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2019

Lipid-Conjugated Rigidochromic Probe Discloses Membrane Alteration in Model Cells of Krabbe Disease

Abbandonato, G., Storti, B., Tonazzini, I., Stöckl, M., Subramaniam, V., Montis, C., Nifosì, R., Cecchini, M., Signore, G. & Bizzarri, R., 5 Feb 2019, In : Biophysical Journal. 116, 3, p. 477-486 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Psychosine
Globoid Cell Leukodystrophy
Lipids
Membranes
Cell Membrane
2018

Hydrophobic-Interaction-Induced Stiffening of α -Synuclein Fibril Networks

Semerdzhiev, S. A., Lindhoud, S., Stefanovic, A., Subramaniam, V., Van Der Schoot, P. & Claessens, M. M. A. E., 17 May 2018, In : Physical Review Letters. 120, 20, p. 1-6 6 p., 208102.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
stiffening
interactions
elastic properties
enthalpy
deposits

Orthogonal supramolecular protein assembly on patterned bifunctional surfaces

Wasserberg, D., Cabanas-Danés, J., Subramaniam, V., Huskens, J. & Jonkheijm, P., 14 Feb 2018, In : Chemical Communications. 54, 13, p. 1615-1618 4 p.

Research output: Contribution to JournalArticleAcademicpeer-review

File
His-His-His-His-His-His
Proteins
Peptides
red fluorescent protein
Open Access
File
Synucleins
Fluorescence
Binding Sites
Amyloid
thioflavin T

Spermine induced reversible collapse of deoxyribonucleic acid-bridged nanoparticle-based assemblies

Göeken, K. L., Schasfoort, R. B. M., Subramaniam, V. & Gill, R., Jan 2018, In : Nano Research. 11, 1, p. 383–396 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Spermine
DNA
Nanoparticles
Surface plasmon resonance
Geometry
2017

Alpha-Synuclein Disease Mutations Are Structurally Defective and Locally Affect Membrane Binding

Robotta, M., Cattani, J., Martins, J. C., Subramaniam, V. & Drescher, M., 20 Mar 2017, In : Journal of the American Chemical Society.

Research output: Contribution to JournalArticleAcademicpeer-review

alpha-Synuclein
Parkinson Disease
Mutation
Membranes
Intrinsically Disordered Proteins

Controlling Protein Surface Orientation by Strategic Placement of Oligo-Histidine Tags

Wasserberg, D., Cabanas-Danés, J., Prangsma, J., O'Mahony, S., Cazade, P. A., Tromp, E., Blum, C., Thompson, D., Huskens, J., Subramaniam, V. & Jonkheijm, P., 26 Sep 2017, In : ACS Nano. 11, 9, p. 9068-9083 16 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
His-His-His-His-His-His
histidine
Histidine
Membrane Proteins
proteins

C-Terminal Truncated α-Synuclein Fibrils Contain Strongly Twisted β-Sheets

Iyer, A., Roeters, S. J., Kogan, V., Woutersen, S., Claessens, M. M. A. E. & Subramaniam, V., 1 Nov 2017, In : Journal of the American Chemical Society. 139, 43, p. 15392-15400 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
Amyloid
Circular Dichroism
Polymorphism
Parkinson Disease

Direct Visualization of Model Membrane Remodeling by α-Synuclein Fibrillization

Chaudhary, H., Subramaniam, V. & Claessens, M. M. A. E., 20 Jun 2017, In : ChemPhysChem. 18, 12, p. 1620-1626 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
Visualization
membranes
Membranes
lipids

Distinct Mechanisms Determine α-Synuclein Fibril Morphology during Growth and Maturation

Sidhu, A., Segers-Nolten, I., Raussens, V., Claessens, M. M. A. E. & Subramaniam, V., 15 Mar 2017, In : ACS Chemical Neuroscience. 8, 3, p. 538-547 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
Polymorphism
Amyloid
Growth
Assays

Evidence for Intramolecular Antiparallel Beta-Sheet Structure in Alpha-Synuclein Fibrils from a Combination of Two-Dimensional Infrared Spectroscopy and Atomic Force Microscopy

