The DOI matches its Crossref record; 55 of the 55 references it cites were found in a registry or an index.
Trace_y: Software algorithms for structural analysis of individual helical filaments by three-dimensional contact point reconstruction atomic force microscopy
Open accessPublished version of a preprint
Abstract
ABSTRACT Atomic force microscopy (AFM) is a powerful and increasingly accessible technology that has a wide range of imaging applications. AFM is capable of producing detailed three-dimensional topographical height images with a high signal-to-noise ratio. This is a key capability of AFM, which enables the structural features of individual molecules to be studied without the need for ensemble averaging, and could offer structural analysis applications where heterogeneity of molecular populations, structural variations between individual molecules, or population distribution properties in general, hold important information. Here, a software tool called Trace_y designed to reconstruct the three-dimensional (3D) surface envelopes of individual helical filament structures from topographical AFM height images is presented. Workflow using Trace_y is demonstrated on the structural analysis of individual helical amyloid protein fibrils where the assembly mechanism of heterogeneous, complex and diverse fibril populations from a single amino-acid sequence due to structural polymorphism is not fully understood. The software and the workflow presented here allows the structural information encoded in topographical AFM height images to be extracted and understood as 3D contact point clouds. This approach will facilitate the use of AFM in structural biology, in integrated methodologies together with other structural analysis tools to understand the structures and behaviours at individual molecule level.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Gwyddion: an open-source software for SPM data analysis
Nečas, D., & Klapetek, P. (2012) · Open Physics · doi:10.2478/s11534-011-0096-2 · Cited by 4,454
The amyloid state and its association with protein misfolding diseases.
Knowles, T. P. J., Vendruscolo, M., & Dobson, C. M. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3810 · Cited by 2,382
The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy
Gross, L., Mohn, F., Moll, N., Liljeroth, P., & Meyer, G. (2009) · Science · doi:10.1126/science.1176210 · Cited by 1,842
The Amyloid State of Proteins in Human Diseases
Eisenberg, D., & Jucker, M. (2012) · Cell · doi:10.1016/j.cell.2012.02.022 · Cited by 1,744
Force-distance curves by atomic force microscopy
Cappella, B., & Dietler, G. (1999) · Surface Science Reports · doi:10.1016/s0167-5729(99)00003-5 · Cited by 1,694
Kernel density estimation via diffusion
Botev, Z. I., Grotowski, J. F., & Kroese, D. P. (2010) · The Annals of Statistics · doi:10.1214/10-aos799 · Cited by 1,689
Imaging Crystals, Polymers, and Processes in Water with the Atomic Force Microscope
Drake, B., Prater, C. B., Weisenhorn, A. L., Gould, S. A. C., Albrecht, T. R., Quate, C. F., Cannell, D. S., Hansma, H. G., & Hansma, P. K. (1989) · Science · doi:10.1126/science.2928794 · Cited by 1,033
Imaging modes of atomic force microscopy for application in molecular and cell biology
Dufrêne, Y. F., Ando, T., Garcia, R., Alsteens, D., Martinez-Martin, D., Engel, A., Gerber, C., & Müller, D. J. (2017) · Nature Nanotechnology · doi:10.1038/nnano.2017.45 · Cited by 945
Fourier shell correlation threshold criteria
van Heel, M., & Schatz, M. (2005) · Journal of Structural Biology · doi:10.1016/j.jsb.2005.05.009 · Cited by 927
