Literature DB >> 27794211

How to fold intricately: using theory and experiments to unravel the properties of knotted proteins.

Sophie E Jackson1, Antonio Suma2, Cristian Micheletti3.   

Abstract

Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native state. Here, we review such developments by paying particular attention to the complementarity of experimental and computational studies. Key open issues that could be tackled with either or both approaches are finally pointed out.
Copyright © 2016 Elsevier Ltd. All rights reserved.

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Year:  2016        PMID: 27794211     DOI: 10.1016/j.sbi.2016.10.002

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  23 in total

1.  Pore translocation of knotted DNA rings.

Authors:  Antonio Suma; Cristian Micheletti
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-28       Impact factor: 11.205

2.  Characterization of the Folding of a 52-Knotted Protein Using Engineered Single-Tryptophan Variants.

Authors:  Hongyu Zhang; Sophie E Jackson
Journal:  Biophys J       Date:  2016-12-20       Impact factor: 4.033

3.  KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers.

Authors:  Luca Tubiana; Guido Polles; Enzo Orlandini; Cristian Micheletti
Journal:  Eur Phys J E Soft Matter       Date:  2018-06-07       Impact factor: 1.890

4.  Genus for biomolecules.

Authors:  Paweł Rubach; Sebastian Zajac; Borys Jastrzebski; Joanna I Sulkowska; Piotr Sułkowski
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

5.  Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.

Authors:  Agata P Perlinska; Adam Stasiulewicz; Ewa K Nawrocka; Krzysztof Kazimierczuk; Piotr Setny; Joanna I Sulkowska
Journal:  PLoS Comput Biol       Date:  2020-05-26       Impact factor: 4.475

6.  Investigation of the structural dynamics of a knotted protein and its unknotted analog using molecular dynamics.

Authors:  José Cícero Alves Silva; Elton José Ferreira Chaves; Gabriel Aires Urquiza de Carvalho; Gerd Bruno Rocha
Journal:  J Mol Model       Date:  2022-03-31       Impact factor: 1.810

7.  The exclusive effects of chaperonin on the behavior of proteins with 52 knot.

Authors:  Yani Zhao; Pawel Dabrowski-Tumanski; Szymon Niewieczerzal; Joanna I Sulkowska
Journal:  PLoS Comput Biol       Date:  2018-03-16       Impact factor: 4.475

8.  Knotting a molecular strand can invert macroscopic effects of chirality.

Authors:  Nathalie Katsonis; Federico Lancia; David A Leigh; Lucian Pirvu; Alexander Ryabchun; Fredrik Schaufelberger
Journal:  Nat Chem       Date:  2020-08-03       Impact factor: 24.427

9.  Tying up the Loose Ends: A Mathematically Knotted Protein.

Authors:  Shang-Te Danny Hsu; Yun-Tzai Cloud Lee; Kornelia M Mikula; Sofia M Backlund; Igor Tascón; Adrian Goldman; Hideo Iwaï
Journal:  Front Chem       Date:  2021-05-24       Impact factor: 5.221

10.  Effects of turn-structure on folding and entanglement in artificial molecular overhand knots.

Authors:  Yiwei Song; Fredrik Schaufelberger; Zoe Ashbridge; Lucian Pirvu; Iñigo J Vitorica-Yrezabal; David A Leigh
Journal:  Chem Sci       Date:  2020-12-08       Impact factor: 9.825

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