Roeters, S. J., Iyer, A., Pletikapić, G., Kogan, V., Subramaniam, V. & Woutersen, S., 23 Jan 2017, In : Scientific Reports. 7, p. 41051

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
alpha-Synuclein
Atomic Force Microscopy
Spectrum Analysis
Buffers
Osmolar Concentration

Intracellular Manipulation of Phagosomal Transport and Maturation Using Magnetic Tweezers

Shekhar, S., Subramaniam, V. & Kanger, J. S., 2017, In : Methods in Molecular Biology. 1519, p. 93-112 20 p.

Research output: Contribution to JournalArticleAcademic

Phagosomes
Calibration
Immune System Phenomena
Phagocytes
Microspheres

Membrane Binding of Parkinson's Protein α-Synuclein: Effect of Phosphorylation at Positions 87 and 129 by the S to D Mutation Approach

Kumar, P., Schilderink, N., Subramaniam, V. & Huber, M., 1 Jul 2017, In : Israel Journal of Chemistry. 57, 7, p. 762-770 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
Phosphorylation
Membranes
Proteins
Spin Labels

Non-uniform self-assembly: On the anisotropic architecture of α-synuclein supra-fibrillar aggregates

Semerdzhiev, S. A., Shvadchak, V. V., Subramaniam, V. & Claessens, M. M. A. E., 1 Dec 2017, In : Scientific Reports. 7, 1, 7699.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
self assembly
anisotropy
proteins
biopolymers
polarity

Room-temperature in-cell EPR spectroscopy: Alpha-Synuclein disease variants remain intrinsically disordered in the cell

Cattani, J., Subramaniam, V. & Drescher, M., 2017, In : Physical Chemistry Chemical Physics. 19, 28, p. 18147-18151 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

alpha-Synuclein
Paramagnetic resonance
Spectroscopy
Parkinson disease
Conformations

Solubilization of lipids and lipid phases by the styrene-maleic acid copolymer

Dominguez Pardo, J. J., Dörr, J. M., Iyer, A., Cox, R. C., Scheidelaar, S., Koorengevel, M. C., Subramaniam, V. & Killian, J. A., Jan 2017, In : European Biophysics Journal. 46, 1, p. 91-101 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Styrene
Lipids
Membranes
Membrane Lipids
maleic acid
2016

Chip based common-path optical coherence tomography system with an on-chip microlens and multi-reference suppression algorithm

Chang, L., Weiss, N., van Leeuwen, T. G., Pollnau, M., de Ridder, R. M., Wörhoff, K., Subramaniam, V. & Kanger, J. S., 13 Jun 2016, In : Optics Express. 24, 12, p. 12635-50 16 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
optical paths
tomography
chips
retarding
lenses

Conformational Compatibility Is Essential for Heterologous Aggregation of α-Synuclein

Sidhu, A., Segers-Nolten, I. & Subramaniam, V., 15 Jun 2016, In : ACS Chemical Neuroscience. 7, 6, p. 719-27 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
Seed
Seeds
Agglomeration
Monomers

Direct Observation of α-Synuclein Amyloid Aggregates in Endocytic Vesicles of Neuroblastoma Cells

Apetri, M. M., Harkes, R., Subramaniam, V., Canters, G. W., Schmidt, T. & Aartsma, T. J., 2016, In : PLoS ONE. 11, 4, p. e0153020

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
Transport Vesicles
protein aggregates
amyloid
Neuroblastoma

Fluorescence Methods for Unraveling Oligomeric Amyloid Intermediates

Zijlstra, N., Schilderink, N. & Subramaniam, V., 2016, In : Methods in Molecular Biology. 1345, p. 151-69 19 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Amyloid
Synucleins
Fluorescence
Photobleaching
Poisons

Functionally different α-synuclein inclusions yield insight into Parkinson's disease pathology

