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Fragasso, A. (author), De Franceschi, N. (author), Stömmer, Pierre (author), van der Sluis, E.O. (author), Dietz, Hendrik (author), Dekker, C. (author)Molecular traffic across lipid membranes is a vital process in cell biology that involves specialized biological pores with a great variety of pore diameters, from fractions of a nanometer to >30 nm. Creating artificial membrane pores covering similar size and complexity will aid the understanding of transmembrane molecular transport in...journal article 2021
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Dekker, W.J.C. (author), Ortiz Merino, R.A. (author), Kaljouw, Astrid (author), Battjes, Julius (author), Wiering, Frank W. (author), Mooiman, C. (author), de la Torre, P. (author), Pronk, J.T. (author)Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae. Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae,...journal article 2021
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Brinkerhoff, H.D. (author), Kang, A.S.W. (author), Liu, Jingqian (author), Aksimentiev, Aleksei (author), Dekker, C. (author)A proteomics tool capable of identifying single proteins would be important for cell biology research and applications. Here, we demonstrate a nanopore-based single-molecule peptide reader sensitive to single-amino acid substitutions within individual peptides. A DNA-peptide conjugate was pulled through the biological nanopore MspA by the DNA...journal article 2021
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Schmid, S. (author), Dekker, C. (author)This paper provides a perspective on potential applications of a new single-molecule technique, viz., the nanopore electro-osmotic trap (NEOtrap). This solid-state nanopore-based method uses locally induced electro-osmosis to form a hydrodynamic trap for single molecules. Ionic current recordings allow one to study an unlabeled protein or...review 2021
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Schmid, S. (author), Dekker, C. (author)Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing.While static 3D structures are now readily available, observing the functional cycle of proteins-involving conformational changes and...review 2021
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Bohländer, P.R. (author), Filius, M. (author), van Kooten, Xander F. (author), Pomorski, A.K. (author), Schmid, S. (author), Dekker, C. (author), Eelkema, R. (author), Kim, S.H. (author), Joo, C. (author)Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside...review 2021
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Whitley, K.D. (author), Jukes, Calum (author), Tregidgo, Nicholas (author), Karinou, Eleni (author), Almada, Pedro (author), Cesbron, Yann (author), Henriques, Ricardo (author), Dekker, C. (author), Holden, Séamus (author)Despite the central role of division in bacterial physiology, how division proteins work together as a nanoscale machine to divide the cell remains poorly understood. Cell division by cell wall synthesis proteins is guided by the cytoskeleton protein FtsZ, which assembles at mid-cell as a dense Z-ring formed of treadmilling filaments. However...journal article 2021
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Dekker, R. (author), van der Meer, F.P. (author), Maljaars, J. (author), Sluys, Lambertus J. (author)This study presents calibration and validation of a cohesive extended finite element model for fatigue crack propagation in ductile materials. The approach relies on a separation between plasticity around the crack tip and fatigue crack growth at the crack tip such that the influence of plasticity on fatigue driving forces is predicted. This...journal article 2021
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Loeff, L. (author), Kerssemakers, J.W.J. (author), Joo, C. (author), Dekker, C. (author)Single-molecule techniques allow the visualization of the molecular dynamics of nucleic acids and proteins with high spatiotemporal resolution. Valuable kinetic information of biomolecules can be obtained when the discrete states within single-molecule time trajectories are determined. Here, we present a fast, automated, and bias-free step...journal article 2021
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Brauns, Fridtjof (author), Pawlik, G. (author), Halatek, Jacob (author), Kerssemakers, J.W.J. (author), Frey, Erwin (author), Dekker, C. (author)Self-organisation of Min proteins is responsible for the spatial control of cell division in Escherichia coli, and has been studied both in vivo and in vitro. Intriguingly, the protein patterns observed in these settings differ qualitatively and quantitatively. This puzzling dichotomy has not been resolved to date. Using reconstituted...journal article 2021
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Kawasaki, S. (author), Dijkema, E. (author), Saccher, M. (author), Giagka, Vasiliki (author), Schleipen, J.J.H.B. (author), Dekker, R. (author)In the bioelectronic medicine field, vagus nerve stimulation (VNS) is a promising technique that is expected to treat numerous inflammatory conditions, in addition to the currently FDA approved treatment for epilepsy, depression and obesity [1]. However, current VNS techniques are still limited in the spatial resolution that they can achieve,...conference paper 2021
