Academic Appointments

  • Basic Life Science Research Associate, Bioengineering

Honors & Awards

  • Long term cross-disciplinary fellowship, Human Frontier Science Program (2012)
  • Cum Laude graduate MSc Physics, Leiden University (2007)

All Publications

  • Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity. eLife Gurel, P. S., Kim, L. Y., Ruijgrok, P. V., Omabegho, T., Bryant, Z., Alushin, G. M. 2017; 6


    Despite extensive scrutiny of the myosin superfamily, the lack of high-resolution structures of actin-bound states has prevented a complete description of its mechanochemical cycle and limited insight into how sequence and structural diversification of the motor domain gives rise to specialized functional properties. Here we present cryo-EM structures of the unique minus-end directed myosin VI motor domain in rigor (4.6 Å) and Mg-ADP (5.5 Å) states bound to F-actin. Comparison to the myosin IIC-F-actin rigor complex reveals an almost complete lack of conservation of residues at the actin-myosin interface despite preservation of the primary sequence regions composing it, suggesting an evolutionary path for motor specialization. Additionally, analysis of the transition from ADP to rigor provides a structural rationale for force sensitivity in this step of the mechanochemical cycle. Finally, we observe reciprocal rearrangements in actin and myosin accompanying the transition between these states, supporting a role for actin structural plasticity during force generation by myosin VI.

    View details for PubMedID 29199952

  • Controllable molecular motors engineered from myosin and RNA. Nature nanotechnology Omabegho, T., Gurel, P. S., Cheng, C. Y., Kim, L. Y., Ruijgrok, P. V., Das, R., Alushin, G. M., Bryant, Z. 2017


    Engineering biomolecular motors can provide direct tests of structure-function relationships and customized components for controlling molecular transport in artificial systems 1 or in living cells 2 . Previously, synthetic nucleic acid motors 3-5 and modified natural protein motors 6-10 have been developed in separate complementary strategies to achieve tunable and controllable motor function. Integrating protein and nucleic-acid components to form engineered nucleoprotein motors may enable additional sophisticated functionalities. However, this potential has only begun to be explored in pioneering work harnessing DNA scaffolds to dictate the spacing, number and composition of tethered protein motors 11-15 . Here, we describe myosin motors that incorporate RNA lever arms, forming hybrid assemblies in which conformational changes in the protein motor domain are amplified and redirected by nucleic acid structures. The RNA lever arm geometry determines the speed and direction of motor transport and can be dynamically controlled using programmed transitions in the lever arm structure 7,9 . We have characterized the hybrid motors using in vitro motility assays, single-molecule tracking, cryo-electron microscopy and structural probing 16 . Our designs include nucleoprotein motors that reversibly change direction in response to oligonucleotides that drive strand-displacement 17 reactions. In multimeric assemblies, the controllable motors walk processively along actin filaments at speeds of 10-20 nm s-1. Finally, to illustrate the potential for multiplexed addressable control, we demonstrate sequence-specific responses of RNA variants to oligonucleotide signals.

    View details for PubMedID 29109539

  • Damping of Acoustic Vibrations of Single Gold Nanoparticles Optically Trapped in Water NANO LETTERS Ruijgrok, P. V., Zijlstra, P., Tchebotareva, A. L., Orrit, M. 2012; 12 (2): 1063-1069


    We combine ultrafast pump-probe spectroscopy with optical trapping to study homogeneous damping of the acoustic vibrations of single gold nanospheres (80 nm diameter) and nanorods (25 nm diameter by 60 nm length) in water. We find a significant particle-to-particle variation in damping times. Our results indicate that vibrational damping occurs not only by dissipation into the liquid, but also by damping mechanisms intrinsic to the particle. Our experiment opens the study of mechanisms of intrinsic mechanical dissipation in metals at frequencies 1-1000 GHz, a range that has been difficult to access thus far.

    View details for DOI 10.1021/nl204311q

    View details for Web of Science ID 000299967800090

    View details for PubMedID 22251064

  • Brownian Fluctuations and Heating of an Optically Aligned Gold Nanorod PHYSICAL REVIEW LETTERS Ruijgrok, P. V., Verhart, N. R., Zijlstra, P., Tchebotareva, A. L., Orrit, M. 2011; 107 (3)


    We present the first quantitative measurements of the torque exerted on a single gold nanorod in a polarized three-dimensional optical trap. We determined the torque both by observing the time-averaged orientation distribution and by measuring the dynamics of the rotational brownian fluctuations. The measurements are in good agreement with calculations, where the temperature profile around the hot nanorod gives rise to a reduced, effective viscosity. The maximum torque on a 60  nm×25  nm nanorod was 100  pN·nm, large enough to address single-molecule processes in soft and biological matter.