Raiss, C. C., Braun, T. S., Konings, I. B. M., Grabmayr, H., Hassink, G. C., Sidhu, A., le Feber, J., Bausch, A. R., Jansen, C., Subramaniam, V. & Claessens, M. M. A. E., 17 Mar 2016, In : Scientific Reports. 6, p. 23116

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
Lewy Bodies
Parkinson Disease
Pathology
Proteasome Endopeptidase Complex

Membrane-Bound Alpha Synuclein Clusters Induce Impaired Lipid Diffusion and Increased Lipid Packing

Iyer, A., Schilderink, N., Claessens, M. M. A. E. & Subramaniam, V., 6 Dec 2016, In : Biophysical Journal. 111, 11, p. 2440-2449 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
alpha-Synuclein
Lipids
Membranes
Phospholipids
Synucleins

p53 Specifically Binds Triplex DNA In Vitro and in Cells

Brázdová, M., Tichý, V., Helma, R., Bažantová, P., Polášková, A., Krejčí, A., Petr, M., Navrátilová, L., Tichá, O., Nejedlý, K., Bennink, M. L., Subramaniam, V., Bábková, Z., Martínek, T., Lexa, M. & Adámik, M., 2016, In : PLoS ONE. 11, 12, p. e0167439

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
DNA
cells
consensus sequence
Consensus Sequence
Transcription

Size-selective analyte detection with a Young interferometer sensor using multiple wavelengths

Mulder, H. K. P., Blum, C., Subramaniam, V. & Kanger, J. S., 18 Apr 2016, In : Optics Express. 24, 8, p. 8594-619 26 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
interferometers
sensors
wavelengths
beads
proteins

The Impact of N-terminal Acetylation of α-Synuclein on Phospholipid Membrane Binding and Fibril Structure

Iyer, A., Roeters, S. J., Schilderink, N., Hommersom, B., Heeren, R. M. A., Woutersen, S., Claessens, M. M. A. E. & Subramaniam, V., 30 Sep 2016, In : Journal of Biological Chemistry. 291, 40, p. 21110-21122 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
Acetylation
Phospholipids
Membranes
Agglomeration

α-Synuclein Oligomers Stabilize Pre-Existing Defects in Supported Bilayers and Propagate Membrane Damage in a Fractal-Like Pattern

Chaudhary, H., Iyer, A., Subramaniam, V. & Claessens, M. M. A. E., 15 Nov 2016, In : Langmuir. 32, 45, p. 11827-11836 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
oligomers
Oligomers
Fractals
fractals
2015

Alpha-synuclein amyloid oligomers act as multivalent nanoparticles to cause hemifusion in negatively charged vesicles

Stefanovic, A. N. D., Claessens, M. M. A. E., Blum, C. & Subramaniam, V., 2015, In : Small. 11, 19, p. 2257-62 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

alpha-Synuclein
Oligomers
Amyloid
Nanoparticles
Membranes

Direct patterning of nanoparticles and biomolecules by liquid nanodispensing

Fabié, L., Agostini, P., Stopel, M. H. W., Blum, C., Lassagne, B., Subramaniam, V. & Ondarçuhu, T., 14 Mar 2015, In : Nanoscale. 7, 10, p. 4497-504 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Biomolecules
Nanoparticles
Proteins
Liquids
Lithography

Enhancing spectral shifts of plasmon-coupled noble metal nanoparticles for sensing applications

Göeken, K. L., Subramaniam, V. & Gill, R., 7 Jan 2015, In : Physical Chemistry Chemical Physics - PCCP. 17, 1, p. 422-7 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metal Nanoparticles
Nanoparticles
Dimerization
Color
Light

Fibril breaking accelerates α-synuclein fibrillization

Shvadchak, V. V., Claessens, M. M. A. E. & Subramaniam, V., 5 Feb 2015, In : Journal of Physical Chemistry B. 119, 5, p. 1912-8 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
Agglomeration
monomers
Monomers
Parkinson disease

Microcantilever based distance control between a probe and a surface

Molenaar, R., Prangsma, J. C., van der Werf, K. O., Bennink, M. L., Blum, C. & Subramaniam, V., Jun 2015, In : Review of Scientific Instruments. 86, 6, p. 063706

