ArticleScientific reports2020
GLN: a method to reveal unique properties of lasso type topology in proteins.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 3 citations in OpenAlex.
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- Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families.PLoS computational biology · 2026Article
- Phosphoglycerate Kinase Can Adopt Topologically Misfolded Forms That Are More Stable Than Its Native State.Journal of the American Chemical Society · 2026Article
- Link node: A method to characterize the chain topology of intrinsically disordered proteins.Quantitative biology (Beijing, China) · 2025Article
- Non-native entanglement protein misfolding observed in all-atom simulations and supported by experimental structural ensembles.Science advances · 2025Article
- AlphaLasso-a web server to identify loop and lasso motifs in 3D structure of biopolymers.Nucleic acids research · 2025Article
- Noncovalent Lasso Entanglements are Common in Experimentally Derived Intrinsically Disordered Protein Ensembles and Strongly Influenced by Protein Length and Charge.The journal of physical chemistry. B · 2025Article
- Folds from fold: Exploring topological isoforms of a single-domain protein.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Pulling Forces Differentially Affect Refolding Pathways Due to Entangled Misfolded States in SARS-CoV-1 and SARS-CoV-2 Receptor Binding Domain.Biomolecules · 2024Article
- Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.Nucleic acids research · 2024Article
- Mathematical topology and geometry-based classification of tauopathies.Scientific reports · 2024Article
- Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance.Journal of molecular biology · 2024Article
- Is Posttranslational Folding More Efficient Than Refolding from a Denatured State: A Computational Study.The journal of physical chemistry. B · 2023Article
- Are there double knots in proteins? Prediction andFrontiers in molecular biosciences · 2023Article
- Lasso Proteins-Unifying Cysteine Knots and Miniproteins.Polymers · 2021Article
- Topoly: Python package to analyze topology of polymers.Briefings in bioinformatics · 2021Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
Geometry and topology are the main factors that determine the functional properties of proteins. In this work, we show how to use the Gauss linking integral (GLN) in the form of a matrix diagram-for a pair of a loop and a tail-to study both the geometry and topology of proteins with closed loops e.g. lassos. We show that the GLN method is a significantly faster technique to detect entanglement in lasso proteins in comparison with other methods. Based on the GLN technique, we conduct comprehensive analysis of all proteins deposited in the PDB and compare it to the statistical properties of the polymers. We show how high and low GLN values correlate with the internal exibility of proteins, and how the GLN in the form of a matrix diagram can be used to study folding and unfolding routes. Finally, we discuss how the GLN method can be applied to study entanglement between two structures none of which are closed loops. Since this approach is much faster than other linking invariants, the next step will be evaluation of lassos in much longer molecules such as RNA or loops in a single chromosome.
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