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The molecular architecture of amyloids formed in vivo can be interrogated using luminescent conjugated oligothiophenes (LCOs), a unique class of amyloid dyes. When bound to amyloid, LCOs yield fluorescence emission spectra that reflect the 3D structure of the protein aggregates. Given that synthetic amyloid-β peptide (Aβ) has been shown to adopt distinct structural conformations with different biological activities, we asked whether Aβ can assume structurally and functionally distinct conformations within the brain. To this end, we analyzed the LCO-stained cores of β-amyloid plaques in postmortem tissue sections from frontal, temporal, and occipital neocortices in 40 cases of familial Alzheimer's disease (AD) or sporadic (idiopathic) AD (sAD). The spectral attributes of LCO-bound plaques varied markedly in the brain, but the mean spectral properties of the amyloid cores were generally similar in all three cortical regions of individual patients. Remarkably, the LCO amyloid spectra differed significantly among some of the familial and sAD subtypes, and between typical patients with sAD and those with posterior cortical atrophy AD. Neither the amount of Aβ nor its protease resistance correlated with LCO spectral properties. LCO spectral amyloid phenotypes could be partially conveyed to Aβ plaques induced by experimental transmission in a mouse model. These findings indicate that polymorphic Aβ-amyloid deposits within the brain cluster as clouds of conformational variants in different AD cases. Heterogeneity in the molecular architecture of pathogenic Aβ among individuals and in etiologically distinct subtypes of AD justifies further studies to assess putative links between Aβ conformation and clinical phenotype.
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http://dx.doi.org/10.1073/pnas.1713215114 | DOI Listing |
ArXiv
August 2025
Department of Genetics, Yale University, New Haven, CT 06510, USA.
A key output of the NIH-Common Fund 4D Nucleome (4DN) project is the open publication of datasets related to the structure of the human cell nucleus and the genome. Recent years have seen a rapid expansion of multiplexed Fluorescence In Situ Hybridization (FISH) or FISH-omics methods, which quantify the spatial organization of chromatin in single cells, sometimes together with RNA and protein measurements, and provide an expanded understanding of how 3D higher-order chromosome structure relates to transcriptional activity and cell development in both health and disease. Despite this progress, results from Chromatin Tracing FISH-omics experiments are difficult to share, reuse, and subject to third-party downstream analysis due to the lack of standard specifications for data exchange.
View Article and Find Full Text PDFJ Bioinform Comput Biol
August 2025
Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China.
To date, the study of single-stranded DNA (ssDNA) similarity has focused mainly on the similarity of bases in the same position in the nucleic acid sequence. However, focusing only on the similarity of base sequences has limitations. This similarity evaluation considers only the one-dimensional similarity of ssDNA and cannot fully capture the three-dimensional (3D) structural consistency of aptamers for nucleic acids with 3D structures.
View Article and Find Full Text PDFJ Phys Chem Lett
August 2025
Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States.
Electrostatic interactions mediated by surrounding ions critically influence RNA behavior, yet flexible RNAs remain underexplored. We performed molecular dynamics simulations to examine three RNAs across the structural continuum: unstructured poly uridylic tract (rU), a semiflexible cytosine-adenine-guanine (CAG) repeat, and a tightly folded pseudoknot. Despite similar net charges, rU attracts a diffuse Mg cloud extending beyond two hydration shells, while the CAG repeat and pseudoknot favor more compact outer-sphere Mg binding.
View Article and Find Full Text PDFGenome Res
September 2025
Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore-560012, India;
long noncoding RNA is the master regulator of the X-Chromosome inactivation (XCI) process. is expressed from the inactive X and coats the inactive X to facilitate XCI. -regulation of expression remains poorly understood in the context of maintenance of XCI.
View Article and Find Full Text PDFJ Chem Inf Model
July 2025
College of Artificial Intelligence, Tianjin Normal University, Tianjin 300387, China.
Exploring drug-target interactions (DTIs) is crucial for drug discovery. Most existing methods for predicting DTIs rely solely on the linear structures of molecules, such as SMILES or the amino acid sequence. However, these linear features fail to reflect the substructures of molecules or the relative positions of atoms.
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