Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.09.11.675362

Selective and Controllable Trapping of Single Proteins in Nanopores using Reversible Covalent Bonds

Li, Y.·Awasthi, S.·Liu, P.·Protopopova, A.·Mayer, M.
View original source ↗Export metadata ↓

Abstract

Analysis of individual proteins using nanopores makes it possible to determine their size and shape in a label-free approach, within minutes, and from L sample volumes. Short residence times of proteins in the nanopore, high electrical current noise, and bandwidth limitations of the recording electronics during resistive pulse recordings, however, limit the accuracy of size and shape analysis of individual proteins. The work presented here introduces a polymer surface coating of solid-state nanopores to minimize non-specific interactions of proteins with the nanopore wall while functionalizing it covalently with phenylboronic acid (PBA) groups. These PBA groups make it possible to trap selectively glycated proteins by taking advantage of the formation of reversible covalent bonds between PBA and vicinal diol groups of glycated amino acid residues on proteins. Dwell time analysis revealed two populations of resistive pulses: short pulses with dwell times td below 0.4 ms from free translocation of proteins and resistive pulses that we term "long events" that last from 0.4 ms to 2 s and result from intended transient covalent bonds between glycated proteins and PBA groups in the nanopore lumen. The choice of applied potential differences during nanopore recordings or the pH value of the recording buffer makes it possible to control and extend the most probable trapping time of proteins in the nanopore within one to two orders of magnitude. This approach provides the highest accuracy for the determination of protein volume and shape achieved to date with solid-state nanopores and reveals that a trapping time of 1 to 20 ms is ideal to achieve reliable volume and shape analysis while retaining high throughput of the analysis. This approach, hence, extends the residence time of natively glycated proteins or of proteins that are intentionally glycated by straightforward incubation in a glucose solution, thereby providing selectivity and improving the accuracy of nanopore-based characterization of single proteins.

Source connections

Explore related subjects

biophysicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Li, Y., Awasthi, S., Liu, P., Protopopova, A., Mayer, M.. 2025-09-16. Selective and Controllable Trapping of Single Proteins in Nanopores using Reversible Covalent Bonds. https://doi.org/10.1101/2025.09.11.675362

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A Minimally Perturbative DARPin Probe for Quantitative Fluorescence Imaging of the Human TCR-CD3 Complex

Fluorescence microscopy is a powerful tool for dissecting the molecular mechanisms of T-cell antigen recognition in living cells, but its quantitative insight critically depends on non-perturbative, high-quality probes. Here, we repurpose a small (~15 kDa) CD3epsilon-binding DARPin (designed ankyrin repeat proteins) to a fluorescent label for T-cell receptor (TCR)/CD3 complexes on primary human CD8+ T-cells, with the aim of generating a powerful tool for quantitative analysis, single-molecule tracking, and advanced imaging of TCR dynamics. We show that the DARPin binds CD3{varepsilon} with high affinity and selectivity and using single molecule tracking and brightness analysis, we characterize the TCR-CD3 diffusion behavior and show that the DARPin binds to both CD3epsilon; subunits. Importantly, labeling preserves antigen sensitivity: on supported lipid bilayers presenting cognate pMHC, T-cells remain responsive, assemble synapses, form TCR microclusters, and initiate signaling similar to unlabeled controls. We further demonstrate compatibility with lattice light-sheet microscopy for volumetric imaging of T-cell - APC interactions in living cells. Together, these results establish DARPins as versatile, minimally perturbative probes for high resolution, quantitative studies of T cell synapse organization and signaling.

biophysics↗
bioRxiv2026

Monitoring intramolecular dynamics across two regions of the mouse prion protein during misfolding and oligomerization using fluorescence correlation spectroscopy

It is important to determine whether native state dynamics drive the misfolding and oligomerization of the prion protein, which are important events in prion disease, and how they are modulated by conformational conversion. Native (N) mouse prion protein (moPrP) is known to form small (OS) and large (OL) oligomers rich in {beta}-sheet, and in this study, photoinduced electron transfer-fluorescence correlation spectroscopy (PET-FCS) has been used to characterize intramolecular dynamics within individual monomeric units in both isolated OS and OL, as well as the diffusion properties of the oligomers. It is estimated that OS and OL comprise of about 15 and 55 monomeric units, respectively. Microsecond dynamics at each of the two regions that are the 1-3 and 2-3 interfaces of native protein are distinct in N, OS and OL, although they occur on very similar timescales. Analysis of the evolution of the distribution of diffusion times, determined using the maximum entropy method, indicates heterogeneity in the oligomerization reaction. Analysis of the change in the fluctuations which occur in two different timescales in the native state ensemble shows that they are damped more at the erstwhile 1-3 interface than the erstwhile 2-3 interface. The difference in the extent of damping at the erstwhile 1-3 and 2-3 interfaces can be explained on the basis of the structural changes known to occur across each region. The changes in dynamics occur concurrently in both regions, indicating that the structural changes accompanying conformational conversion also occur simultaneously during the oligomerization of moPrP.

biophysics↗
bioRxiv2026

Combining CHARMM36m with OPC water improves accuracy

Atomistic simulations of intrinsically disordered proteins (IDPs) are notoriously sensitive to force field inaccuracies, either regarding the protein or the water model, yielding inaccurate observables such as compactness, secondary structure propensities, or kinetics. The currently most widely used IDP force fields are Amber99sb-disp (A99disp) and Charmm36m (C36m). A99disp includes a new water model and thus optimized both, the protein and the water interactions. In contrast, C36m used the Tip3p water model and optimized only protein interactions. In many cases, C36m+Tip3p underestimates radii of gyration compared to FRET or SAXS experiments. Such overly compact structural ensembles are believed to arise from an imbalance between protein-protein, protein-water, and water-water interactions, which might be due to Tip3p inaccuracies. Here, we aim at re-balancing these interactions by combining C36m with the Optimal Point Charge (OPC) water model. Recently, this C36m+OPC combination showed improved accuracy for the disordered domain of the measles virus nucleoprotein. Here we present a systematic assessment, comparing C36m+OPC, C36m+Tip3p, C36m+Tip4p, C22*, A03ws, A99sb-ws, and A99disp for five IDPs, as well as a subset of those for five globular proteins, a set of disordered AGQ-repeat peptides, and the fast folding miniprotein CLN025. We compared extensive MD simulations (> 8.5 ms) with SAXS, NMR, circular dichroism, photo-induced electron transfer (PET), T-jump infrared spectroscopy, and X-ray crystallography measurements. We found that combining C36m with OPC improved accuracy over C36m+Tip3p for IDP ensembles without compromising its accuracy for globular proteins. While also the kinetics of the AGQ-peptides were more accurate for C36m+OPC, those of CLN025 folding were less accurate. Overall, C36m+OPC showed similar accuracy as A99sb-ws and A99disp, the latter is currently considered among the most accurate protein force fields.

biophysics↗