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Lacham-Hartman S, Shmidov Y, Radisky ES, Bitton R, Lukatsky DB, Papo N. Avidity observed between a bivalent inhibitor and an enzyme monomer with a single active site. PLoS One 2021; 16:e0249616. [PMID: 34847142 PMCID: PMC8631645 DOI: 10.1371/journal.pone.0249616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 11/13/2021] [Indexed: 12/16/2022] Open
Abstract
Although myriad protein–protein interactions in nature use polyvalent binding, in which multiple ligands on one entity bind to multiple receptors on another, to date an affinity advantage of polyvalent binding has been demonstrated experimentally only in cases where the target receptor molecules are clustered prior to complex formation. Here, we demonstrate cooperativity in binding affinity (i.e., avidity) for a protein complex in which an engineered dimer of the amyloid precursor protein inhibitor (APPI), possessing two fully functional inhibitory loops, interacts with mesotrypsin, a soluble monomeric protein that does not self-associate or cluster spontaneously. We found that each inhibitory loop of the purified APPI homodimer was over three-fold more potent than the corresponding loop in the monovalent APPI inhibitor. This observation is consistent with a suggested mechanism whereby the two APPI loops in the homodimer simultaneously and reversibly bind two corresponding mesotrypsin monomers to mediate mesotrypsin dimerization. We propose a simple model for such dimerization that quantitatively explains the observed cooperativity in binding affinity. Binding cooperativity in this system reveals that the valency of ligands may affect avidity in protein–protein interactions including those of targets that are not surface-anchored and do not self-associate spontaneously. In this scenario, avidity may be explained by the enhanced concentration of ligand binding sites in proximity to the monomeric target, which may favor rebinding of the multiple ligand binding sites with the receptor molecules upon dissociation of the protein complex.
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Affiliation(s)
- Shiran Lacham-Hartman
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yulia Shmidov
- Deprtment of Chemical Engineering and the Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America
| | - Ronit Bitton
- Deprtment of Chemical Engineering and the Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - David B. Lukatsky
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail: (NP); (DBL)
| | - Niv Papo
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail: (NP); (DBL)
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2
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Brückner S, Schubert R, Kraushaar T, Hartmann R, Hoffmann D, Jelli E, Drescher K, Müller DJ, Oliver Essen L, Mösch HU. Kin discrimination in social yeast is mediated by cell surface receptors of the Flo11 adhesin family. eLife 2020; 9:55587. [PMID: 32286952 PMCID: PMC7156268 DOI: 10.7554/elife.55587] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/03/2020] [Indexed: 02/06/2023] Open
Abstract
Microorganisms have evolved specific cell surface molecules that enable discrimination between cells from the same and from a different kind. Here, we investigate the role of Flo11-type cell surface adhesins from social yeasts in kin discrimination. We measure the adhesion forces mediated by Flo11A-type domains using single-cell force spectroscopy, quantify Flo11A-based cell aggregation in populations and determine the Flo11A-dependent segregation of competing yeast strains in biofilms. We find that Flo11A domains from diverse yeast species confer remarkably strong adhesion forces by establishing homotypic interactions between single cells, leading to efficient cell aggregation and biofilm formation in homogenous populations. Heterotypic interactions between Flo11A domains from different yeast species or Saccharomyces cerevisiae strains confer weak adhesive forces and lead to efficient strain segregation in heterogenous populations, indicating that in social yeasts Flo11A-mediated cell adhesion is a major mechanism for kin discrimination at species and sub-species levels. These findings, together with our structure and mutation analysis of selected Flo11A domains, provide a rationale of how cell surface receptors have evolved in microorganisms to mediate kin discrimination.
