To understand how the interior of the cell influences biochemical processes, such as biocatalysis and organization of the biopolymers, we need to know what the important parameters in the cell are, and quantify their contribution to the intracellular organization.
By creative design, we developed a series FRET sensors for macromolecular crowding and the ionic strength: Cells are crowded with macromolecules that occupy space, generating a force that influences the organization of biomolecules in cells. The crowding sensors compress akin a polymer in crowded solutions. The sensors provide a readout for the excluded volume in bacteria, yeasts, and mammalian cells. Our efforts are towards improving these sensors, as well as applying them in different species. Further, we apply the sensors in dynamic soft materials.
Further reading:
Nature Methods, 2015, 227-229
Biophys J. 2017, 1929-1939
Nature Rev. Microbiol 2017, 309-318
Collaborators:
Prof. Veenhoff (UMCG Groningen)
Prof. Sheets and Prof. Heikal (Univ Minnesota)
Prof. Fitter (RWTH Aachen)
Dr. Aberg (UMCG Groningen)
Dr. Kedrov (HHU Düsseldorf)
IONIC STRENGTH SENSING
The other sensor that we developed measures the ionic strength. The ionic strength is important for anything charged, which includes pretty much every molecule in the living cell (apart from a few small molecules). Our FRET-based ionic strength sensor allows to determine the ionic strength inside living cells, with all the advantages of FRET-based genetically-encoded sensors, such as high spatiotemporal resolution, and easy targeting to different compartments.
Further reading:
ACS Chem Biol 2017, 2510-2514
LIFE-LIKE SYSTEMS, INFORMATION TRANSFER, DIAGNOSTIC TOOLS, AND MORE
We will provide more information in due course.
NEWS
SARA PUBLISHES IN ELIFE ON PHYSICAL CHEMICAL PARAMETERS IN YEAST DURING AGING
October 10, 2020
With our optimized crowding sensor in yeast in a dedicated microfluidics device, we show that crowding is relatively stable during yeast aging, contrasting with our initial expectations, with the note that longer-lived cells show higher crowding stability. On larger length scales (at least more than the 8-nm crowding sensor), we show with CLEM (correlative light-electron microscopy) that there are drastic changes in the organellar volume fractions. We tentatively name this organellar crowding to distinguish the µm-scale crowding with nm-scale macromolecular crowding. Using pHluorin, a green fluorescent protein sensitive to the pH, we observe small but significant acidification of the cytoplasm, which decreases sharply after senescence. We hoped to show that several physical and chemical parameters drift during aging, and the levels at which they arrive should be considered when describing molecular events in old cells
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ILARIA, MENG-RUO, AND NUNO JOIN THE LAB
August 8, 2020
We are stoked to be joined by three new members in the lab at the same time (partially due to delays induced by Covid...). Ilaria will perform her master thesis on synthetic cells, while Meng-Ruo will do his postdoc studies on chemistry on proteins and in cells, and Nuno will perform his postdoc studies on the intracellular physicochemical properties. The lab is getting ever more busy and vibrant!
SELECTED IN RISING STARS IN SENSIGN VIRTUAL ISSUE
August 8, 2020
We are honored to be included in the rising stars of sensing virtual issue of ACS Sensors. This is a great recognition of the work the team has been performing in the last few years. You can find the issue here.
PROTOCOL ON CROWDING MEASUREMENTS
July 26, 2020
Sara wrote a very informative chapter in Methods in Molecular Biology on how to perform accurate crowding measurements inside yeast cells. This protocol is included in a topic on The Nucleus, edited by Ronald Hancock. One of our main messages that we convey in our notes is that cells need to be treated gently because the organization in their interior is affected relatively quickly!
MEET THE TEAM
ARNOLD BOERSMA
Principle Investigator
SARA MOUTON
PhD Student (shared with Liesbeth Veenhoff)
QI WAN
PhD student
WEIYAN ZUO
PhD student
THEODOROS PITTAS
PhD Student
MILARA KALACHEVA
PhD Student
BURAK ÖZÇIFÇI
PhD Student
JAKUB HADULA
PhD student
LUIS PAULO BUSCA GUERZONI
Postdoc
NUNO DA SILVA
Postdoc
MENG-RUO HUANG
Postdoc
ILARIA PALUMBO
Master thesis
FABIAN SCHMITZ
Research assistant / Lab manager
PUBLISHED WORK
2020
Engineering Crowding Sensitivity into Protein Linkers.
