Biology subjects

van Noort, J.

Publications and source records attributed to van Noort, J..

10 recordsLinked to original sources

bioRxiv2026

Irregular nucleosome positioning governs a crystalline to liquid-like phase transition and tunes chromatin accessibility

Chromatin must fold tightly enough to protect the genome while being sufficiently accessible for DNA dependent processes such as transcription. The physical rules that balance these competing roles remain unclear, as DNA sequence encodes both biochemical information such as transcription factor binding sites, and biophysical cues that shape chromatin structure. Here, using synthetic chromatin fibres assembled from physiologically relevant DNA sequences, we show that nucleosome positioning dictates the material state of chromatin. Heterochromatin-like sequences produce compact fibres stabilised by nucleosome stacking, whereas euchromatin-like sequences generate irregular nucleosome positioning that yields disrupted, heterogeneous, and mechanically deformable fibres. Quantitative polymer modelling reveals that these irregular arrays are highly dynamic, continually sampling a broad ensemble of conformations as nucleosome stacking breaks down. We identify two previously unrecognised thresholds encoded by nucleosome positioning: minimal positional irregularity (2-3 bp) triggers a transition from an ordered paracrystalline state to a liquid-like phase, whereas an order of magnitude greater irregularity (~18 bp) is required to generate accessibility and mechanical fragility permissive for transcription factor binding. Euchromatin-like arrays reside at this accessibility threshold. These findings indicate that nucleosome positioning tunes chromatin toward or away from critical structural states that couple genome protection, chromatin dynamics, and transcriptional potential, providing a physical mechanism that helps connect DNA sequence to gene expression.

molecular biology↗

bioRxiv2026

Topological Investigation of Protein Folding and Intrinsic Disorder

Mapping protein conformations into a space of fold topologies offers an unprecedented perspective on the long-standing protein folding problem. In this study, we apply circuit topology to investigate the folding landscape of both stably folded and intrinsically disordered proteins. This topological approach quantifies intra-chain contact arrangements within a polypeptide chain. We demonstrate that ordered and disordered proteins can be distinguished by their topological organization, and that a topology-based model can predict chain compaction and folding state. Furthermore, topology relates to folding and unfolding kinetics and thermodynamics. These findings establish topology as a fundamental concept for understanding protein folding and disorder.

biophysics↗

bioRxiv2025

Modulation of archaeal hypernucleosome structure and stability by Mg2+

DNA-wrapping histone proteins play a central role in chromatin organization, gene expression and regulation in most eukaryotes and archaea. While the structure and function of eukaryotic histones are well-characterized, archaeal histones and their complexes with DNA require further scrutiny. Distinct from their eukaryotic counterparts, previously characterized canonical archaeal histones assemble on DNA into an endless superhelical nucleoprotein complex called a hypernucleosome. In this study, we explored whether hypernucleosome formation is a conserved feature of canonical archaeal histones. Moreover, to further elucidate how hypernucleosomes are regulated, we also explored how changes in the physico-chemical conditions, particularly the presence of Mg2+, influence the hypernucleosome. Using a combination of Tethered Particle Motion (TPM) and single-molecule force spectroscopy, we established that T. kodakarensis histones assemble into hypernucleosomes on DNA, similar to the M. fervidus histones HMfA and HMfB, the only canonical histones structurally characterized in previous studies. However, the effects of Mg2+ ions are distinct despite the histones high sequence- and structural similarity. We propose a model in which Mg2+ ions exert a generic effect on hypernucleosome compactness and stability due to electrostatic DNA shielding, with additional differential effects depending on histone identity.

molecular biology↗

bioRxiv2024

Phosphorylation regulated conformational diversity and topological dynamics of an intrinsically disordered nuclear receptor

Site-specific phosphorylation of disordered proteins is often considered as a marker of protein activity, yet it is unclear how phosphorylation alters conformational dynamics of disordered protein chains, such as those in the nuclear receptor superfamily. In the case of disordered human glucocorticoid receptor N-terminal domain (GR NTD), a negatively charged region known as core activation function 1 (AF1c) features three phosphorylation sites, regulating its function and intracellular localization. Deletion of this sequence reduces GR transcriptional activation ability dramatically in cell experiments. By developing a circuit topology-based fold analysis approach, combined with atomistic simulations, we reveal that site-specific phosphorylation facilitates formation of non-local contacts, leading to the emergence of disordered compact topologies with significant entanglement, which are distinct from solvent exposed topologies. While we observe that the topological buildup of solvent-exposed states is similar in different phosphovariants, it depends on the exact phosphorylation site for the disordered compact states. This study thus reveals the complex regulatory role of the GR phosphorylation and introduces a unique analysis framework that can be broadly applied to studying topological dynamics of disordered proteins.

