LaserLaB - Molecular Biophysics

Research Output 1999 2019

2018

The Soft Side of Extracellular Vesicles

Sorkin, R., Huisjes, R., Boskovic, F., Vorselen, D., Pignatelli, S., Ofir-Birin, Y., Leal, J. K. F., Schiller, J., Roos, W. H., Bosman, G., Regev-Rudzki, N., Schiffelers, R. M. & Wuite, G. J. L., 2 Feb 2018, In : Biophysical Journal. 114, 3, p. 562A-562A

Research output: Contribution to JournalMeeting AbstractAcademic

Towards Dense Object Tracking in a 2D Honeybee Hive

Bozek, K., Hebert, L., Mikheyev, A. S. & Stephens, G. J., 14 Dec 2018, Proceedings - 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, CVPR 2018. IEEE Computer Society, p. 4185-4193 9 p. 8578538. (IEEE/CVF Conference on Computer Vision and Pattern Recognition).

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Neural networks
Video recording
Network architecture
Labeling
Image analysis

Two distinct conformational states define the interaction of human RAD51-ATP with single-stranded DNA

Brouwer, I., Moschetti, T., Candelli, A., Garcin, E. B., Modesti, M., Pellegrini, L., Wuite, G. J. L. & Peterman, E. J. G., Apr 2018, In : EMBO Journal. 37, 7, p. 1-26 26 p., e98162.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Single-Stranded DNA
Adenosine Triphosphate
DNA
Molecules
Nucleoproteins

Viruses under the loop: Their assembly process and capsid stiffness

van Rosmalen, M. G. M., 2018, 198 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Viscoelastic properties of vimentin originate from nonequilibrium conformational changes

Block, J., Witt, H., Candelli, A., Danes, J. C., Peterman, E. J. G., Wuite, G. J. L., Janshoff, A. & Köster, S., 13 Jun 2018, In : Science advances. 4, 6, eaat1161.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
filaments
materials science
durability
helices
folding
2017

Cell volume change through water efflux impacts cell stiffness and stem cell fate

Guo, M., Pegoraro, A. F., Mao, A., Zhou, E. H., Arany, P. R., Han, Y., Burnette, D. T., Jensen, M. H., Kasza, K. E., Moore, J. R., Mackintosh, F. C., Fredberg, J. J., Mooney, D. J., Lippincott-Schwartz, J. & Weitz, D. A., 10 Oct 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 41, p. E8618-E8627

Research output: Contribution to JournalArticleAcademicpeer-review

Cell Size
Stem Cells
Water
Osmotic Pressure
Cell Biology

Collective Dynamics of Cooperating Homodimeric and Heterotrimeric Kinesin-2 Motor Proteins Unraveled

Kushwaha, V. S., Miedema, D. M., Denisov, D. V., Acar, S., Nienhuis, B., Schall, P. & Peterman, E. J. G., 3 Feb 2017, In : Biophysical Journal. 112, 3, p. 273A-273A Supplement 1.

Research output: Contribution to JournalMeeting AbstractAcademic

Competition between Bending and Internal Pressure Governs the Mechanics of Fluid Nanovesicles

Vorselen, D., MacKintosh, F. C., Roos, W. H. & Wuite, G. J. L., Mar 2017, In : ACS Nano. 11, 3, p. 2628-2636

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Correlation Imaging Reveals Specific Crowding Dynamics of Kinesin Motor Proteins

Miedema, D. M., Kushwaha, V. S., Denisov, D. V., Acar, S., Nienhuis, B., Peterman, E. J. G. & Schall, P., 16 Nov 2017, In : Physical Review X. 7, 4, 41037.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Corrigendum: Sliding sleeves of XRCC4-XLF bridge DNA and connect fragments of broken DNA

Brouwer, I., Sitters, G., Candelli, A., Heerema, S. J., Heller, I., Melo de, A. J., Zhang, H., Normanno, D., Modesti, M., Peterman, E. J. G. & Wuite, G. J. L., 30 Mar 2017, In : Nature. 543, 7647, p. 742

Research output: Contribution to JournalArticleAcademicpeer-review

Dual wavelength Scanning Light Ophthalmoscope with concentric circle scanning

Damodaran, M., Vienola, K. V., Vermeer, K. A. & De Boer, J. F., Jun 2017, In : Investigative ophthalmology & visual science. 58, 8, p. 3132 1 p.

