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Piejko M, Niewieczerzal S, Sulkowska JI. The Folding of Knotted Proteins: Distinguishing the Distinct Behavior of Shallow and Deep Knots. Isr J Chem 2020. [DOI: 10.1002/ijch.202000036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Maciej Piejko
- Faculty of ChemistryUniversity of Warsaw Pasteura 1 Warsaw 02-093 Poland
- Centre of New TechnologiesUniversity of Warsaw Banacha 2c Warsaw 02-097 Poland
| | | | - Joanna I. Sulkowska
- Faculty of ChemistryUniversity of Warsaw Pasteura 1 Warsaw 02-093 Poland
- Centre of New TechnologiesUniversity of Warsaw Banacha 2c Warsaw 02-097 Poland
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2
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Rubach P, Zajac S, Jastrzebski B, Sulkowska JI, Sułkowski P. Genus for biomolecules. Nucleic Acids Res 2020; 48:D1129-D1135. [PMID: 31584078 PMCID: PMC6943057 DOI: 10.1093/nar/gkz845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/17/2019] [Accepted: 10/02/2019] [Indexed: 01/03/2023] Open
Abstract
The 'Genus for biomolecules' database (http://genus.fuw.edu.pl) collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given chain and its subchains. For each biomolecule, this information is shown in the form of a genus trace plot, as well as a genus matrix diagram. We assemble such information for all and RNA structures deposited in the Protein Data Bank (PDB). This database presents also various statistics and extensive information about the biological function of the analyzed biomolecules. The database is regularly self-updating, once new structures are deposited in the PDB. Moreover, users can analyze their own structures.
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Affiliation(s)
- Paweł Rubach
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Warsaw School of Economics, Al. Niepodległości 162, 02-554 Warsaw, Poland
| | - Sebastian Zajac
- Warsaw School of Economics, Al. Niepodległości 162, 02-554 Warsaw, Poland
| | - Borys Jastrzebski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Piotr Sułkowski
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
- Walter Burke Institute for Theoretical Physics, California Institute of Technology, Pasadena, CA 91125, USA
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Dabrowski-Tumanski P, Rubach P, Goundaroulis D, Dorier J, Sułkowski P, Millett KC, Rawdon EJ, Stasiak A, Sulkowska JI. KnotProt 2.0: a database of proteins with knots and other entangled structures. Nucleic Acids Res 2019; 47:D367-D375. [PMID: 30508159 PMCID: PMC6323932 DOI: 10.1093/nar/gky1140] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/24/2018] [Accepted: 11/30/2018] [Indexed: 01/08/2023] Open
Abstract
The KnotProt 2.0 database (the updated version of the KnotProt database) collects information about proteins which form knots and other entangled structures. New features in KnotProt 2.0 include the characterization of both probabilistic and deterministic entanglements which can be formed by disulfide bonds and interactions via ions, a refined characterization of entanglement in terms of knotoids, the identification of the so-called cysteine knots, the possibility to analyze all or a non-redundant set of proteins, and various technical updates. The KnotProt 2.0 database classifies all entangled proteins, represents their complexity in the form of a knotting fingerprint, and presents many biological and geometrical statistics based on these results. Currently the database contains >2000 entangled structures, and it regularly self-updates based on proteins deposited in the Protein Data Bank (PDB).
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland
| | - Pawel Rubach
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland
- Warsaw School of Economics, Al. Niepodlegosci 162, Warsaw, Poland
| | - Dimos Goundaroulis
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Julien Dorier
- Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Piotr Sułkowski
- Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, Poland
- Walter Burke Institute for Theoretical Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kenneth C Millett
- Department of Mathematics, University of California, Santa Barbara, CA 93106, USA
| | - Eric J Rawdon
- Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Joanna I Sulkowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland
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Dabrowski-Tumanski P, Piejko M, Niewieczerzal S, Stasiak A, Sulkowska JI. Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting from the Ribosome Exit Channel. J Phys Chem B 2018; 122:11616-11625. [PMID: 30198720 DOI: 10.1021/acs.jpcb.8b07634] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The mechanism of folding of deeply knotted proteins into their native structure is still not understood. Current thinking about protein folding is dominated by the Anfinsen dogma, stating that the structure of the folded proteins is uniquely dictated by the amino acid sequence of a given protein and that the folding is driven uniquely by the energy gained from interactions between amino acids that contact each other in the native structure of the protein. The role of ribosomes in protein folding was only seen as permitting the folding to progress from the N-terminal part of nascent protein chains. We propose here that ribosomes can participate actively in the folding of knotted proteins by actively threading nascent chains emerging from the ribosome exit channels through loops formed by a synthesized earlier portion of the same protein. Our simulations of folding of deeply knotted protein Tp0624 positively verify the proposed ribosome-driven active threading mechanism leading to the formation of deeply knotted proteins.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 , Warsaw , Poland.,Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
| | - Maciej Piejko
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 , Warsaw , Poland.,Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
| | - Szymon Niewieczerzal
- Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
| | - Andrzej Stasiak
- Center for Integrative Genomics , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Joanna I Sulkowska
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 , Warsaw , Poland.,Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
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