LaserLaB - Molecular Biophysics

Research Output 1999 2019

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2019

Adaptive, locally linear models of complex dynamics

Costa, A. C., Ahamed, T. & Stephens, G. J., 29 Jan 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 5, p. 1501-1510 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Caenorhabditis elegans
Linear Models
Space Simulation
Visual Cortex
Posture

Inhibition of autotransporter biogenesis by small molecules

Steenhuis, M., Abdallah, A. M., de Munnik, S. M., Kuhne, S., Sterk, G. J., van den Berg van Saparoea, B., Westerhausen, S., Wagner, S., van der Wel, N. N., Wijtmans, M., van Ulsen, P., Jong, W. S. P. & Luirink, J., 1 Jul 2019, In : Molecular Microbiology. 112, 1, p. 81-98 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Membrane Proteins
Virulence Factors
Libraries
Hemoglobins
Peptide Hydrolases

Isoniazid bactericidal activity involves electron transport chain perturbation

Zeng, S., Soetaert, K., Ravon, F., Vandeput, M., Bald, D., Kauffmann, J. M., Mathys, V., Wattiez, R. & Fontaine, V., 1 Mar 2019, In : Antimicrobial Agents and Chemotherapy. e01841-18.

Research output: Contribution to JournalArticleAcademicpeer-review

Isoniazid
Electron Transport
Adenosine Triphosphate
Electron Transport Complex IV
NADH Dehydrogenase

Maturation of adenovirus primes the protein nano-shell for successful endosomal escape

Denning, D., Bennett, S., Mullen, T., Moyer, C., Vorselen, D., Wuite, G. J. L., Nemerow, G. & Roos, W. H., 7 Mar 2019, In : Nanoscale. 11, 9, p. 3799-3803 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

DNA
Genes
Fatigue of materials
Proteins
Medical nanotechnology

Origin of Slow Stress Relaxation in the Cytoskeleton

Mulla, Y., Mackintosh, F. C. & Koenderink, G. H., 29 May 2019, In : Physical Review Letters. 122, 21, 218102.

Research output: Contribution to JournalArticleAcademicpeer-review

biopolymers
stress relaxation
rheology
residual stress
nonlinearity

Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA

Backer, A. S., Biebricher, A. S., King, G. A., Wuite, G. J. L., Heller, I. & Peterman, E. J. G., 22 Mar 2019, In : Science advances. 5, 3, p. 1-11 11 p., eaav1083.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
deoxyribonucleic acid
microscopy
polarization
molecules
biotechnology
2018

Acetylation and phosphorylation of human TFAM regulate TFAM-DNA interactions via contrasting mechanisms

Shabestari, M. H., King, G. A., Taris, K-K. H., Pandey, A. K., Venkatesh, S., Thilagavathi, J., Singh, K., Koppisetti, R. K., Temiakov, D., Roos, W. H., Suzuki, C. K. & Wuite, G. J. L., 20 Apr 2018, In : Nucleic Acids Research. 46, 7, p. 3633-3642

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Adaptive, locally-linear models of complex dynamics (preprint)

Costa, A. C., Ahamed, T. & Stephens, G. J., 25 Jul 2018, In : arXiv preprint arXiv:1501.03933.

Research output: Contribution to JournalArticleAcademic

File
brain
posture
eigenvalue
bifurcation
nematode

Adaptive optics via self-interference digital holography for non-scanning three-dimensional imaging in biological samples

Man, T., Wan, Y., Yan, W., Wang, X. H., Peterman, E. J. G. & Wang, D., 1 Jun 2018, In : Biomedical Optics Express. 9, 6, p. 2614-2626 13 p., #326210.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Holography
Three-Dimensional Imaging
adaptive optics
holography
aberration

A polarized view on DNA under tension

Van Mameren, J., Vermeulen, K., Wuite, G. J. L. & Peterman, E. J. G., 28 Mar 2018, In : Journal of Chemical Physics. 148, 12, 123306.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
deoxyribonucleic acid
DNA
Coloring Agents
dyes
Fluorescence microscopy

A single point mutation in precursor protein VI doubles the mechanical strength of human adenovirus

van Rosmalen, M. G. M., Nemerow, G. R., Wuite, G. J. L. & Roos, W. H., Jun 2018, In : Journal of Biological Physics. 44, 2, p. 119-132 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
adenoviruses
Human Adenoviruses
Protein Precursors
Capsid
mutations

Atomic force microscopy-based mechanobiology

Krieg, M., Fläschner, G., Alsteens, D., Gaub, B. M., Roos, W. H., Wuite, G. J. L., Gaub, H. E., Gerber, C., Dufrêne, Y. F. & Müller, D. J., 1 Nov 2018, In : Nature Reviews Physics. 1, January, p. 41-57 17 p.