    View details for DOI 10.1103/PhysRevLett.107.037401

    View details for Web of Science ID 000292597400024

    View details for PubMedID 21838403

  • Making gold nanoparticles fluorescent for simultaneous absorption and fluorescence detection on the single particle level PHYSICAL CHEMISTRY CHEMICAL PHYSICS Gaiduk, A., Ruijgrok, P. V., Yorulmaz, M., Orrit, M. 2011; 13 (1): 149-153


    We demonstrate a simple way of making individual 20 nm gold nanoparticles fluorescent (with a fluorescence quantum yield of about 10(-6)) in glycerol. Gold NPs prepared in such a way have bright fluorescence for a long time under moderate excitation, and their fluorescence remains when the solvent is exchanged to water. We propose to use these nanoparticles as a calibration standard for simultaneous detection of fluorescence and absorption (by means of photothermal detection), and experimentally demonstrate the theoretically predicted shift in axial positions of these signals. Simultaneous absorption and fluorescence detection of such stable labels makes them attractive for multidimensional tracking and screening applications.

    View details for DOI 10.1039/c0cp01389g

    View details for Web of Science ID 000285099800017

    View details for PubMedID 21042602

  • Room-Temperature Detection of a Single Molecule's Absorption by Photothermal Contrast SCIENCE Gaiduk, A., Yorulmaz, M., Ruijgrok, P. V., Orrit, M. 2010; 330 (6002): 353-356


    So far, single-molecule imaging has predominantly relied on fluorescence detection. We imaged single nonfluorescent azo dye molecules in room-temperature glycerol by the refractive effect of the heat that they release in their environment upon intense illumination. This photothermal technique provides contrast for the absorbing objects only, irrespective of scattering by defects or roughness, with a signal-to-noise ratio of ~10 for a single molecule in an integration time of 300 milliseconds. In the absence of oxygen, virtually no bleaching event was observed, even after more than 10 minutes of illumination. In a solution saturated with oxygen, the average bleaching time was of the order of 1 minute. No blinking was observed in the absorption signal. On the basis of bleaching steps, we obtained an average absorption cross section of 4 angstroms(2) for a single chromophore.

    View details for DOI 10.1126/science.1195475

    View details for Web of Science ID 000282986700036

    View details for PubMedID 20947760

  • Spontaneous emission of a nanoscopic emitter in a strongly scattering disordered medium OPTICS EXPRESS Ruijgrok, P. V., Wuest, R., Rebane, A. A., Renn, A., Sandoghdar, V. 2010; 18 (6): 6360-6365


    Fluorescence lifetimes of nitrogen-vacancy color centers in individual diamond nanocrystals were measured at the interface between a glass substrate and a strongly scattering medium. Comparison of the results with values recorded from the same nanocrystals at the glass-air interface revealed fluctuations of fluorescence lifetimes in the scattering medium. After discussing a range of possible systematic effects, we attribute the observed lengthening of the lifetimes to the reduction of the local density of states. Our approach is very promising for exploring the strong threedimensional localization of light directly on the microscopic scale.

    View details for Web of Science ID 000276002500109

    View details for PubMedID 20389659

  • Probing the acoustic vibrations of single gold nanoparticle by ultrashort laser pulses Laser Photonics Rev. Tcheborateva AL, Ruijgrok PV, Zijlstra P, Orrit M 2010; 4 (4): 581-597
  • Detection limits in photothermal microscopy Chem. Sci. Gaiduk A, Ruijgrok PV, Yorulmaz M, Orrit M 2010; 1 (3): 343-350
  • Acoustic and Optical Modes of Single Dumbbells of Gold Nanoparticles CHEMPHYSCHEM Tchebotareva, A. L., van Dijk, M. A., Ruijgrok, P. V., Fokkema, V., Hesselberth, M. H., Lippitz, M., Orrit, M. 2009; 10 (1): 111-114

    View details for DOI 10.1002/cphc.200800289

    View details for Web of Science ID 000262870500015

    View details for PubMedID 18688828