Pittas T, Zuo W, Boersma AJ.
Methods Enzymol. 2020 doi: 10.1016/bs.mie.2020.09.007
Controlling Optical and Catalytic Activity of Genetically Engineered Proteins by Ultrasound.
Zhou Y, Huo S, Loznik M, Göstl R, Boersma AJ, Herrmann A.
Angew Chem Int Ed Engl. 2020 Oct 26. doi: 10.1002/anie.202010324. Online ahead of print.
Mouton SN, Thaller DJ, Crane MM, Rempel IL, Terpstra OT, Steen A, Kaeberlein M, Lusk CP, Boersma AJ, Veenhoff LM.
Elife. 2020 Sep 29;9:e54707. doi: 10.7554/eLife.54707.
Mouton SN, Veenhoff LM, Boersma AJ.
Methods Mol Biol. 2020; 2175:169-180. doi: 10.1007/978-1-0716-0763-3_12.
Löwe M, Kalacheva M, Boersma AJ, Kedrov A.
FEBS J. 2020 May 28. doi: 10.1111/febs.15429. Online ahead of print.
Modular and Versatile trans-Encoded Genetic Switches.
Paul A, Warszawik EM, Loznik M, Boersma AJ, Herrmann A
Angew Chem Int Ed Engl. 2020 Apr 30. doi: 10.1002/anie.202001372. Online ahead of print.
Miller RC, Aplin CP, Kay TM, Leighton R, Libal C, Simonet R, Cembran A, Heikal AA, Boersma AJ, Sheets ED
J Phys Chem B. 2020 Apr 30;124(17):3447-3458. doi: 10.1021/acs.jpcb.9b10498. Epub 2020 Apr 16.
Supercharged Proteins and Polypeptides.
Ma C, Malessa A, Boersma AJ, Liu K, Herrmann A.
Adv Mater. 2020 Jan 15:e1905309. doi: 10.1002/adma.201905309
This article is part of the Special Issue: From Responsive Materials to Interactive Materials
2019
Syga Ł, de Vries RH, van Oosterhout H, Bartelds R, Boersma AJ, Roelfes G, Poolman B.
Chembiochem. 2019 Dec 9. doi: 10.1002/cbic.201900655.
DNA Nanotechnology Enters Cell Membranes.
Huo S, Li H, Boersma AJ, Herrmann A.
Adv Sci (Weinh). 2019 Mar 20;6(10):1900043. doi: 10.1002/advs.201900043
Highlighted in Advanced Science News, April 2019.
This article is part of the Advanced Science 5th anniversary interdisciplinary article series.
Decreased Effective Macromolecular Crowding in Escherichia coli Adapted to Hyperosmotic Stress.
Liu B, Hasrat Z, Poolman B, Boersma AJ.
J Bacteriol. 2019 Apr 24;201(10). pii: e00708-18. doi: 10.1128/JB.00708-18
Selected as Article of Significant Interest (spotlight) in J. Bacteriol.
Schwarz J, J Leopold H, Leighton R, Miller RC, Aplin CP, Boersma AJ, Heikal AA, Sheets ED.
Methods Appl Fluoresc. 2019 Feb 19;7(2):025002. doi: 10.1088/2050-6120/ab0242
Leopold HJ, Leighton R, Schwarz J, Boersma AJ, Sheets ED, Heikal AA.
J Phys Chem B. 2019 Jan 17;123(2):379-393. doi: 10.1021/acs.jpcb.8b09829
2018
How Important Is Protein Diffusion in Prokaryotes?
Schavemaker PE, Boersma AJ, Poolman B.
Front Mol Biosci. 2018 Nov 13;5:93. doi: 10.3389/fmolb.2018.00093.