Research output: Contribution to JournalArticleAcademicpeer-review

biophysics
atomic force microscopy
mechanical properties
microscopy
fluorescence emission spectroscopy

Comparing autotransporter β-domain configurations for their capacity to secrete heterologous proteins to the cell surface

Jong, W. S. P., Schillemans, M., ten Hagen-Jongman, C. M., Luirink, J. & van Ulsen, P., 7 Feb 2018, In : PLoS ONE. 13, 2, e0191622.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
IgA-specific serine endopeptidase
recombinant proteins
Membrane Proteins
Recombinant Proteins
Membranes

Display of recombinant proteins on bacterial outer membrane vesicles by using protein ligation

van den Berg van Saparoea, H. B., Houben, D., de Jonge, M. I., Jong, W. S. P. & Luirink, J., Apr 2018, In : Applied and Environmental Microbiology. 84, 8, p. 1-17 17 p., e02567-17.

Research output: Contribution to JournalArticleAcademicpeer-review

hemoglobin
vesicle
Recombinant Proteins
recombinant proteins
Ligation

Effect of dsDNA on the Assembly Pathway and Mechanical Strength of SV40 VP1 Virus-like Particles

van Rosmalen, M. G. M., Li, C., Zlotnick, A., Wuite, G. J. L. & Roos, W. H., 6 Nov 2018, In : Biophysical Journal. 115, 9, p. 1656-1665 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Simian virus 40
Virion
DNA Viruses
DNA
Buffers

Immunization with Skp delivered on outer membrane vesicles protects mice against enterotoxigenic Escherichia coli CHALLENGE

Hays, M. P., Houben, D., Yang, Y., Luirink, J. & Hardwidge, P. R., 1 May 2018, In : Frontiers in Cellular and Infection Microbiology. 8, MAY, 132.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Enterotoxigenic Escherichia coli
Immunization
Glutathione Transferase
Membranes
Antigens

Interplay between Ciliary Ultrastructure and IFT-Train Dynamics Revealed by Single-Molecule Super-resolution Imaging

Oswald, F., Prevo, B., Acar, S. & Peterman, E. J. G., 2 Oct 2018, In : Cell Reports. 25, 1, p. 224-235 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Cilia
Axoneme
Imaging techniques
Molecules
Wild Animals

In vivo retinal imaging for fixational eye motion detection using a high-speed digital micromirror device (DMD)-based ophthalmoscope

Vienola, K. V., Damodaran, M., Braaf, B., Vermeer, K. A. & de Boer, J. F., 1 Feb 2018, In : Biomedical Optics Express. 9, 2, p. 591-602 12 p., #313640.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Ophthalmoscopes
high speed
Equipment and Supplies
retina
Artifacts

Ionophoric effects of the antitubercular drug bedaquiline

Hards, K., McMillan, D. G. G., Schurig-Briccio, L. A., Gennis, R. B., Lill, H., Bald, D. & Cook, G. M., 10 Jul 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 28, p. 7326-7331 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

File
bedaquiline
Antitubercular Agents
Adenosine Triphosphate
Escherichia coli
Proton-Motive Force

Multilamellar nanovesicles show distinct mechanical properties depending on their degree of lamellarity

Vorselen, D., Marchetti, M., López-Iglesias, C., Peters, P. J., Roos, W. H. & Wuite, G. J. L., 21 Mar 2018, In : Nanoscale. 10, 11, p. 5318-5324 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Atomic force microscopy
Mechanical properties
Unilamellar Liposomes
Lipid bilayers
Nanoindentation

Nanomechanics of Extracellular Vesicles Reveals Vesiculation Pathways

Sorkin, R., Huisjes, R., Bošković, F., Vorselen, D., Pignatelli, S., Ofir-Birin, Y., Freitas Leal, J. K., Schiller, J., Mullick, D., Roos, W. H., Bosman, G., Regev-Rudzki, N., Schiffelers, R. M. & Wuite, G. J. L., 27 Sep 2018, In : Small. 14, 39, p. 1-8 8 p., 1801650.

Research output: Contribution to JournalArticleAcademicpeer-review

Nanomechanics
Lipids
Proteins
Blood
Erythrocytes

Normal stresses in semiflexible polymer hydrogels

Vahabi, M., Vos, B. E., De Cagny, H. C. G., Bonn, D., Koenderink, G. H. & Mackintosh, F. C., 28 Mar 2018, In : Physical Review E. 97, 3, p. 1-11 11 p., 032418.

