A method for the analysis of domain movements in large biomolecular complexes

Proteins
Guru Prasad PoornamSteven Hayward

Abstract

A new method for the analysis of domain movements in large, multichain, biomolecular complexes is presented. The method is applicable to any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement. The method is blind to atomic bonding and atom type and can, therefore, be applied to biomolecular complexes containing different constituent molecules such as protein, RNA, or DNA. At the heart of the method is the use of blocks located at grid points spanning the whole molecule. The rotation vector for the rotation of atoms from each block between the two conformations is calculated. Treating components of these vectors as coordinates means that each block is associated with a point in a "rotation space" and that blocks with atoms that rotate together, perhaps as part of the same rigid domain, will have colocated points. Thus a domain can be identified from the clustering of points from blocks that span it. Domain pairs are accepted for analysis of their relative movements in terms of screw axes based upon a set of reasonable criteria. Here, we report on the application of the method to biomolecules covering a considerable size range: hemoglobin, liver alco...Continue Reading

References

Apr 5, 1979·Journal of Molecular Biology·J Baldwin, C Chothia
Nov 1, 1978·Proceedings of the National Academy of Sciences of the United States of America·H L MonacoW N Lipscomb
Mar 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·K L KrauseW N Lipscomb
Dec 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·R B Honzatko, W N Lipscomb
Sep 1, 1995·Trends in Biochemical Sciences·R A Sayle, E J Milner-White
Jan 1, 1997·Annual Review of Biochemistry·P D Boyer
Feb 19, 1999·Proteins·K HinsenM J Field
Apr 5, 2001·Protein Engineering·F Tama, Y H Sanejouand
Sep 11, 2002·Journal of Molecular Biology·Yue YuanChien Ho
Dec 5, 2002·Journal of Molecular Graphics & Modelling·Steven Hayward, Richard A Lee
Jul 2, 2003·Bioinformatics·Richard A LeeSteven Hayward
Jul 1, 1997·Acta Crystallographica. Section D, Biological Crystallography·J F HuntJ Deisenhofer
Apr 2, 2005·Bioinformatics·Guoying QiSteven Hayward
Sep 7, 2005·Current Opinion in Structural Biology·Ivet Bahar, A J Rader
Jan 21, 2006·Current Opinion in Structural Biology·Joanna F Swain, Lila M Gierasch

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Citations

Dec 22, 2011·Proceedings of the National Academy of Sciences of the United States of America·Fumiaki YumotoRobert J Fletterick
Mar 19, 2013·PloS One·Charles K AllerstonOpher Gileadi
Nov 22, 2013·PloS One·Daniel TaylorSteven Hayward
Nov 6, 2015·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Christopher Girdlestone, Steven Hayward
May 20, 2015·Computational and Structural Biotechnology Journal·Nivedita Rai, Amutha Ramaswamy
Mar 10, 2016·Acta Crystallographica. Section D, Structural Biology·Richard D Bunker
Sep 5, 2015·Journal of Biomolecular Structure & Dynamics·Daniela BaroneLuigi Vitagliano
Aug 17, 2010·Archives of Biochemistry and Biophysics·Stéphane MouilleronBéatrice Golinelli-Pimpaneau
Mar 1, 2012·Journal of Molecular Biology·Jason C Porta, Gloria E O Borgstahl
Feb 7, 2012·Journal of Molecular Biology·Justyna Aleksandra WojdylaColin Kleanthous
Apr 22, 2016·Protein Engineering, Design & Selection : PEDS·S R SalinasL Ielpi
Jan 28, 2014·Journal of Structural Biology·Matthias ZebischNorbert Sträter
Jan 1, 2012·Computational and Structural Biotechnology Journal·Rajni VermaDanilo Roccatano
Jan 28, 2015·Proceedings of the National Academy of Sciences of the United States of America·Solmaz SobhanifarNatalie C J Strynadka
Jun 17, 2016·Proceedings of the National Academy of Sciences of the United States of America·Yi MiaoRichard G Brennan
Nov 18, 2015·Enzyme Research·Paola R BeassoniAngela T Lisa
Sep 3, 2016·Bioinformatics·Thach Nguyen, Michael Habeck
Oct 11, 2016·Journal of Chemical Theory and Computation·Aravind ChandrasekaranLee-Wei Yang
Sep 15, 2015·PLoS Computational Biology·Stephan KöhlerGiovanni Settanni
Jun 16, 2017·Journal of Biomolecular Structure & Dynamics·Prabu Manoharan, Nanda Ghoshal
May 3, 2018·Acta Crystallographica. Section F, Structural Biology Communications·Yong Ju Kim
Feb 7, 2014·Nature Communications·Patricia CasinoAlberto Marina
Jan 1, 2014·SIAM Journal on Scientific Computing : a Publication of the Society for Industrial and Applied Mathematics·Chandrajit BajajAntje Vollrath
Apr 23, 2013·Nature·Yong Ju KimMartha E Sommer
Dec 11, 2019·The Journal of Biological Chemistry·Jakob H MikkelsenChristian B F Andersen
Apr 17, 2020·Protein Science : a Publication of the Protein Society·Kathryn M FergusonMark A Lemmon
Oct 5, 2019·Acta Crystallographica. Section F, Structural Biology Communications·Clement Angkawidjaja, Takashi Torashima

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