Literature DB >> 22105789

Knot theory in understanding proteins.

Rama Mishra1, Shantha Bhushan.   

Abstract

This paper aims to enthuse mathematicians, especially topologists, knot theorists and geometers to examine problems in the study of proteins. We have highlighted those advances and breakthroughs in knot theory that directly and indirectly help in understanding proteins. We have discussed the phenomena of knotting of protein backbone. This paper also provides a few open questions for knot theorists, the answers to which will help in further understanding of proteins.

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Year:  2011        PMID: 22105789     DOI: 10.1007/s00285-011-0488-3

Source DB:  PubMed          Journal:  J Math Biol        ISSN: 0303-6812            Impact factor:   2.259


  27 in total

1.  An enzyme with a deep trefoil knot for the active-site architecture.

Authors:  Osamu Nureki; Mikako Shirouzu; Kyoko Hashimoto; Ryuichiro Ishitani; Takaho Terada; Masatada Tamakoshi; Tairo Oshima; Masao Chijimatsu; Koji Takio; Dmitry G Vassylyev; Takehiko Shibata; Yorinao Inoue; Seiki Kuramitsu; Shigeyuki Yokoyama
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-06-20

2.  Experimental detection of knotted conformations in denatured proteins.

Authors:  Anna L Mallam; Joseph M Rogers; Sophie E Jackson
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-14       Impact factor: 11.205

3.  Untangling the folding mechanism of the 5(2)-knotted protein UCH-L3.

Authors:  Fredrik I Andersson; David G Pina; Anna L Mallam; Georg Blaser; Sophie E Jackson
Journal:  FEBS J       Date:  2009-03-24       Impact factor: 5.542

4.  A knot or not a knot? SETting the record 'straight' on proteins.

Authors:  William R Taylor; Bing Xiao; Steven J Gamblin; Kuang Lin
Journal:  Comput Biol Chem       Date:  2003-02       Impact factor: 2.877

5.  Threading a peptide through a peptide: protein loops, rotaxanes, and knots.

Authors:  John W Blankenship; Philip E Dawson
Journal:  Protein Sci       Date:  2007-06-13       Impact factor: 6.725

6.  Rapid knot detection and application to protein structure prediction.

Authors:  Firas Khatib; Matthew T Weirauch; Carol A Rohl
Journal:  Bioinformatics       Date:  2006-07-15       Impact factor: 6.937

7.  Are there knots in proteins?

Authors:  M L Mansfield
Journal:  Nat Struct Biol       Date:  1994-04

8.  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

9.  Statistics of knots, geometry of conformations, and evolution of proteins.

Authors:  Rhonald C Lua; Alexander Y Grosberg
Journal:  PLoS Comput Biol       Date:  2006-05-19       Impact factor: 4.475

10.  Intricate knots in proteins: Function and evolution.

Authors:  Peter Virnau; Leonid A Mirny; Mehran Kardar
Journal:  PLoS Comput Biol       Date:  2006-07-28       Impact factor: 4.475

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  3 in total

1.  A Knot Polynomial Invariant for Analysis of Topology of RNA Stems and Protein Disulfide Bonds.

Authors:  Wei Tian; Xue Lei; Louis H Kauffman; Jie Liang
Journal:  Mol Based Math Biol       Date:  2017-01

2.  Topological dynamics of an intrinsically disordered N-terminal domain of the human androgen receptor.

Authors:  Vahid Sheikhhassani; Barbara Scalvini; Julian Ng; Laurens W H J Heling; Yosri Ayache; Tom M J Evers; Eva Estébanez-Perpiñá; Iain J McEwan; Alireza Mashaghi
Journal:  Protein Sci       Date:  2022-06       Impact factor: 6.993

Review 3.  The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations.

Authors:  Roberto Covino; Tatjana Skrbić; Silvio A Beccara; Pietro Faccioli; Cristian Micheletti
Journal:  Biomolecules       Date:  2013-12-24
  3 in total

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