Special issue on biochemical reactions in cytomimetic media edited by A.P. Minton and G. Rivas
Lee HB, Cong A, Leopold H, Currie M, Boersma AJ, Sheets ED, Heikal AA.
Phys Chem Chem Phys. 2018 Oct 7;20(37):24045-24057. doi: 10.1039/c8cp03873b
Influence of Fluorescent Protein Maturation on FRET Measurements in Living Cells.
Liu B, Mavrova SN, van den Berg J, Kristensen SK, Mantovanelli L, Veenhoff LM, Poolman B, Boersma AJ.
ACS Sens. 2018 Sep 28;3(9):1735-1742. doi: 10.1021/acssensors.8b00473
Selected in "Rising Stars in Sensing" virtual issue of ACS Sensors 2020
Höfig H, Otten J, Steffen V, Pohl M, Boersma AJ, Fitter J.
ACS Sens. 2018 Aug 24;3(8):1462-1470. doi: 10.1021/acssensors.8b00143
2017
Ionic Strength Sensing in Living Cells.
Liu B, Poolman B, Boersma AJ.
ACS Chem Biol. 2017 Oct 20;12(10):2510-2514. doi: 10.1021/acschembio.7b00348
Highlighted in Chemical & Engineering News, October 2017
Cover image ACS Chem. Biol. October 2017
Meet our authors highlight Boqun Liu
Fluorescence Dynamics of a FRET Probe Designed for Crowding Studies.
Currie M, Leopold H, Schwarz J, Boersma AJ, Sheets ED, Heikal AA.
J Phys Chem B. 2017 Jun 15;121(23):5688-5698. doi: 10.1021/acs.jpcb.7b01306.
Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding.
Liu B, Åberg C, van Eerden FJ, Marrink SJ, Poolman B, Boersma AJ.
Biophys J. 2017 May 9;112(9):1929-1939. doi: 10.1016/j.bpj.2017.04.004.
Microorganisms maintain crowding homeostasis.
van den Berg J, Boersma AJ, Poolman B.
Nat Rev Microbiol. 2017 May;15(5):309-318. doi: 10.1038/nrmicro.2017.17
2016
Semisynthetic Nanoreactor for Reversible Single-Molecule Covalent Chemistry.
Lee J, Boersma AJ, Boudreau MA, Cheley S, Daltrop O, Li J, Tamagaki H, Bayley H.
ACS Nano. 2016 Sep 27;10(9):8843-50. doi: 10.1021/acsnano.6b04663
Highlighted in Nanotechweb.org, 2016.
2015
Associative Interactions in Crowded Solutions of Biopolymers Counteract Depletion Effects.
Groen J, Foschepoth D, te Brinke E, Boersma AJ, Imamura H, Rivas G, Heus HA, Huck WT.
J Am Chem Soc. 2015 Oct 14;137(40):13041-8. doi: 10.1021/jacs.5b07898
Highlighted in Derek Lowe’s “in the pipeline” blog
Protein engineering: The power of four.
Boersma AJ, Roelfes G.
Nat Chem. 2015 Apr;7(4):277-9. doi: 10.1038/nchem.2220
A sensor for quantification of macromolecular crowding in living cells.
Boersma AJ, Zuhorn IS, Poolman B.
Nat Methods. 2015 Mar;12(3):227-9, 1 p following 229. doi: 10.1038/nmeth.3257
Highlighted in NWO newsletter, 2015
Highlighted in Biophysical Society newsletter (with interview), 2015
News articles in kennislink.nl, University of Groningen website, AzoSensors.com, Science Newsline, Phys.org, Technobahn, EurekAlert!, Science Daily, Bioportfolio, Nanowerk Nanotechnology News, and others.
Draksharapu A, Boersma AJ, Browne WR, Roelfes G.
Dalton Trans. 2015 Feb 28;44(8):3656-63. doi: 10.1039/c4dt02734e.
Draksharapu A, Boersma AJ, Leising M, Meetsma A, Browne WR, Roelfes G.
Dalton Trans. 2015 Feb 28;44(8):3647-55. doi: 10.1039/c4dt02733g.