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Affiliation(s)
- Stefan Brückner
- Department of Genetics, Philipps-Universität Marburg, Marburg, Germany
| | - Rajib Schubert
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Timo Kraushaar
- Department of Biochemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniel Hoffmann
- Department of Genetics, Philipps-Universität Marburg, Marburg, Germany
| | - Eric Jelli
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Lars Oliver Essen
- Department of Biochemistry, Philipps-Universität Marburg, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Hans-Ulrich Mösch
- Department of Genetics, Philipps-Universität Marburg, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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3
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Li M, Ding H, Lin M, Yin F, Song L, Mao X, Li F, Ge Z, Wang L, Zuo X, Ma Y, Fan C. DNA Framework-Programmed Cell Capture via Topology-Engineered Receptor-Ligand Interactions. J Am Chem Soc 2019; 141:18910-18915. [PMID: 31691568 DOI: 10.1021/jacs.9b11015] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Receptor-ligand interactions (RLIs) that play pivotal roles in living organisms are often depicted with the classic keys-and-locks model. Nevertheless, RLIs on the cell surface are generally highly complex and nonlinear, partially due to the noncontinuous and dynamic distribution of receptors on extracellular membranes. Here, we develop a tetrahedral DNA framework (TDF)-programmed approach to topologically engineer RLIs on the cell membrane, which enables active recruitment-binding of clustered receptors for high-affinity capture of circulating tumor cells (CTCs). The four vertices of a TDF afford orthogonal anchoring of ligands with spatial organization, based on which we synthesized n-simplexes harboring 1-3 aptamers targeting epithelial cell adhesion molecule (EpCAM) that are overexpressed on the membrane of tumor cells. The 2-simplex with three aptamers not only shows increased binding affinity (∼19-fold) but prevents endocytosis by cells. By using 2-simplex as the capture probe, we demonstrate the high-efficiency CTC capture, which is challenged in real clinical breast cancer patient samples. This TDF-programmed platform thus provides a powerful means for studying RLIs in physiological settings and for cancer diagnosis.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Hongming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology , Soochow University , Suzhou 215006 , China
| | - Meihua Lin
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , Wuhan 430074 , China
| | - Fangfei Yin
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200127 , China.,Division of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China
| | - Lu Song
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200127 , China.,Division of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China
| | - Xiuhai Mao
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Fan Li
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Zhilei Ge
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Lihua Wang
- Division of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Yuqiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures , Nanjing University , Nanjing 210093 , China
| | - Chunhai Fan
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200127 , China
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4
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Affiliation(s)
- Gadiel Saper
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
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5
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Tang NC, Chilkoti A. Combinatorial codon scrambling enables scalable gene synthesis and amplification of repetitive proteins. NATURE MATERIALS 2016; 15:419-24. [PMID: 26726995 PMCID: PMC4809025 DOI: 10.1038/nmat4521] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/25/2015] [Indexed: 05/08/2023]
Abstract
Most genes are synthesized using seamless assembly methods that rely on the polymerase chain reaction (PCR). However, PCR of genes encoding repetitive proteins either fails or generates nonspecific products. Motivated by the need to efficiently generate new protein polymers through high-throughput gene synthesis, here we report a codon-scrambling algorithm that enables the PCR-based gene synthesis of repetitive proteins by exploiting the codon redundancy of amino acids and finding the least-repetitive synonymous gene sequence. We also show that the codon-scrambling problem is analogous to the well-known travelling salesman problem, and obtain an exact solution to it by using De Bruijn graphs and a modern mixed integer linear programme solver. As experimental proof of the utility of this approach, we use it to optimize the synthetic genes for 19 repetitive proteins, and show that the gene fragments are amenable to PCR-based gene assembly and recombinant expression.
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Affiliation(s)
- Nicholas C Tang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
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6
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Quiroz FG, Chilkoti A. Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers. NATURE MATERIALS 2015; 14:1164-71. [PMID: 26390327 PMCID: PMC4618764 DOI: 10.1038/nmat4418] [Citation(s) in RCA: 293] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 08/04/2015] [Indexed: 05/17/2023]
Abstract
Proteins and synthetic polymers that undergo aqueous phase transitions mediate self-assembly in nature and in man-made material systems. Yet little is known about how the phase behaviour of a protein is encoded in its amino acid sequence. Here, by synthesizing intrinsically disordered, repeat proteins to test motifs that we hypothesized would encode phase behaviour, we show that the proteins can be designed to exhibit tunable lower or upper critical solution temperature (LCST and UCST, respectively) transitions in physiological solutions. We also show that mutation of key residues at the repeat level abolishes phase behaviour or encodes an orthogonal transition. Furthermore, we provide heuristics to identify, at the proteome level, proteins that might exhibit phase behaviour and to design novel protein polymers consisting of biologically active peptide repeats that exhibit LCST or UCST transitions. These findings set the foundation for the prediction and encoding of phase behaviour at the sequence level.
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Affiliation(s)
- Felipe García Quiroz
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
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7
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Varner CT, Rosen T, Martin JT, Kane RS. Recent advances in engineering polyvalent biological interactions. Biomacromolecules 2015; 16:43-55. [PMID: 25426695 PMCID: PMC4294584 DOI: 10.1021/bm5014469] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/11/2014] [Indexed: 12/21/2022]
Abstract
Polyvalent interactions, where multiple ligands and receptors interact simultaneously, are ubiquitous in nature. Synthetic polyvalent molecules, therefore, have the ability to affect biological processes ranging from protein-ligand binding to cellular signaling. In this review, we discuss recent advances in polyvalent scaffold design and applications. First, we will describe recent developments in the engineering of polyvalent scaffolds based on biomolecules and novel materials. Then, we will illustrate how polyvalent molecules are finding applications as toxin and pathogen inhibitors, targeting molecules, immune response modulators, and cellular effectors.
