Literature DB >> 26958882

Untangling the Influence of a Protein Knot on Folding.

Dominique T Capraro1, Patricia A Jennings2.   

Abstract

Entanglement and knots occur across all aspects of the physical world. Despite the common belief that knots are too complicated for incorporation into proteins, knots have been identified in the native fold of a growing number of proteins. The discovery of proteins with this unique backbone characteristic has challenged the preconceptions about the complexity of biological structures, as well as current folding theories. Given the intricacies of the knotted geometry, the interplay between a protein's fold, structure, and function is of particular interest. Interestingly, for most of these proteins, the knotted region appears critical both in folding and function, although full understanding of these contributions is still incomplete. Here, we experimentally reveal the impact of the knot on the landscape, the origin of the bistable nature of the knotted protein, and broaden the view of knot formation as uniquely decoupled from folding.
Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2016        PMID: 26958882      PMCID: PMC4788744          DOI: 10.1016/j.bpj.2016.01.017

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  37 in total

1.  Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins.

Authors:  Anna L Mallam; Sophie E Jackson
Journal:  Nat Chem Biol       Date:  2011-12-18       Impact factor: 15.040

2.  Conservation of complex knotting and slipknotting patterns in proteins.

Authors:  Joanna I Sułkowska; Eric J Rawdon; Kenneth C Millett; Jose N Onuchic; Andrzej Stasiak
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-08       Impact factor: 11.205

3.  β-Bulge triggers route-switching on the functional landscape of interleukin-1β.

Authors:  Dominique T Capraro; Melinda Roy; José N Onuchic; Shachi Gosavi; Patricia A Jennings
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-17       Impact factor: 11.205

4.  The rough energy landscape of superfolder GFP is linked to the chromophore.

Authors:  Benjamin T Andrews; Andrea R Schoenfish; Melinda Roy; Geoffrey Waldo; Patricia A Jennings
Journal:  J Mol Biol       Date:  2007-08-15       Impact factor: 5.469

5.  Energy landscape of knotted protein folding.

Authors:  Joanna I Sułkowska; Jeffrey K Noel; Jose N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2012-08-13       Impact factor: 11.205

6.  Protein folding. Translational tuning optimizes nascent protein folding in cells.

Authors:  Soo Jung Kim; Jae Seok Yoon; Hideki Shishido; Zhongying Yang; LeeAnn A Rooney; Jose M Barral; William R Skach
Journal:  Science       Date:  2015-04-24       Impact factor: 47.728

7.  Mechanistic insights into the folding of knotted proteins in vitro and in vivo.

Authors:  Nicole C H Lim; Sophie E Jackson
Journal:  J Mol Biol       Date:  2014-09-16       Impact factor: 5.469

8.  Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons.

Authors:  H Roder; K Wüthrich
Journal:  Proteins       Date:  1986-09

9.  Knotted vs. unknotted proteins: evidence of knot-promoting loops.

Authors:  Raffaello Potestio; Cristian Micheletti; Henri Orland
Journal:  PLoS Comput Biol       Date:  2010-07-29       Impact factor: 4.475

10.  Chromophore packing leads to hysteresis in GFP.

Authors:  Benjamin T Andrews; Melinda Roy; Patricia A Jennings
Journal:  J Mol Biol       Date:  2009-07-03       Impact factor: 5.469

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  6 in total

1.  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

2.  Converging experimental and computational views of the knotting mechanism of a small knotted protein.

Authors:  Cristina Paissoni; Sarita Puri; Iren Wang; Szu-Yu Chen; Carlo Camilloni; Shang-Te Danny Hsu
Journal:  Biophys J       Date:  2021-04-01       Impact factor: 3.699

3.  The energy cost of polypeptide knot formation and its folding consequences.

Authors:  Andrés Bustamante; Juan Sotelo-Campos; Daniel G Guerra; Martin Floor; Christian A M Wilson; Carlos Bustamante; Mauricio Báez
Journal:  Nat Commun       Date:  2017-11-17       Impact factor: 14.919

4.  Topological descriptions of protein folding.

Authors:  Erica Flapan; Adam He; Helen Wong
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-18       Impact factor: 11.205

5.  The AAA+ protease ClpXP can easily degrade a 31 and a 52-knotted protein.

Authors:  Elin M Sivertsson; Sophie E Jackson; Laura S Itzhaki
Journal:  Sci Rep       Date:  2019-02-20       Impact factor: 4.379

6.  Folding analysis of the most complex Stevedore's protein knot.

Authors:  Iren Wang; Szu-Yu Chen; Shang-Te Danny Hsu
Journal:  Sci Rep       Date:  2016-08-16       Impact factor: 4.379

  6 in total

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