ArticleProteins2012
Geofold: topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability.
Article in Proteins, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Anti-CTLA-4 nanobody as a promising approach in cancer immunotherapy.Cell death & disease · 2024Review
- Enhanced Thermostability of D-Psicose 3-Epimerase fromInternational journal of molecular sciences · 2021Article
- The structural basis of nanobody unfolding reversibility and thermoresistance.Scientific reports · 2018Article
- Mapping the Geometric Evolution of Protein Folding Motor.PloS one · 2016Article
- Exploring the folding pathway of green fluorescent protein through disulfide engineering.Protein science : a publication of the Protein Society · 2015Article
- Article
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Authors and funding
7 authors.
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Abstract
Protein unfolding is modeled as an ensemble of pathways, where each step in each pathway is the addition of one topologically possible conformational degree of freedom. Starting with a known protein structure, GeoFold hierarchically partitions (cuts) the native structure into substructures using revolute joints and translations. The energy of each cut and its activation barrier are calculated using buried solvent accessible surface area, side chain entropy, hydrogen bonding, buried cavities, and backbone degrees of freedom. A directed acyclic graph is constructed from the cuts, representing a network of simultaneous equilibria. Finite difference simulations on this graph simulate native unfolding pathways. Experimentally observed changes in the unfolding rates for disulfide mutants of barnase, T4 lysozyme, dihydrofolate reductase, and factor for inversion stimulation were qualitatively reproduced in these simulations. Detailed unfolding pathways for each case explain the effects of changes in the chain topology on the folding energy landscape. GeoFold is a useful tool for the inference of the effects of disulfide engineering on the energy landscape of protein unfolding.
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Registered trials
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