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Affiliation(s)
- Chad T. Varner
- The Howard P. Isermann Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Tania Rosen
- The Howard P. Isermann Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Jacob T. Martin
- The Howard P. Isermann Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Ravi S. Kane
- The Howard P. Isermann Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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8
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Tiwari DK, Dasgupta-Schubert N, Villaseñor Cendejas LM, Villegas J, Carreto Montoya L, Borjas García SE. Interfacing carbon nanotubes (CNT) with plants: enhancement of growth, water and ionic nutrient uptake in maize (Zea mays) and implications for nanoagriculture. APPLIED NANOSCIENCE 2013. [DOI: 10.1007/s13204-013-0236-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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9
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Programmable multivalent display of receptor ligands using peptide nucleic acid nanoscaffolds. Nat Commun 2012; 3:614. [PMID: 22233624 PMCID: PMC3518395 DOI: 10.1038/ncomms1629] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 12/01/2011] [Indexed: 01/05/2023] Open
Abstract
Multivalent effects dictate the binding affinity of multiple ligands on one molecular entity to receptors. Integrins are receptors that mediate cell attachment through multivalent binding to peptide sequences within the extracellular matrix, and overexpression promotes the metastasis of some cancers. Multivalent display of integrin antagonists enhances their efficacy, but current scaffolds have limited ranges and precision for the display of ligands. Here we present an approach to studying multivalent effects across wide ranges of ligand number, density, and three-dimensional arrangement. Using L-lysine γ-substituted peptide nucleic acids, the multivalent effects of an integrin antagonist were examined over a range of 1-45 ligands. The optimal construct improves the inhibitory activity of the antagonist by two orders of magnitude against the binding of melanoma cells to the extracellular matrix in both in vitro and in vivo models.
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10
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Zhou W, Liu X, Ji J. Fast and selective cancer cell uptake of therapeutic gold nanorods by surface modifications with phosphorylcholine and Tat. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm16713a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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11
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Yang Z, Tu Q, Wang J, Lei X, He T, Sun H, Huang N. Bioactive Plasma-Polymerized Bipolar Films for Enhanced Endothelial Cell Mobility. Macromol Biosci 2011; 11:797-805. [DOI: 10.1002/mabi.201000474] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/18/2011] [Indexed: 01/19/2023]
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12
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Amiram M, Quiroz FG, Callahan DJ, Chilkoti A. A highly parallel method for synthesizing DNA repeats enables the discovery of 'smart' protein polymers. NATURE MATERIALS 2011; 10:141-8. [PMID: 21258353 PMCID: PMC3075872 DOI: 10.1038/nmat2942] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 12/09/2010] [Indexed: 05/24/2023]
Abstract
Robust high-throughput synthesis methods are needed to expand the repertoire of repetitive protein-polymers for different applications. To address this need, we developed a new method, overlap extension rolling circle amplification (OERCA), for the highly parallel synthesis of genes encoding repetitive protein-polymers. OERCA involves a single PCR-type reaction for the rolling circle amplification of a circular DNA template and simultaneous overlap extension by thermal cycling. We characterized the variables that control OERCA and demonstrated its superiority over existing methods, its robustness, high-throughput and versatility by synthesizing variants of elastin-like polypeptides (ELPs) and protease-responsive polymers of glucagon-like peptide-1 analogues. Despite the GC-rich, highly repetitive sequences of ELPs, we synthesized remarkably large genes without recursive ligation. OERCA also enabled us to discover 'smart' biopolymers that exhibit fully reversible thermally responsive behaviour. This powerful strategy generates libraries of repetitive genes over a wide and tunable range of molecular weights in a 'one-pot' parallel format.
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Affiliation(s)
- Miriam Amiram
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708-0281, USA
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13
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Lempens EHM, Merkx M, Tirrell M, Meijer EW. Dendrimer Display of Tumor-Homing Peptides. Bioconjug Chem 2011; 22:397-405. [DOI: 10.1021/bc100403e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Edith H. M. Lempens
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Matthew Tirrell
- Department of Chemical Engineering and Materials Research Laboratory, University of California Santa Barbara, California 93106-5080, United States
| | - E. W. Meijer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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