Unambiguous assignment of kinked‐ β sheets leads to insights into molecular grammar of reversibility in biomolecular condensates
Year: 2025
Type: article
Abstract: Kinked- β sheets are short peptide motifs that appear as distortions in β -strands and often mediate formation of reversible amyloid fibrils in prion-like proteins. Standard methods for assigning secondary structures cannot distinguish these esoteric motifs. Here, we provide a supervised machine learning based structural quantification map to unambiguously characterize Kinked- β sheets from coordinate data. We find that these motifs, although deviating from standard β -strand region of the Ramachandran plot, scatter around the allowed regions. We also demonstrate the applicability of our technique in wresting out LARKS, which are kinked β -strands with designated sequence. Additionally, from our exhaustive simulation generated conformations, we create a repository of potential kinked peptide-segments that can be used as a screening-library for assigning beta-kinks in unresolved coordinate dataset. Overall, our map for Kinked- β provides a robust framework for detailed structural and kinetics investigation of these important motifs in prion-like proteins that lead to formation of amyloid fibrils.
Source: Protein Science
DOI: 10.1002/pro.70266
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funders: Indian Institute of Science, Johns Hopkins University, Wellcome Trust, Compute Canada, Department of Biotechnology, Ministry of Science and Technology, India, Department of Science and Technology, Ministry of Science and Technology, India, Ministry of Education, India, The Wellcome Trust DBT India Alliance, Indian Institute of Science Education and Research Mohali
OpenAlex ID: W4413140736