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Yang, W.W.W. (author), van Dijk, M.C. (author), Primavera, Christian (author), Dekker, C. (author)We have developed a fabrication methodology for label-free optical trapping of individual nanobeads and proteins in inverted-bowtie-shaped plasmonic gold nanopores. Arrays of these nanoapertures can be reliably produced using focused ion beam (FIB) milling with gap sizes of 10–20 nm, single-nanometer variation, and with a remarkable stability...journal article 2021
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Janissen, R. (author), Woodman, Andrew (author), Shengjuler, Djoshkun (author), Vallet, Thomas (author), Lee, Kuo Ming (author), Kuijpers, L.C. (author), Moustafa, Ibrahim M. (author), Fitzgerald, Fiona (author), Dekker, N.H. (author)Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics...journal article 2021
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Boogaard, Bob (author), Tas, Ali (author), Nijssen, J.P.A. (author), Broeren, F.G.J. (author), van den Dobbelsteen, J.J. (author), Verhoeven, Vincent (author), Pluim, Jip (author), Dekker, Sing (author), Snijder, Eric J. (author), van Hemert, Martijn J. (author), Herfst, Sander (author)The SARS-CoV-2 pandemic resulted in shortages of production and test capacity of FFP2-respirators. Such facemasks are required to be worn by healthcare professionals when performing aerosol-generating procedures on COVID-19 patients. In response to the high demand and short supply, we designed three models of facemasks that are suitable for...journal article 2021
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Deshpande, Siddharth (author), Dekker, C. (author)Cells organize their interior through membrane-bound organelles and through membraneless condensates that are formed by liquid–liquid phase separation (LLPS). The complex process of coacervation that is involved in LLPS is challenging to study in living cells. Hence, studying coacervation in cell-mimicking synthetic containers can yield...review 2021
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Klughammer, N. (author), Dekker, C. (author)Holes in metal films do not allow the propagation of light if the wavelength is much larger than the hole diameter, establishing such nanopores as so-called zero-mode waveguides (ZMWs). Molecules, on the other hand, can still pass through these holes. We use this to detect individual fluorophore-labelled molecules as they travel through a ZMW...journal article 2021
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Dekker, R. (author), van der Meer, F.P. (author), Maljaars, Johan (author), Sluys, Lambertus J. (author)A numerical model for corrosion pit propagation under mechanical loading is presented. The level set method is used for corrosion front tracking and also enables the domain to be split into a solid and a pit domain. In the pit the diffusion of atoms originating from the dissolution process occurring at the pit front is simulated. The model is...journal article 2021
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Ryu, J.K. (author), Bouchoux, Céline (author), Liu, Hon Wing (author), Kim, E. (author), Minamino, Masashi (author), de Groot, Ralph (author), Katan, A.J. (author), Bonato, Andrea (author), Marenduzzo, Davide (author), Michieletto, Davide (author), Uhlmann, Frank (author), Dekker, C. (author)Structural maintenance of chromosome (SMC) protein complexes are able to extrude DNA loops. While loop extrusion constitutes a fundamental building block of chromosomes, other factors may be equally important. Here, we show that yeast cohesin exhibits pronounced clustering on DNA, with all the hallmarks of biomolecular condensation. DNA...journal article 2021
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Japaridze, A. (author), Yang, W.W.W. (author), Dekker, C. (author), Nasser, William (author), Muskhelishvili, Georgi (author)Nucleoid-associated proteins (NAPs) are a class of highly abundant DNA-binding proteins in bacteria and archaea. While both the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding and stabilizing higher-order nucleoprotein complexes in...journal article 2021
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Fragasso, A. (author), de Vries, Hendrik W. (author), Andersson, John (author), van der Sluis, E.O. (author), van der Giessen, Erik (author), Dahlin, Andreas (author), Onck, Patrick R. (author), Dekker, C. (author)Nuclear Pore Complexes (NPCs) regulate bidirectional transport between the nucleus and the cytoplasm. Intrinsically disordered FG-Nups line the NPC lumen and form a selective barrier, where transport of most proteins is inhibited whereas specific transporter proteins freely pass. The mechanism underlying selective transport through the NPC is...journal article 2021