From Molecules to Cells: Imaging Soft Samples with the Atomic Force Microscope
Radmacher, M., Tillmann, R. W., Fritz, M., & Gaub, H. E. (1992) · Science · doi:10.1126/science.1411505 · Cited by 900
Macromolecular modeling and design in Rosetta: recent methods and frameworks
Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0848-2 · Cited by 888
Algorithms for scanned probe microscope image simulation, surface reconstruction, and tip estimation
Villarrubia, J. S. (1997) · Journal of Research of the National Institute of Standards and Technology · doi:10.6028/jres.102.030 · Cited by 673
Buell, A. K., Galvagnion, C., Gaspar, R., Sparr, E., Vendruscolo, M., Knowles, T. P. J., Linse, S., & Dobson, C. M. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1315346111 · Cited by 664
Half a century of amyloids: past, present and future
Ke, P. C., Zhou, R., Serpell, L. C., Riek, R., Knowles, T. P. J., Lashuel, H. A., Gazit, E., Hamley, I. W., Davis, T. P., Fändrich, M., et al. (2020) · Chemical Society Reviews · doi:10.1039/c9cs00199a · Cited by 568
Cryo-EM structures of amyloid-β 42 filaments from human brains
Yang, Y., Arseni, D., Zhang, W., Huang, M., Lövestam, S., Schweighauser, M., Kotecha, A., Murzin, A. G., Peak-Chew, S. Y., Macdonald, J., et al. (2022) · Science · doi:10.1126/science.abm7285 · Cited by 549
The architecture of the Gram-positive bacterial cell wall
Pasquina-Lemonche, L., Burns, J., Turner, R. D., Kumar, S., Tank, R., Mullin, N., Wilson, J. S., Chakrabarti, B., Bullough, P. A., Foster, S. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2236-6 · Cited by 522
Fibril Fragmentation Enhances Amyloid Cytotoxicity
Xue, W.-F., Hellewell, A. L., Gosal, W. S., Homans, S. W., Hewitt, E. W., & Radford, S. E. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.049809 · Cited by 384
Self-citationAmyloid Polymorphism in the Protein Folding and Aggregation Energy Landscape
Adamcik, J., & Mezzenga, R. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201713416 · Cited by 346
Usov, I., & Mezzenga, R. (2015) · Macromolecules · doi:10.1021/ma502264c · Cited by 333
Lövestam, S., Koh, F. A., van Knippenberg, B., Kotecha, A., Murzin, A. G., Goedert, M., & Scheres, S. H. (2022) · eLife · doi:10.7554/elife.76494 · Cited by 298
Tracking Single Particles and Elongated Filaments with Nanometer Precision
Ruhnow, F., Zwicker, D., & Diez, S. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.04.023 · Cited by 295
Cryo-EM structures of tau filaments
Scheres, S. H., Zhang, W., Falcon, B., & Goedert, M. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.05.011 · Cited by 285
Multiple Assembly Pathways Underlie Amyloid-β Fibril Polymorphisms
Goldsbury, C., Frey, P., Olivieri, V., Aebi, U., & Müller, S. A. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.07.029 · Cited by 273
Localization atomic force microscopy
Heath, G. R., Kots, E. D., Robertson, J., Lansky, S., Khelashvili, G., Weinstein, H., & Scheuring, S. (2021) · Nature · doi:10.1038/s41586-021-03551-x · Cited by 212
Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in Drosophila
Hervás, R., Rau, M., Park, Y., Zhang, W., Murzin, A. G., Fitzpatrick, J. A. J., Scheres, S. H. W., & Si, K. (2020) · Science · doi:10.1126/science.aba3526 · Cited by 195
Pyne, A. L. B., Noy, A., Main, K. H. S., Velasco-Berrelleza, V., Piperakis, M. M., Mitchenall, L. A., Cugliandolo, F. M., Beton, J. G., Stevenson, C. E. M., Hoogenboom, B. W., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21243-y · Cited by 143