biophysics↗

bioRxiv2024

Point set registration for combining fluorescence microscopy methods

SUMMARYImplementation of combined microscopy methods provides valuable information across various scientific applications. However, aligning the datasets and finding the correct point correspondence poses a challenge, especially for large, randomly distributed point sets that are subject to positional errors and missing points. Here, we provide a three-step procedure to perform point set registration, which can be applied to datasets with millions of points and stays robust even when only 10% of the points correspond. In the first global step, the scaling and rotation parameters for the imaging systems are determined once on a smaller calibration dataset using a geometric hashing algorithm. When the global transformation is known, full experimental datasets can be registered by performing step two: a course registration using cross-correlation, and step three: a precise registration to fine-tune the transformation. After these three steps, point correspondence is determined by setting a distance threshold based on a statistical model of random point sets that additionally provides the matching error. We have demonstrated its successful implementation in coupling fluorescence and sequencing methodologies. To enable wide application of these point set registration and correspondence algorithms we provide a python library called MatchPoint.

biophysics↗

bioRxiv2022

Multifocal two-photon excitation fluorescence microscopy reveals hop diffusion of H-Ras membrane anchors in epidermal cells of zebrafish embryos

Developments in fluorescence microscopy techniques have enabled imaging of individual fluorescently labelled proteins in biological systems, and in the current study, a single-molecule microscopy (SMM) technique has been applied in vivo, using the zebrafish embryo model. We have used multifocal two-photon excitation fluorescence microscopy (2PEFM) to study the dynamics of a GFP-fused H-Ras membrane-anchoring domain, GFP-C10H-Ras, in the epidermal cells of living embryos. In previous studies, a fast and a slow diffusing population of GFP-C10H-Ras molecules had been found. The application of the multifocal 2PEFM technique enabled us to focus on the slow diffusing population, which appears to occur in clusters that diffuse within microdomains of the epidermal cell membranes. Based on their mobility on a short timescale ([≤] 1s) we could distinguish between a subpopulation that was diffusing and one that was virtually immobile. Owing to the multifocal 2PEFM imaging mode, we were able to dramatically reduce photobleaching which enabled us to follow the GFP-C10H-Ras particles over a prolonged time (> 3 s) and reconstruct their molecular trajectories of the diffusing subpopulation. These trajectories exhibited that the C10H-Ras particles continuously switch between a diffusing state and brief bursts of increased diffusion. As a result, they display an anomalous mobility pattern that can be referred to as hop diffusion. Taken together, this study demonstrates that multifocal 2PEFM offers a powerful approach to studying individual particles for prolonged periods of time, and that using this approach we were able to uncover the hopping behavior of GFP-C10H-Ras. SUMMARY STATEMENTBy application of the two-photon excitation single-molecule microscopy to living zebrafish embryos, anomalous diffusion modes of individual H-Ras membrane anchors in epidermal cells were found.

biophysics↗

bioRxiv2022

Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins

Single-molecule FRET (smFRET) has become an established tool to study biomolecular structure and dynamics in vitro and in live cells. We performed a worldwide blind study involving 19 labs to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems that undergo distinct conformational changes, we obtained an uncertainty of the FRET efficiency of less than {+/-} 0.06, corresponding to an interdye distance precision of [≤] 0.2 nm and accuracy of [≤] 0.5 nm. We further discuss the limits for detecting distance fluctuations with sensitivity down to [lsim] 10% of the Forster distance and provide guidelines on how to detect potential dye perturbations. The ability of smFRET experiments to simultaneously measure distances and avoid averaging of conformational dynamics slower than the fluorescence lifetime is unique for dynamic structural biology.

biophysics↗

bioRxiv2022

The columnar structure of human telomeric chromatin suggests mechanisms for telomere maintenance

