PMID: 11917144Mar 28, 2002Paper

A Fourier analysis of symmetry in protein structure

Protein Engineering
W R TaylorTomas P Flores

Abstract

The score matrix from a structure comparison program (SAP) was used to search for repeated structures using a Fourier analysis. When tested with artificial data, a simple Fourier transform of the smoothed matrix provided a clear signal of the repeat periodicity that could be used to extract the repeating units with the SAP program. The strength of the Fourier signal was calibrated against the signal from model proteins. The most useful of these was the novel random-walk approach employed to generate realistic 'fake' structures. On the basis of these it was possible to conclude that only a small proportion of protein structures have an unexpected degree of symmetry. Artificially generated 'ideal' folds provided an upper limit on the strength of signal that could be expected from a 'perfectly' repeating compact structure. Unexpectedly, some of the very regular beta-propellor folds attained the same strength but the majority of symmetric structures lay below this region. When native proteins were ranked by the power of their spectrum a wide variety of fold types were seen to score highly. In the betaalpha class, these included the globular betaalpha proteins and the more repetitive leucine-rich betaalpha folds. In the all-beta cla...Continue Reading

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Citations

Jun 25, 2003·Computational Biology and Chemistry·William R TaylorRobert P Bywater
Mar 9, 2012·Bioinformatics·M I Sadowski, W R Taylor
Jun 8, 2010·BMC Bioinformatics·Changhoon KimByungkook Lee
Nov 23, 2006·BMC Bioinformatics·Vijayaraj NagarajanYouping Deng
May 2, 2009·The Journal of Chemical Physics·Kenneth C MillettAndrzej Stasiak
Jun 29, 2011·Journal of Theoretical Biology·Xiaojuan Shen
Jun 14, 2013·The Journal of Physical Chemistry. B·R Gonzalo ParraDiego U Ferreiro
Jul 21, 2009·Computational Biology and Chemistry·Yi HeYi Xiao
Sep 11, 2008·Computational Biology and Chemistry·Hanlin ChenYi Xiao
Jun 19, 2007·Journal of Molecular Graphics & Modelling·Xiaochun WangYi Xiao
Feb 3, 2007·Computational Biology and Chemistry·Xiaofeng JiYi Xiao
Sep 2, 2004·Proteins·Kevin B MurrayJanet M Thornton
Jun 24, 2004·Proteins·William R Taylor, Inge Jonassen
Jun 6, 2006·Proteins·William R TaylorInge Jonassen
Nov 2, 2007·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Julia Hartling, Junhyong Kim
Feb 7, 2006·Journal of Molecular Biology·William R Taylor
Jun 28, 2005·Computational Biology and Chemistry·Andrew A LaskinEugene V Korotkov
Jun 28, 2011·Computational Biology and Chemistry·Rui ZhouYi Xiao
Dec 8, 2015·PloS One·Xiaojuan ShenGuanglin Li
Oct 18, 2016·BioMed Research International·Ashwani JhaDukka B Kc
Nov 26, 2020·Nucleic Acids Research·Lisanna PaladinSilvio C E Tosatto
Sep 5, 2009·Journal of Chemical Information and Modeling·Aysam GuerlerErnst-Walter Knapp

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