Research output: Contribution to JournalMeeting AbstractAcademic

Effect of Cholesterol on the Stability and Lubrication Efficiency of Phosphatidylcholine Surface Layers

Sorkin, R., Kampf, N. & Klein, J., 1 Aug 2017, In : Langmuir. 33, 30, p. 7459-7467 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Cholesterol
cholesterol
lubrication
Phosphatidylcholines
Lubrication

Ensemble and single-molecule dynamics of IFT dynein in Caenorhabditis elegans cilia

Mijalkovic, J., Prevo, B., Oswald, F., Mangeol, P. J. J. & Peterman, E. J. G., 23 Feb 2017, In : Nature Communications. 8, p. 14591

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Dyneins
Cilia
Caenorhabditis elegans
Molecules
locomotion

Exploiting ecology in drug pulse sequences in favour of population reduction

Bauer, M., Graf, I. R., Ngampruetikorn, V., Stephens, G. J. & Frey, E., Sep 2017, In : PLoS Computational Biology. 13, 9

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Force percolation of contractile active gels

Alvarado, J., Sheinman, M., Sharma, A., MacKintosh, F. C. & Koenderink, G. H., 2017, In : Soft Matter. 13, 34, p. 5624-5644 21 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Gels
gels
myosins
Myosins
Actins

How to switch the motor on: RNA polymerase initiation steps at the single-molecule level

Marchetti, M., Malinowska, A., Heller, I. & Wuite, G. J. L., Jul 2017, In : Protein Science. 26, 7, p. 1303-1313

Research output: Contribution to JournalArticleAcademicpeer-review

Human RAD52 Captures and Holds DNA Strands, Increases DNA Flexibility, and Prevents Melting of Duplex DNA: Implications for DNA Recombination

Brouwer, I., Zhang, H., Candelli, A., Normanno, D., Peterman, E. J. G., Wuite, G. J. L. & Modesti, M., 21 Mar 2017, In : Cell Reports. 18, 12, p. 2845-2853

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Hyperstretching DNA

Schakenraad, K., Biebricher, A. S., Sebregts, M., ten Bensel, B., Peterman, E. J. G., Wuite, G. J. L., Heller, I., Storm, C. & van der Schoot, P., 19 Dec 2017, In : Nature Communications. 8, 2197.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Imaging membrane-protein diffusion in living bacteria

Varadarajan, A., 2017, 189 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Intracellular transport studied with dynamic single-molecule super-resolution microscopy

Oswald, F., 2017, 173 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Intraflagellar transport: mechanisms of motor action, cooperation, and cargo delivery

Prevo, B., Scholey, J. M. & Peterman, E. J. G., Sep 2017, In : The FEBS Journal. 284, 18, p. 2905-2931

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Knotty Problems during Mitosis: Mechanistic Insight into the Processing of Ultrafine DNA Bridges in Anaphase

Sarlós, K., Biebricher, A., Petermann, E. J. G., Wuite, G. J. L. & Hickson, I. D., 2017, In : Cold Spring Harbor symposia on quantitative biology. 82, p. 187-195 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Anaphase
Mitosis
DNA
Processing
Chromatids

Nonlinear Loading-Rate-Dependent Force Response of Individual Vimentin Intermediate Filaments to Applied Strain

Block, J., Witt, H., Candelli, A., Peterman, E. J. G., Wuite, G. J. L., Janshoff, A. & Koester, S., 24 Jan 2017, In : Physical Review Letters. 118, 4, 48101.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Order and disorder in the extracellular matrix

van der Horst, A. & Wuite, G. J. L., 1 Jan 2017, The Oxford Handbook of Soft Condensed Matter. Oxford University Press., p. 475-496 22 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

disorders
matrices
collagens
elastin
mechanical properties

Probing DNA-DNA Interactions with a Combination of Quadruple-Trap Optical Tweezers and Microfluidics

Brouwer, I., King, G. A., Heller, I., Biebricher, A. S., Peterman, E. J. G. & Wuite, G. J. L., 2017, Methods in Molecular Biology. Walker, J. M. (ed.). Humana Press, Methods Mol Biol, Vol. 1486. p. 275-293 19 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Optical Tweezers
Microfluidics
DNA
Proteins
Buffers

Probing the mechanical stability of bridged DNA-H-NS protein complexes by single-molecule AFM pulling

Liang, Y., van der Valk, R. A., Dame, R. T., Roos, W. H. & Wuite, G. J. L., 10 Nov 2017, In : Scientific Reports. 7, 15275.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Programming the mechanics of cohesive fiber networks by compression

