LaserLaB - Molecular Biophysics

Research Output 1999 2019

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
brain
resolution cell
monkeys
posture
cortexes

Capturing the Continuous Complexity of Behavior in C. elegans

Ahamed, T., Costa, A. C. & Stephens, G. J., 2019, In : bioRxiv. p. 827535

Research output: Contribution to JournalArticleAcademic

worms
exponents
posture
locomotion
animals

Deconstruction of septin assembly

Szuba, A., 2019, 160 p.

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

Open Access
File

Distinct requirements for tail-anchored membrane protein biogenesis in escherichia coli

Peschke, M., Le Goff, M., Koningstein, G. M., Vischer, N. O., Abdel-Rehim, A., High, S., Van Ulsen, P. & Luirink, J., 1 Jan 2019, In : mBio. 10, 5, e01580-19.

Research output: Contribution to JournalArticleAcademicpeer-review

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

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., 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

Interrogating the essential bacterial cell division protein FtsQ with fragments using target immobilized NMR screening (TINS)

Glas, M., Eiso, A. B., Hollander, J., Siegal, G., Luirink, J. & de Esch, I., 1 Aug 2019, In : International Journal of Molecular Sciences. 20, 15, 3684.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
cell division
Cell Division
affinity
Screening
screening

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

Modelling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behaviour across species

Helms, S. J., Rozemuller, W. M., Costa, A. C., Avery, L., Stephens, G. J. & Shimizu, T. S., 30 Aug 2019, In : Journal of the Royal Society, Interface. 16, 157

Research output: Contribution to JournalArticleAcademicpeer-review

Exploratory Behavior
Phenotype
Caenorhabditis elegans

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

Real-Time Assembly of Viruslike Nucleocapsids Elucidated at the Single-Particle Level

Marchetti, M., Kamsma, D., Cazares Vargas, E., Hernandez García, A., Van Der Schoot, P., De Vries, R., Wuite, G. J. L. & Roos, W. H., 14 Aug 2019, In : Nano Letters. 19, 8, p. 5746-5753 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Nucleocapsid
assembly
Oligomers
Packaging
DNA

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

The Cell: Strong, Soft Matter

Mulla, Y., 2019, 152 p.

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

Open Access
File
2018

A brief introduction to single-molecule fluorescence methods

van den Wildenberg, S. M. J. L., Prevo, B. & Peterman, E. J. G., 2018, Single Molecule Analysis: Methods and Protocols. Humana Press Inc, p. 93-113 21 p. (Methods in Molecular Biology; vol. 1665).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Fluorescence Microscopy
Fluorescence
Fluorescence Polarization
Biological Science Disciplines
Energy Transfer

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 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Acoustic Force Spectroscopy (AFS): From single molecules to single cells

Kamsma, D., 2018, 188 p.

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

Open Access
File

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

Controlled Disturbance of Intraflagellar Transport in C. elegans Chemosensory Cilia Results in Changes of Ciliary Structure

Jona, M., Oswald, F., Girard, J., van Loo, J. & Peterman, E. J. G., 2 Feb 2018, In : Biophysical Journal. 114, 3, p. 655A-656A

Research output: Contribution to JournalMeeting AbstractAcademic

Direct Observation and Quantification of Protein Dynamics on Negatively-Supercoiled DNA

King, G. A., Burla, F., Peterman, E. J. G. & Wuite, G. J. L., 2 Feb 2018, In : Biophysical Journal. 114, 3, p. 168A-168A

Research output: Contribution to JournalMeeting AbstractAcademic

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

Ensemble and single-molecule dynamics of intraflagellar transport in C. elegans

Mijalkovic, J., 2018, 182 p.

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

Open Access
File

Exposing Chromosome Architecture and Mechanics Using Optical Manipulation and Fluorescence Microscopy

Meijering, A. E. C., Sarlos, K., Bizard, A. H., Acar, S., Venegas, A. B., Bhowmick, R., Liu, Y., Heller, I., Hickson, I., Peterman, E. J. G. & Wuite, G. J. L., 2 Feb 2018, In : Biophysical Journal. 114, 3, p. 446A-446A

Research output: Contribution to JournalMeeting AbstractAcademic

Fibrin structure and mechanics: A journey across scales

Vos, B. E., 2018, 218 p.

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

Open Access
File

Hyperstretching DNA

Schakenraad, K., Biebricher, A. S., Sebregts, M., ten Bensel, B., Peterman, E. J. G., Wuite, G. J. L., Storm, C., van der Schoot, P. & Heller, I., 2 Feb 2018, In : Biophysical Journal. 114, 3, p. 90A-90A

Research output: Contribution to JournalMeeting AbstractAcademic

Imaging the structure and the movement of the retina with scanning light ophthalmoscopy

Vienola, K. V., 2018, 117 p.

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

Open Access
File

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

Kinesin motor stepping challenged: The impact of traffic jams and temperature

Kushwaha, V. S., 2018, 140 p.

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

Open Access
File

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

On display: Autotransporter secretion and application

Van Ulsen, P., Zinner, K. M., Jong, W. S. P. & Luirink, J., 1 Sep 2018, In : FEMS Microbiology Letters. 365, 18, p. 1-10 10 p., fny165.

Research output: Contribution to JournalReview articleAcademicpeer-review

Membranes
Proteins
Secretory Pathway
Virulence Factors
Gram-Negative Bacteria

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 Analysis: Methods and Protocols

Peterman, E. (ed.), 2018, 2 ed. New York: Humana Press, Methods Mol Biol. 380 p. (Methods in molecular biology; vol. 1665)

Research output: Book / ReportBook editingAcademic

Molecules
Molecular biology
Cytology
Biophysics
Biochemistry

Single-molecule fluorescence microscopy in living Caenorhabditis elegans

van Krugten, J. & Peterman, E. J. G., 2018, Single Molecule Analysis: Methods and Protocols. Humana Press Inc, p. 145-154 10 p. (Methods in Molecular Biology; vol. 1665).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Caenorhabditis elegans
Fluorescence Microscopy
Cilia
Molecular Dynamics Simulation
Organelles

Single-molecule imaging of Escherichia coli transmembrane proteins

Varadajan, A., Oswald, F. & Bollen, Y. J. M., 2018, Methods in Molecular Biology. Peterman, E. (ed.). Humana Press Inc, Vol. 1665. p. 135-144 10 p. (Methods in Molecular Biology; vol. 1665).

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

Escherichia coli Proteins
Biological Phenomena
Cell Fusion
Gram-Negative Bacteria
Fluorescence Microscopy

Single-molecule measurements using acoustic force spectroscopy (AFS)

Kamsma, D. & Wuite, G. J. L., Jan 2018, Methods in Molecular Biology. New York, NY: Humana Press Inc, p. 341-351 11 p. (Methods in Molecular Biology; vol. 1665).

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

Acoustics
Spectrum Analysis

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