ArticleBiophysical journal2014
The structure of misfolded amyloidogenic dimers: computational analysis of force spectroscopy data.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 32 citations in OpenAlex.
- Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers.International journal of molecular sciences · 2023Review
- Mechanical Stability of a Small, Highly-Luminescent Engineered Protein NanoLuc.International journal of molecular sciences · 2020Article
- Review
- AFM Probing of Amyloid-Beta 42 Dimers and Trimers.Frontiers in molecular biosciences · 2020Article
- Spontaneous self-assembly of amyloid β (1-40) into dimers.Nanoscale advances · 2019Article
- Probing the Basis of α-Synuclein Aggregation by Comparing Simulations to Single-Molecule Experiments.Biophysical journal · 2019Article
- Force clamp approach for characterization of nano-assembly in amyloid beta 42 dimer.Nanoscale · 2019Article
- Probing Intermolecular Interactions within the Amyloid β Trimer Using a Tethered Polymer Nanoarray.Bioconjugate chemistry · 2018Article
- Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes.Journal of physics D: Applied physics · 2018Article
- Single-molecule probing of amyloid nano-ensembles using the polymer nanoarray approach.Physical chemistry chemical physics : PCCP · 2017Article
- Nano-assembly of amyloid β peptide: role of the hairpin fold.Scientific reports · 2017Article
- A novel pathway for amyloids self-assembly in aggregates at nanomolar concentration mediated by the interaction with surfaces.Scientific reports · 2017Article
- Self-assembly of the full-length amyloid Aβ42 protein in dimers.Nanoscale · 2016Article
- Antibody-Based Drugs and Approaches Against Amyloid-β Species for Alzheimer's Disease Immunotherapy.Drugs & aging · 2016Review
- Article
- Article
- Probing of Amyloid Aβ (14-23) Trimers by Single-Molecule Force Spectroscopy.Jacobs journal of molecular and translational medicine · 2016Article
- A Metal-free Click Chemistry Approach for the Assembly and Probing of Biomolecules.Journal of nature and science · 2016Article
- A flexible nanoarray approach for the assembly and probing of molecular complexes.Biophysical journal · 2015Article
- Role of monomer arrangement in the amyloid self-assembly.Biochimica et biophysica acta · 2015Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Progress in understanding the molecular mechanism of self-assembly of amyloidogenic proteins and peptides requires knowledge about their structure in misfolded states. Structural studies of amyloid aggregates formed during the early aggregation stage are very limited. Atomic force microscopy (AFM) spectroscopy is widely used to analyze misfolded proteins and peptides, but the structural characterization of transiently formed misfolded dimers is limited by the lack of computational approaches that allow direct comparison with AFM experiments. Steered molecular dynamics (SMD) simulation is capable of modeling force spectroscopy experiments, but the modeling requires pulling rates 10(7) times higher than those used in AFM experiments. In this study, we describe a computational all-atom Monte Carlo pulling (MCP) approach that enables us to model results at pulling rates comparable to those used in AFM pulling experiments. We tested the approach by modeling pulling experimental data for I91 from titin I-band (PDB ID: 1TIT) and ubiquitin (PDB ID: 1UBQ). We then used MCP to analyze AFM spectroscopy experiments that probed the interaction of the peptides [Q6C] Sup35 (6-13) and [H13C] Aβ (13-23). A comparison of experimental results with the computational data for the Sup35 dimer with out-of-register and in-register arrangements of β-sheets suggests that Sup35 monomers adopt an out-of-register arrangement in the dimer. A similar analysis performed for Aβ peptide demonstrates that the out-of-register antiparallel β-sheet arrangement of monomers also occurs in this peptide. Although the rupture of hydrogen bonds is the major contributor to dimer dissociation, the aromatic-aromatic interaction also contributes to the dimer rupture process.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.