Papers by Joanna Sulkowska
Protein Science, Apr 17, 2023
The fact that proteins can have their chain formed in a knot is known for almost 30 years. Howeve... more The fact that proteins can have their chain formed in a knot is known for almost 30 years. However, as they are not common, only a fraction of such proteins is available in the Protein Data Bank. It was not possible to assess their importance and versatility up until now because we did not have access to the whole proteome of an organism, let alone a human one. The arrival of efficient machine learning methods for protein structure prediction, such as AlphaFold and RoseTTaFold, changed that. We analyzed all proteins from the human proteome (over 20,000) determined with AlphaFold in search for knots and found them in less than 2% of the structures. Using a variety of methods, including homolog search, clustering, quality assessment, and visual inspection, we determined the nature of each of the knotted structures and classified it as either knotted, potentially knotted, or an artifact, and deposited all of them in a database available at: https://knotprot.cent.uw.edu.pl/alphafold. Overall, we found 51 credible knotted proteins (0.2% of human proteome). The set of potentially knotted structures includes a new complex type of a knot not reported in proteins yet. That knot type, denoted 63 in mathematical notation, would necessitate a more complex folding path than any knotted protein characterized to date.
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bioRxiv (Cold Spring Harbor Laboratory), Jun 18, 2023
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TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk, 2016
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Journal of Molecular Biology, 2019
Knots in proteins are increasingly being recognized as an important structural concept, and the f... more Knots in proteins are increasingly being recognized as an important structural concept, and the folding of these peculiar structures still poses considerable challenges. From a functional point of view, most protein knots discovered so far are either enzymes or DNA-binding proteins. Our comprehensive topological analysis of the Protein Data Bank reveals several novel structures including knotted mitochondrial proteins and the most deeply embedded protein knot discovered so far. For the latter, we propose a novel folding pathway based on the idea that a loose knot forms at a terminus and slides to its native position. For the mitochondrial proteins, we discuss the folding problem from the perspective of transport and suggest that they fold inside the mitochondria. We also discuss the evolutionary origin of a novel class of knotted membrane proteins and argue that a novel knotted DNA-binding protein constitutes a new fold. Finally, we have also discovered a knot in an artificially designed protein structure.
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物性研究, Apr 20, 2009
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Journal of Physical Chemistry Letters, Dec 26, 2012
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Acta Biochimica Polonica, 2018
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TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk, 2014
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Reactive & Functional Polymers, Nov 1, 2018
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Bioinformatics, Aug 16, 2019
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PLOS Computational Biology, May 26, 2020
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Bioinformatics, Apr 30, 2018
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Nucleic Acids Research, Jun 14, 2018
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Proceedings of the National Academy of Sciences of the United States of America, Mar 9, 2017
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物性研究, Apr 20, 2009
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Bulletin of the American Physical Society, Mar 4, 2015
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bioRxiv (Cold Spring Harbor Laboratory), Mar 14, 2023
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ACS Chemical Neuroscience, Oct 5, 2022
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Scientific Reports, Sep 16, 2020
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Papers by Joanna Sulkowska