Kodera, N., Noshiro, D., Dora, S. K., Mori, T., Habchi, J., Blocquel, D., Gruet, A., Dosnon, M., Salladini, E., Bignon, C., et al. (2020) · Nature Nanotechnology · doi:10.1038/s41565-020-00798-9 · Cited by 117
Imaging erythrocytes under physiological conditions by atomic force microscopy
Nowakowski, R., Luckham, P. F., & Winlove, P. (2001) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/s0005-2736(01)00365-0 · Cited by 103
Single-molecule kinetics of pore assembly by the membrane attack complex
Parsons, E. S., Stanley, G. J., Pyne, A. L. B., Hodel, A. W., Nievergelt, A. P., Menny, A., Yon, A. R., Rowley, A., Richter, R. P., Fantner, G. E., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10058-7 · Cited by 98
Amyot, R., & Flechsig, H. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008444 · Cited by 86
Ruggeri, F. S., Flagmeier, P., Kumita, J. R., Meisl, G., Chirgadze, D. Y., Bongiovanni, M. N., Knowles, T. P. J., & Dobson, C. M. (2020) · ACS Nano · doi:10.1021/acsnano.9b09676 · Cited by 79
A pentameric TRPV3 channel with a dilated pore
Lansky, S., Betancourt, J. M., Zhang, J., Jiang, Y., Kim, E. D., Paknejad, N., Nimigean, C. M., Yuan, P., & Scheuring, S. (2023) · Nature · doi:10.1038/s41586-023-06470-1 · Cited by 74
An Imaging and Systems Modeling Approach to Fibril Breakage Enables Prediction of Amyloid Behavior
Xue, W., & Radford, S. E. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2013.10.034 · Cited by 66
Self-citationNSs amyloid formation is associated with the virulence of Rift Valley fever virus in mice
Léger, P., Nachman, E., Richter, K., Tamietti, C., Koch, J., Burk, R., Kummer, S., Xin, Q., Stanifer, M. L., Bouloy, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17101-y · Cited by 62
Aubrey, L. D., Blakeman, B. J. F., Lutter, L., Serpell, C. J., Tuite, M. F., Serpell, L. C., & Xue, W. (2020) · Communications Chemistry · doi:10.1038/s42004-020-00372-3 · Cited by 61
Self-citationTopoStats – A program for automated tracing of biomolecules from AFM images
Beton, J. G., Moorehead, R., Helfmann, L., Gray, R., Hoogenboom, B. W., Joseph, A. P., Topf, M., & Pyne, A. L. B. (2021) · Methods · doi:10.1016/j.ymeth.2021.01.008 · Cited by 56
Moreno‐Herrero, F., Pérez, M., Baró, A. M., & Ávila, J. (2004) · Biophysical Journal · doi:10.1016/s0006-3495(04)74130-2 · Cited by 55
On the Structural Diversity and Individuality of Polymorphic Amyloid Protein Assemblies
Lutter, L., Aubrey, L. D., & Xue, W. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167124 · Cited by 54
Self-citationLutter, L., Serpell, C. J., Tuite, M. F., & Xue, W. (2019) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2019.07.010 · Cited by 48
Self-citationHigh resolution atomic force microscopy of double-stranded RNA
Ares, P., Fuentes-Perez, M. E., Herrero‐Galán, E., Valpuesta, J., Gil, A., Gómez‐Herrero, J., & Moreno‐Herrero, F. (2016) · Nanoscale · doi:10.1039/c5nr07445b · Cited by 47
Amyloid particles facilitate surface-catalyzed cross-seeding by acting as promiscuous nanoparticles
Koloteva‐Levine, N., Aubrey, L. D., Marchante, R., Purton, T. J., Hiscock, J. R., Tuite, M. F., & Xue, W. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2104148118 · Cited by 45
Self-citationLutter, L., Al‐Hilaly, Y. K., Serpell, C. J., Tuite, M. F., Wischik, C. M., Serpell, L. C., & Xue, W. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167466 · Cited by 44
Self-citationForce-induced remodelling of proteins and their complexes
Chen, Y., Radford, S. E., & Brockwell, D. J. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.02.001 · Cited by 42
