Amyloid fibril formation and tissue deposition are associated with many diseases. Studies have shown that prefibrillar intermediates, such as oligomers, are the most toxic proteospecies of the amyloidogenic cascade. Thus, understanding the mechanisms of formation and the conformational ensemble of prefibrillar species is critical. Due to their transient and heterogeneous nature, detection and characterization of prefibrillar species remain challenging. The fluorogenic probe fluorescein arsenical hairpin (FlAsH), which recognizes a tetracysteine motif, has been recently used to detect the oligomerization of amyloidogenic peptides encompassing a Cys-Cys tag. In this study, we extended the FlAsH detection method to gain novel kinetic and conformational insights into the self-assembly of islet amyloid polypeptide (IAPP), a 37-residue peptide hormone whose deposition is associated with type II diabetes. By positional scanning of the Cys-Cys motif, the stability of the noncontiguous tetracysteine FlAsH-binding sites formed during self-assembly was evaluated and revealed rapid monomer self-recognition through the convergence of C-terminal domains. On the other hand, the N-terminal domains come close to each other only upon the formation of the cross-β-sheet amyloid structure. We demonstrated that this method is well-suited to detect thioflavin T-negative fibrils and to screen inhibitors of amyloid formation. This study highlights that with positional scanning of the split-tetracysteine motif (Cys-Cys), the FlAsH detection method offers unique time-dependent conformational insights on the proteospecies assembled throughout the amyloidogenic pathway.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/acs.bioconjchem.7b00827 | DOI Listing |
Soft Matter
January 2025
College of Chemistry, Sichuan University, Chengdu 610064, China.
Biomolecules usually adopt ubiquitous circular structures which are important for their functionality. Based on three-dimensional Langevin dynamics simulations, we investigate the conformational change of a polymer confined in a spherical cavity. Both passive and active polymers with either homogeneous or heterogeneous stiffness are analyzed in a comparative manner.
View Article and Find Full Text PDFIn eukaryotes, mismatch repair begins with M ut S h omolog (MSH) complexes, which scan newly replicated DNA for mismatches. Upon mismatch detection, MSH complexes recruit the PCNA- stimulated endonuclease Mlh1-Pms1/PMS2 (yeast/human), which nicks the DNA to allow downstream proteins to remove the mismatch. Past work has shown that although Mlh1-Pms1 is an ATPase and this activity is important , ATP is not required to nick DNA.
View Article and Find Full Text PDFACS Omega
January 2025
School of Bio-Chemical Engineering and Technology, Sirindhorn International Institute of Technology, Thammasat University, 99 Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
The integration of molecular docking and AM1 calculations has elucidated the complexation behavior of butylone enantiomers with methylated β-cyclodextrin derivatives. Our study reveals that butylone can adopt two distinct conformations within the β-cyclodextrin cavity, with one conformation being preferentially stabilized due to its favorable binding energy. This conformation preference is influenced by the methylation at the O2, O3, and O6 positions of β-cyclodextrin, which significantly affects complex stability and solvation properties.
View Article and Find Full Text PDFPeerJ
January 2025
Department of Biological Science, University of Ulsan, Ulsan, Republic of South Korea.
The genus , a group of ciliated protists, has attracted attention as a model organism due to its widespread distribution and ease of cultivation. This study examines the evolutionary patterns of the SSU rRNA secondary structure within this genus, aiming to elucidate its role in supporting evolutionary relationships and uncovering cryptic species. By predicting the secondary structure of SSU rRNA and applying the CBC (Compensatory Base Change) concept analysis, we examined 69 species of the genus , with 57 SSU rRNA gene sequences retrieved from GenBank and 12 newly sequenced specimens from South Korea.
View Article and Find Full Text PDFHeliyon
January 2025
Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.
The myeloid-specific triggering receptors expressed on myeloid cells 2 (TREM2) is a group of class I receptors expressed in brain microglia plays a decisive role in neurodegenerative diseases such as Alzheimer's disease (AD) and Nasu Hakola disease (NHD). The extracellular domain (ECD) of TREM2 interacts with a wide-range of ligands, yet the molecular mechanism underlying recognition of such ligands to this class I receptor remains underexplored. Herein, we undertook a systematic investigation for exploring the mode of ligand recognition in immunoglobulin-like ectodomain by employing both knowledge-based and machine-learning guided molecular docking approach followed by the state-of-the-art all atoms molecular dynamics (MD) simulations.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!