Vos, B. E., Liebrand, L. C., Vahabi, M., Biebricher, A., Wuite, G. J. L., Peterman, E. J. G., Kurniawan, N. A., MacKintosh, F. C. & Koenderink, G. H., 21 Dec 2017, In : Soft Matter. 13, 47, p. 8886-8893

Research output: Contribution to JournalArticleAcademicpeer-review

Recent Advances in Biological Single-Molecule Applications of Optical Tweezers and Fluorescence Microscopy

Hashemi Shabestari, M., Meijering, A. E. C., Roos, W. H., Wuite, G. J. L. & Peterman, E., 2017, Single-Molecule Enzymology: Nanomechanical Manipulation and Hybrid Methods. Elsevier, Vol. 582. p. 85-119

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Optical tweezers
Fluorescence microscopy
Molecules
Biomolecules
Biological systems

Single-molecule observation of DNA compaction by meiotic protein SYCP3

Syrjanen, J. L., Heller, I., Candelli, A., Davies, O. R., Peterman, E. J. G., Wuite, G. J. L. & Pellegrini, L., 13 Mar 2017, In : eLife. 6

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

SRP, FtsY, DnaK and YidC Are Required for the Biogenesis of the E. coli Tail-Anchored Membrane Proteins DjlC and Flk

Peschke, M., Le Goff, M., Koningstein, G. M., Karyolaimos, A., de Gier, J. W., van Ulsen, P. & Luirink, J., 1 Jan 2017, (Accepted/In press) In : Journal of Molecular Biology.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Signal Recognition Particle
Membrane Proteins
Escherichia coli
Membranes
Hydrophobic and Hydrophilic Interactions

Super-Resolution Imaging of Unlabeled Proteins on DNA

Meijering, A. E. C., Biebricher, A. S., Peterman, E. J. G., Wuite, G. J. L. & Heller, I., 3 Feb 2017, In : Biophysical Journal. 112, 3, p. 20A-20A

Research output: Contribution to JournalMeeting AbstractAcademic

Supported Planar Mammalian Membranes as Models of in Vivo Cell Surface Architectures

Liu, H-Y., Grant, H., Hsu, H-L., Sorkin, R., Boskovic, F., Wuite, G. & Daniel, S., 18 Oct 2017, In : ACS Applied Materials and Interfaces. 9, 41, p. 35526-35538

Research output: Contribution to JournalArticleAcademicpeer-review

Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity

Hoekstra, T. P., Depken, M., Lin, S-N., Cabanas-Danes, J., Gross, P., Dame, R. T., Peterman, E. J. G. & Wuite, G. J. L., 28 Feb 2017, In : Biophysical Journal. 112, 4, p. 575-583

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Th17-mediated cross protection against pneumococcal carriage by vaccination with a variable antigen

Kuipers, K., Jong, W. S. P., van der Gaast-de Jongh, C. E., Houben, D., van Opzeeland, F., Simonetti, E., van Selm, S., de Groot, R., Koenders, M. I., Azarian, T., Pupo, E., van der Ley, P., Langereis, J. D., Zomer, A., Luirink, J. & de Jonge, M. I., 1 Jan 2017, In : Infection and Immunity. 85, 10, e00281-17.

Research output: Contribution to JournalArticleAcademicpeer-review

Cross Protection
Vaccination
Vaccines
Antigens
Salmonella enterica

The Interplay between a Bacterial Chromatin Protein and DNA Polymerase

Lin, S-N., Dame, R. T. & Wuite, G. J. L., 3 Feb 2017, In : Biophysical Journal. 112, 3, p. 513A-513A

Research output: Contribution to JournalMeeting AbstractAcademic

Turning Around at the Tip: Single-Molecule Dynamics of Intraflagellar Transport in C-elegans Chemosensory Cilia

Mijalkovic, J., van Krugten, J., Oswald, F., Acar, S. & Peterman, E. J., 3 Feb 2017, In : Biophysical Journal. 112, 3, p. 262A-262A

Research output: Contribution to JournalMeeting AbstractAcademic

Understanding Adenovirus maturation: A nanomechanics approach

Denning, D., Bennett, S., Mullen, T., Moyer, C., Wuite, G. J., Nemerow, G. & Roos, W. H., Jul 2017, In : European Biophysics Journal. 46, p. S184-S184 1 p., Supplement 1.