Telomeres, the ends of eukaryotic chromosomes, play pivotal roles in ageing and cancer and are targets of DNA damage and response. However, little is known about the structure and organization of telomeric chromatin at the molecular level. We used electron microscopy and single-molecule magnetic tweezers to characterize well-defined telomeric chromatin fibers of kilobasepair length. The cryo-EM structure of the compact telomeric tetranucleosome revealed a novel columnar folding, unusually short nucleosome repeat length of [~]132bp and the role of the histone N-terminal tails in stabilizing this structure. This is the first near-high resolution structure of chromatin with a native DNA sequence. The columnar structure exposes the DNA, making them susceptible to DNA damage. The telomeric tetranucleosome also exists in an alternative well-defined state, with one nucleosome open, accessible to protein factors. This suggests that protein factors, which plays a role in maintaining telomeres, can bind to telomeric chromatin in its compact heterochromatic form. The features of the telomeric chromatin structure reveals important insights of significant relevance for telomere function in vivo that provides information on mechanisms of nucleosome recognition by chromatin factors

molecular biology↗

bioRxiv2021

Analysis of the H-Ras mobility pattern in vivo shows cellular heterogeneity inside epidermal tissue

Over the last two decades, developments in single-molecule microscopy (SMM) have enabled imaging and tracking of individual, fluorescently labelled proteins in biological systems, and most of these studies have focused on the analysis of protein mobility patterns inside cultured cells. In the present study, SMM was applied in vivo, using the zebrafish embryo model. We studied the protein dynamics of the membrane protein H-Ras, mutants of this protein, and its membrane-anchoring domain, C10H-Ras, in epidermal cells of living two-day-old embryos, using a total internal reflection fluorescence microscopy (TIRFM) setup. For all proteins studied, our results consistently confirm the presence of a fast- and a slow-diffusing subpopulations of molecules, which both confine to microdomains within the plasma membrane. Although the mobility patterns of H-Ras, mutants of this proteins and its membrane-anchoring domain were remarkably similar, the constitutively active H-Ras mutant, H-RasV12, exhibited significantly higher diffusion rates than the wild-type H-Ras and its inactive mutant, H-RasN17. Ultimately, we characterized variability in our data obtained using the zebrafish embryo model and demonstrated that differences between cells within the same embryo are the largest source of variation in our data. Our findings are in line with a model in which the cellular architecture of individual cells within a tissue determine the mobility of H-Ras proteins anchored in the plasma membrane cytoplasmic leaflet. Thereby, our results underline the growing importance of performing SMM imaging in vivo in order to better understand factors influencing the protein dynamics in an intact living organism. SUMMARY STATEMENTBy application of single-molecule microscopy to living zebrafish embryos, factors altering the in vivo dynamics of H-Ras proteins in epidermal cells were analyzed.

biophysics↗

bioRxiv2019

Multiplexed Nanometric 3D Tracking of Microbeads using a FFT-Phasor Algorithm

Many single-molecule biophysical techniques rely on nanometric tracking of microbeads to obtain quantitative information about the mechanical properties of biomolecules such as chromatin fibers. Their three-dimensional position can be resolved by holographic analysis of the diffraction pattern in wide-field imaging. Fitting this diffraction pattern to Lorentz Mie scattering theory yields the bead position with nanometer accuracy in three dimensions but is computationally expensive. Real-time multiplexed bead tracking therefore requires a more efficient tracking method. Here, we introduce 3D phasor tracking, a fast and robust bead tracking algorithm with nanometric localization accuracy in a z-range of over 10 {micro}m. The algorithm is based on a 2D cross-correlation using Fast Fourier Transforms with computer-generated reference images, yielding a processing rate of up to 10.000 regions of interest per second. We implemented the technique in magnetic tweezers and tracked the 3D position of over 100 beads in real-time on a generic CPU. Its easy implementation, efficiency, and robustness can improve multiplexed biophysical bead tracking applications, especially where high throughput is required.\n\nSignificanceMicrobeads are often used in biophysical single-molecule manipulation experiments and accurately tracking their position in 3 dimensions is key for quantitative analysis. Holographic imaging of these beads allows for multiplexing bead tracking but image analysis can be a limiting factor. Here we present a 3D tracking algorithm based on Fast Fourier Transforms that is fast, has nanometric precision, is robust against common artifacts and is accurate over 10s of micrometers. We show its real-time application for magnetic tweezers based force spectroscopy on more than 100 chromatin fibers in parallel, but we anticipate that many other bead-based biophysical essays can benefit from this simple and robust 3 phasor algorithm.

biophysics↗