EARLIER
Continuous stochastic detection of amino acid enantiomers with a protein nanopore.
Boersma, A.J.; Bayley, H. Angew. Chem. Int. Ed. 2012, 51, 9606.
Real-time detection of multiple neurotransmitters with a protein nanopore.
Boersma, A.J.; Brain, K.L.; Bayley, H. ACS Nano 2012, 6, 5304.
Highlighted in Nanomedicine, 2012.
Ligand denticity controls enantiomeric preference in DNA-based asymmetric catalysis.
Boersma, A.J.; de Bruin, B.; Feringa, B.L.; Roelfes, G. Chem. Commun. 2012, 2394.
Highlighted in Chemistry & Industry, 2012.
Catalytic enantioselective syn hydration of enones in water using a DNA-based catalyst.
Boersma, A.J.; Coquière, D.; Geerdink, D.; Rosati, F.; Feringa, B.L.; Roelfes, G. Nature Chem. 2010, 2, 991.
Highlighted on the NWO website, Chemisch2Weekblad
Synfacts highlight of the month February
Selected in Faculty of 1000
On the role of DNA in DNA-based catalytic enantioselective conjugate addition reactions.
Dijk, E.W.; Boersma, A.J.; Feringa, B.L.; Roelfes, G. Org. Biomol. Chem. 2010, 8, 3868.
DNA-based asymmetric catalysis.
Boersma, A.J.; Megens, R.P.; Feringa, B.L.; Roelfes, G. Chem. Soc. Rev. 2010, 39, 2083.
A kinetic and structural investigation of DNA-based asymmetric catalysis using the first generation ligands.
Rosati, F.; Boersma, A.J.; Klijn, J.E.; Meetsma, A.; Feringa, B.L.; Roelfes, G. Chem. Eur. J. 2009, 15, 9596.
Enantioselective Friedel-Crafts reactions in water using a DNA-based catalyst.
Boersma, A.J.; Feringa, B.L.; Roelfes, G. Angew. Chem. Int. Ed. 2009, 48, 3346.
Highlighted in Synfacts 2009(7)
DNA-based asymmetric catalysis: Sequence-dependent rate acceleration and enantioselectivity.
Boersma, A.J.; Klijn, J.E.; Feringa, B.L.; Roelfes, G. J. Am. Chem. Soc. 2008, 130, 11783.
Highlighted in JACS Select #4
α,β-Unsaturated 2-acyl imidazoles as a practical class of dienophiles for the DNA-based catalytic asymmetric Diels-Alder reaction in water.
Boersma, A.J.; Feringa, B.L.; Roelfes, G. Org. Lett. 2007, 9, 3647.
Highlighted on organic-chemistry.org, august 2008
Highly enantioselective DNA-based catalysis.
Roelfes, G.; Boersma, A.J.; Feringa, B.L. Chem. Commun. 2006, 635.
Hot paper in Chemical Communications.
Highlighted in Chemistry World, march 2006
Highlighted in Nature news & views, 7 dec 2006
Metal-catalyzed cotrimerization of arynes and alkenes.
Quintana, I.; Boersma, A.J.; Peña, D.; Pérez, D.; Guitián, E. Org. Lett. 2006, 8, 3347.
Catalytic enantioselective conjugate addition of dialkylzinc reagents to N-substituted-2,3-dehydro-4-piperidones.
Sebesta, R.; Pizzuti, M.G.; Boersma, A.J.; Minnaard, A.J.; Feringa, B.L. Chem. Commun. 2005, 1711.
AVAILABLE POSITIONS
STUDENT INTERNSHIPS
Student internships: Students that would like to obtain experience in one of our research topics, please contact Arnold
RESEARCH ASSISTANT
We are looking for a research assistant with experience in biochemistry/molecular biology. More information here
NO POSITION ADVERTIZED, BUT INTERESTED?
Strong PhD and Postdoc candidates are encouraged to get in contact with Arnold.
CONTACT US
DWI Leibniz Institut für Interaktive Materialien
Forckenbeckstrasse 50
D-52056 Aachen, Germany
boersma[at]dwi.rwth-aachen.de