Research output: Contribution to JournalMeeting AbstractAcademic

Versatile Quadruple-Trap Optical Tweezers for Dual DNA Experiments

Heller, I., Laurens, N., Vorselen, D., Broekmans, O. D., Biebricher, A. S., King, G. A., Brouwer, I., Wuite, G. J. L. & Peterman, E. J. G., 2017, In : Methods in Molecular Biology. 1486, p. 257-272 16 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Optical Tweezers
DNA
Molecular Probes
Microfluidics
Fluorescence Microscopy

Vertex-Specific Proteins pUL17 and pUL25 Mechanically Reinforce Herpes Simplex Virus Capsids

Snijder, J., Radtke, K., Anderson, F., Scholtes, L., Corradini, E., Baines, J., Heck, A. J. R., Wuite, G. J. L., Sodeik, B. & Roos, W. H., Jun 2017, In : Journal of Virology. 91, 12, UNSP e00123-17.

Research output: Contribution to JournalArticleAcademicpeer-review

2016

A Combined Imaging and Force Spectroscopy Approach Reveals the Material Properties of Viral Nanoparticles

Denning, D., Wuite, G. J. L. & Roos, W. H., 2016, In : Biophysical Journal. 110, 3, p. 500A-500A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Acoustic Force Spectroscopy: An Instrument to Perform Highly Parallel Single Molecule Measurements

Sitters, G., Oswald, F., Kamsma, D., Langeveld, J., Peutz, W., Peterman, E. J. G., Wuite, G. J. L. & Heyning, O. T., 2016, In : Biophysical Journal. 110, 3, p. 516A-516A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Assembly and Mechanical Properties of the Cargo-Free and Cargo Loaded Bacterial Nanocompartment Encapsulin

Snijder, J., Kononova, O., Barbu, I. M., Uetrecht, C., Rurup, W. F., Koay, M. S. T., Cornelissen, J. J. L. M., Roos, W. H., Barsegov, V., Wuite, G. J. L. & Heck, A. J. R., 2016, In : Biomacromolecules. 17, 8, p. 2522-2529

Research output: Contribution to JournalArticleAcademicpeer-review

Viruses
Mechanical properties
Enzymes
Proteins
Molecular modeling
Open Access
Atomic Force Microscopy
Virion
Virology
Capsid
Observation

Bias, belief, and consensus: Collective opinion formation on fluctuating networks

Ngampruetikorn, V. & Stephens, G. J., 18 Nov 2016, In : Physical Review E. 2016, 94, p. 052312

Research output: Contribution to JournalArticleAcademicpeer-review

Broken detailed balance at mesoscopic scales in active biological systems

Battle, C., Broedersz, C. P., Fakhri, N., Geyer, V. F., Howard, J., Schmidt, C. F. & MacKintosh, F. C., 2016, In : Science. 352, 6285, p. 604-607

Research output: Contribution to JournalArticleAcademicpeer-review

thermodynamic equilibrium
probes
configurations
cells

Broken Detailed Balance of Filament Dynamics in Active Networks

Gladrow, J., Fakhri, N., MacKintosh, F. C., Schmidt, C. F. & Broedersz, C. P., 2016, In : Physical Review Letters. 116, 24, 248301.

Research output: Contribution to JournalArticleAcademicpeer-review

filaments
myosins
probes
biopolymers
coupled modes

Comment on "Anomalous Discontinuity at the Percolation Critical Point of Active Gels" Reply

Sheinman, M., Sharma, A. & MacKintosh, F. C., 2016, In : Physical Review Letters. 116, 18, 189802.

Research output: Contribution to JournalArticleAcademicpeer-review

Controlled tip wear on high roughness surfaces yields gradual broadening and rounding of cantilever tips

Vorselen, D., Kooreman, E. S., Wuite, G. J. L. & Roos, W. H., 11 Nov 2016, In : Scientific Reports. 6, 36972.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Critical behaviour in the nonlinear elastic response of hydrogels

Dennison, M., Jaspers, M., Kouwer, P. H. J., Storm, C., Rowan, A. E. & MacKintosh, F. C., 2016, In : Soft Matter. 12, 33, p. 6995-7004

Research output: Contribution to JournalArticleAcademicpeer-review

Hydrogels
Shear stress
Gels
Biopolymers
Polymers

Detection and Mechanical Characterization of Small Multilamellar Vesicles using Atomic Force Microscopy

Marchetti, M., Vorselen, D., Roos, W. H. & Wuite, G. J. L., 2016, In : Biophysical Journal. 110, 3, p. 73A-73A-73A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access