Research output: Contribution to JournalArticleAcademicpeer-review

Feedback
probes
atomic force microscopy
Hysteresis
micrometers

Oligomers of Parkinson's Disease-Related α-Synuclein Mutants Have Similar Structures but Distinctive Membrane Permeabilization Properties

Stefanovic, A. N. D., Lindhoud, S., Semerdzhiev, S. A., Claessens, M. M. A. E. & Subramaniam, V., 2015, In : Biochemistry. 54, 20, p. 3142-50 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Synucleins
Oligomers
Parkinson Disease
Membranes
Mutation

Parkinson's Protein α-Synuclein Binds Efficiently and with a Novel Conformation to Two Natural Membrane Mimics

Kumar, P., Segers-Nolten, I. M. J., Schilderink, N., Subramaniam, V. & Huber, M., 2015, In : PLoS ONE. 10, 11, p. e0142795

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
Conformations
electrons
Membranes
Parkinson disease

Photonic effects on the fluorescence lifetimes of dyes in thin PVA layers

Prangsma, J. C., Molenaar, R., Subramaniam, V. & Blum, C., 2015, Nanoimaging and Nanospectroscopy III. SPIE, Vol. 9554. 95540G

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

Fluorescence Lifetime
Fluorophores
Thin Layer
Dyes
Photonics

Spatiotemporal proliferation of human stromal cells adjusts to nutrient availability and leads to stanniocalcin-1 expression in vitro and in vivo

Higuera, G. A., Fernandes, H., Spitters, T. W. G. M., van de Peppel, J., Aufferman, N., Truckenmueller, R., Escalante, M., Stoop, R., van Leeuwen, J. P., Boer, J. D., Subramaniam, V., Karperien, M., van Blitterswijk, C., van Boxtel, A. & Moroni, L., Aug 2015, In : Biomaterials. 61, p. 190-202 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Stromal Cells
Nutrients
Availability
Food
Mesenchymal Stromal Cells

Supporting data of spatiotemporal proliferation of human stromal cells adjusts to nutrient availability and leads to stanniocalcin-1 expression in vitro and in vivo

Higuera, G. A., Fernandes, H., Spitters, T. W. G. M., van de Peppel, J., Aufferman, N., Truckenmueller, R., Escalante, M., Stoop, R., van Leeuwen, J. P., Boer, J. D., Subramaniam, V., Karperien, M., van Blitterswijk, C., van Boxtel, A. & Moroni, L., Dec 2015, In : Data in brief. 5, p. 84-94 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Stromal Cells
Food
Extracellular Matrix
Bioreactors
Blood Vessels

Three Long-Range Distance Constraints and an Approach Towards a Model for the α-Synuclein-Fibril Fold

Hashemi Shabestari, M., Kumar, P., Segers-Nolten, I. M. J., Claessens, M. M. A. E., van Rooijen, B. D., Subramaniam, V. & Huber, M., 2015, In : Applied Magnetic Resonance. 46, 4, p. 369-388 20 p.

Research output: Contribution to JournalArticleAcademicpeer-review

strands
Parkinson disease
proteins
paramagnetic resonance
interactions

Two distinct β-sheet structures in Italian-mutant amyloid-beta fibrils: a potential link to different clinical phenotypes

Hubin, E., Deroo, S., Schierle, G. K., Kaminski, C., Serpell, L., Subramaniam, V., van Nuland, N., Broersen, K., Raussens, V. & Sarroukh, R., Dec 2015, In : Cellular and Molecular Life Sciences. 72, 24, p. 4899-913 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Amyloid
Alzheimer Disease
Cerebral Amyloid Angiopathy
Phenotype
Mutation

Waveguide-coupled micro-ball lens array suitable for mass fabrication

Chang, L., Dijkstra, M., Ismail, N., Pollnau, M., de Ridder, R. M., Wörhoff, K., Subramaniam, V. & Kanger, J. S., 24 Aug 2015, In : Optics Express. 23, 17, p. 22414-23 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

balls
lenses
waveguides
fabrication
divergence
2014

A four-amino acid linker between repeats in the α-synuclein sequence is important for fibril formation