Research output: Contribution to JournalArticleAcademicpeer-review

Hydrogel
fibrin
Polymers
gels
polymers

Probing cellular mechanics with acoustic force spectroscopy

Sorkin, R., Bergamaschi, G., Kamsma, D., Brand, G., Dekel, E., Ofir-Birin, Y., Rudik, A., Gironella, M., Ritort, F., Regev-Rudzki, N., Roos, W. H. & Wuite, G. J. L., 8 Aug 2018, In : Molecular Biology of the Cell. 29, 16, p. 2005-2011 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Mechanics
Acoustics
Spectrum Analysis
Erythrocytes
Biophysics

Quantifying Local Molecular Tension Using Intercalated DNA Fluorescence

King, G. A., Biebricher, A. S., Heller, I., Peterman, E. J. G. & Wuite, G. J. L., 11 Apr 2018, In : Nano Letters. 18, 4, p. 2274-2281 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
DNA
deoxyribonucleic acid
Fluorescence
fluorescence
Catenated DNA

Reconstitution of anaphase DNA bridge recognition and disjunction

Sarlós, K., Biebricher, A. S., Bizard, A. H., Bakx, J. A. M., Ferreté-Bonastre, A. G., Modesti, M., Paramasivam, M., Yao, Q., Peterman, E. J. G., Wuite, G. J. L. & Hickson, I. D., 3 Sep 2018, In : Nature Structural and Molecular Biology. 25, 9, p. 868-876 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Anaphase
DNA
Chromosome Segregation
Proteins
Chromatids

Single-Cell Acoustic Force Spectroscopy: Resolving Kinetics and Strength of T Cell Adhesion to Fibronectin

Kamsma, D., Bochet, P., Oswald, F., Alblas, N., Goyard, S., Wuite, G. J. L., Peterman, E. J. G. & Rose, T., 11 Sep 2018, In : Cell Reports. 24, 11, p. 3008-3016 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
T-cells
Cell adhesion
Fibronectins
Acoustics
Cell Adhesion

Single-Molecule Turnarounds of Intraflagellar Transport at the C. elegans Ciliary Tip

Mijalkovic, J., van Krugten, J., Oswald, F., Acar, S. & Peterman, E. J. G., 13 Nov 2018, In : Cell Reports. 25, 7, p. 1701-1707.e2 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Cilia
Dyneins
Fluorescence microscopy
Fluorescence Microscopy
Microtubules

Structural analysis of the interaction between the bacterial cell division proteins FTSQ and FTSB

Kureisaite-Ciziene, D., Varadajan, A., McLaughlin, S. H., Glas, M., Silva, A. M., Luirink, R., Mueller, C., Blaauwen, T. D., Grossmann, T. N., Luirink, J. & Löwe, J., 11 Sep 2018, In : mBio. 9, 5, p. 1-17 17 p., e01346-18.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Cell Division
Proteins
Bacteria
Periplasm
Membrane Proteins

The anti-mycobacterial activity of the cytochrome bcc inhibitor Q203 can be enhanced by small-molecule inhibition of cytochrome bd.

Lu, P., Asseri, A. H. O., Kremer, M., Maaskant, J., Ummels, R., Lill, H. & Bald, D., 8 Feb 2018, In : Scientific Reports. 8

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Cytochromes
Electron Transport
Mycobacterium tuberculosis
Energy Metabolism
Mycobacterium smegmatis

The fluid membrane determines mechanics of erythrocyte extracellular vesicles and is softened in hereditary spherocytosis

Vorselen, D., van Dommelen, S. M., Sorkin, R., Piontek, M. C., Schiller, J., Döpp, S. T., Kooijmans, S. A. A., van Oirschot, B. A., Versluijs, B. A., Bierings, M. B., van Wijk, R., Schiffelers, R. M., Wuite, G. J. L. & Roos, W. H., 23 Nov 2018, In : Nature Communications. 9, p. 1-9 9 p., 4960.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Hereditary Spherocytosis
erythrocytes
Mechanics
Blood
Erythrocytes

The Role of Network Architecture in Collagen Mechanics

Jansen, K. A., Licup, A. J., Sharma, A., Rens, R., MacKintosh, F. C. & Koenderink, G. H., 5 Jun 2018, In : Biophysical Journal. 114, 11, p. 2665-2678 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Mechanics
Collagen
Polymerization
Extracellular Matrix
Rheology

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

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

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

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

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

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

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