دورية أكاديمية
AlphaFold predicts novel human proteins with knots.
| العنوان: | AlphaFold predicts novel human proteins with knots. |
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| المؤلفون: | Perlinska AP; Centre of New Technologies, University of Warsaw, Warsaw, Poland., Niemyska WH; Centre of New Technologies, University of Warsaw, Warsaw, Poland.; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland., Gren BA; Centre of New Technologies, University of Warsaw, Warsaw, Poland.; Faculty of Physics, University of Warsaw, Warsaw, Poland., Bukowicki M; Faculty of Physics, University of Warsaw, Warsaw, Poland., Nowakowski S; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.; Faculty of Physics, University of Warsaw, Warsaw, Poland., Rubach P; Centre of New Technologies, University of Warsaw, Warsaw, Poland.; Warsaw School of Economics, Warsaw, Poland., Sulkowska JI; Centre of New Technologies, University of Warsaw, Warsaw, Poland. |
| المصدر: | Protein science : a publication of the Protein Society [Protein Sci] 2023 May; Vol. 32 (5), pp. e4631. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: 2001- : Woodbury, NY : Cold Spring Harbor Laboratory Press Original Publication: New York, N.Y. : Cambridge University Press, c1992- |
| مواضيع طبية MeSH: | Protein Folding* , Proteome*, Humans ; Protein Conformation |
| مستخلص: | 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 6 (© 2023 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.) |
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| فهرسة مساهمة: | Keywords: biological function; evolution; folding; new knotted folds |
| المشرفين على المادة: | 0 (Proteome) |
| تواريخ الأحداث: | Date Created: 20230324 Date Completed: 20230501 Latest Revision: 20230601 |
| رمز التحديث: | 20231215 |
| مُعرف محوري في PubMed: | PMC10108431 |
| DOI: | 10.1002/pro.4631 |
| PMID: | 36960558 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1469-896X |
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| DOI: | 10.1002/pro.4631 |