NanoLocz: Image Analysis Platform for AFM, High‐Speed AFM, and Localization AFM
Heath, G. R., Micklethwaite, E., & Storer, T. M. (2024) · Small Methods · doi:10.1002/smtd.202301766 · Cited by 42
Heterotypic Amyloid β interactions facilitate amyloid assembly and modify amyloid structure
Konstantoulea, K., Guerreiro, P. S., Ramakers, M., Louros, N. N., Aubrey, L. D., Houben, B., Michiels, E., Vleeschouwer, M. D., Lampi, Y., Ribeiro, L. F., et al. (2021) · The EMBO Journal · doi:10.15252/embj.2021108591 · Cited by 40
Self-citationLutter, L., Serpell, C. J., Tuite, M. F., Serpell, L. C., & Xue, W. (2020) · BioMolecular Concepts · doi:10.1515/bmc-2020-0009 · Cited by 33
Self-citationProtein dynamics by the combination of high-speed AFM and computational modeling
Flechsig, H., & Ando, T. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102591 · Cited by 33
The physical dimensions of amyloid aggregates control their infective potential as prion particles
Marchante, R., Beal, D. M., Koloteva‐Levine, N., Purton, T. J., Tuite, M. F., & Xue, W. (2017) · eLife · doi:10.7554/elife.27109 · Cited by 31
Self-citationDisease-relevant β2-microglobulin variants share a common amyloid fold
Wilkinson, M., Gallardo, R. U., Maya‐Martinez, R., Guthertz, N., So, M., Aubrey, L. D., Radford, S. E., & Ranson, N. A. (2023) · Nature Communications · doi:10.1038/s41467-023-36791-8 · Cited by 31
Beal, D. M., Tournus, M., Marchante, R., Purton, T. J., Smith, D. P., Tuite, M. F., Doumic, M., & Xue, W.-F. (2020) · iScience · doi:10.1016/j.isci.2020.101512 · Cited by 29
Self-citationProduction and Use of Recombinant Aβ for Aggregation Studies
O’Malley, T. T., Linse, S. S., & Walsh, D. M. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7811-3_19 · Cited by 10
Sanami, S., Purton, T. J., Smith, D. P., Tuite, M. F., & Xue, W. (2022) · Biomolecules · doi:10.3390/biom12050630 · Cited by 10
Self-citationChitty, C., Kuliga, K., & Xue, W. (2024) · Biochemical Society Transactions · doi:10.1042/bst20230857 · Cited by 8
Self-citationAubrey, L. D., Lutter, L., Fennell, K., Purton, T., Ward, N. L., Serpell, L., & Xue, W.-F. (2023) · bioRxiv · doi:10.1101/2023.07.14.549001 · Cited by 4
Self-citation
Research works printed but not linked: 1
- Feuillie, 2020, Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in Drosophila, Front. Mol. Biosci., 7
Metadata
- Authors
- Xue, W.-F.
- Affiliations
- University of Kent (GB)
- Corresponding author
- Xue, Wei-Feng
- ORCID
- Xue, Wei-Feng
- Venue
- Structure
- Publisher
- Elsevier BV
- Published
- 2025-02
- Volume
- 33
- Issue
- 2
- Pages
- 363-371.e2
- ISSN
- 0969-2126 (ISSN-L)
- OpenAlex
- W4405069410
- Cited by
- 14
- References
- 55
- Citations by year
- 2026: 6 · 2025: 3
- FWCI
- 1.91
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- creativecommons.org/licenses/by/4.0/ (vor)
- Locations
- Structure (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- Kent Academic Repository (University of Kent) (submittedVersion)
- Funders
- Engineering and Physical Sciences Research Council (EP/X01729X/1)
- Biotechnology and Biological Sciences Research Council (BB/S003312/1, BB/J008001/1, BB/M02427X/1)
- Topics
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Force Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Keywords
- helical filaments, amyloid fibrils, structural polymorphism
- MeSH terms
- Algorithms, Amyloid, Models, Molecular, Software, Microscopy, Atomic Force, Imaging, Three-Dimensional
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