Shvadchak, V. V. & Subramaniam, V., 21 Jan 2014, In : Biochemistry. 53, 2, p. 279-81 3 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Synucleins
Membranes
Amino Acids
Immersion
Membrane Lipids

Alpha-synuclein binds to the inner membrane of mitochondria in an α-helical conformation

Robotta, M., Gerding, H. R., Vogel, A., Hauser, K., Schildknecht, S., Karreman, C., Leist, M., Subramaniam, V. & Drescher, M., 24 Nov 2014, In : ChemBioChem. 15, 17, p. 2499-502 4 p.

Research output: Contribution to JournalArticleAcademicpeer-review

alpha-Synuclein
Mitochondria
Mitochondrial Membranes
Conformations
Electron Spin Resonance Spectroscopy

Amyloids of alpha-synuclein affect the structure and dynamics of supported lipid bilayers

Iyer, A., Petersen, N. O., Claessens, M. M. A. E. & Subramaniam, V., 17 Jun 2014, In : Biophysical Journal. 106, 12, p. 2585-94 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
alpha-Synuclein
Lipid Bilayers
Amyloid
Membranes
Lipids

Application of MALDI-TOF mass spectrometry for study on fibrillar and oligomeric aggregates of alpha-synuclein

Severinovskaya, O. V., Kovalska, V. B., Losytskyy, M. Y., Cherepanov, V. V., Subramaniam, V. & Yarmoluk, S. M., 2014, In : Biopolymers and Cell. 30, 3, p. 190-196 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
alpha-Synuclein
Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Mass spectrometry
Mass Spectrometry
Proteolysis

Background reduction in a young interferometer biosensor

Mulder, H. K. P., Subramaniam, V. & Kanger, J. S., 21 Jul 2014, Optical Sensors, 2014. Optical Society of America (OSA)

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

Biosensors
Interferometers
Refractive index
Sensors
Glucose

Classification of dynamical diffusion states in single molecule tracking microscopy

Bosch, P. J., Kanger, J. S. & Subramaniam, V., 5 Aug 2014, In : Biophysical Journal. 107, 3, p. 588-98 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Proteins
Membrane Proteins
Bayes Theorem
Single Molecule Imaging
Cellular Structures

Coming to grips with amyloid oligomers: Single molecule photobleaching approaches

Subramaniam, V., 21 Jul 2014, Optical Sensors, 2014. Optical Society of America (OSA)

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

Neurodegenerative diseases
Photobleaching
Oligomers
Self assembly
Agglomeration

Elucidating the aggregation number of dopamine-induced α-synuclein oligomeric assemblies

Zijlstra, N., Claessens, M. M. A. E., Blum, C. & Subramaniam, V., 21 Jan 2014, In : Biophysical Journal. 106, 2, p. 440-6 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Synucleins
Dopamine
Photobleaching
Amyloid
Parkinson Disease

Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single-molecule tracking microscopy in live cells

Bosch, P. J., Corrêa, I. R., Sonntag, M. H., Ibach, J., Brunsveld, L., Kanger, J. S. & Subramaniam, V., 19 Aug 2014, In : Biophysical Journal. 107, 4, p. 803-14 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Coloring Agents
Proteins
Photobleaching
Single Molecule Imaging
Eukaryotic Cells

Excitation Spectra and Stokes Shift Measurements of Single Organic Dyes at Room Temperature

Stopel, M. H. W., Blum, C. & Subramaniam, V., 18 Sep 2014, In : Journal of Physical Chemistry Letters. 5, 18, p. 3259-64 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Coloring Agents
Dyes
dyes
Molecules
shift

Integrated polymer micro-ball lenses for two-dimensional divergence reduction of light from single-mode optical waveguides

Chang, L., Dijkstra, M., de Ridder, R. M., Wörhoff, K., Subramaniam, V. & Kanger, J. S., 21 Jul 2014, European Conference on Lasers and Electro-Optics, CLEO 2015. OSA - The Optical Society

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