PMID: 11321674Apr 26, 2001Paper

Concerted motions in copper plastocyanin and azurin: an essential dynamics study

Biophysical Chemistry
C ArcangeliS Cannistraro

Abstract

Essential dynamics analysis of molecular dynamics simulation trajectories (1.1 ns) of two copper containing electron transfer proteins, plastocyanin and azurin, has been performed. The protein essential modes have been analysed in order to identify large concerted motions which could be relevant for the electron transfer function exerted by these proteins. The analysis, conducted for temporal windows of different lengths along the protein trajectories, shows a rapid convergence and indicates that for both the proteins the predominant internal motions occur in a subspace of only a few degrees of freedom. Moreover, it is found that for both the proteins the likely binding sites (i.e. the hydrophobic and negative patches) with the reaction partners move in a concerted fashion with a few structural regions far from the active site. Such results are discussed in connection with the possible involvement of large concerted motions in the recognition and binding interaction with physiological electron transfer partners.

References

Mar 1, 1990·Journal of Molecular Graphics·G Vriend
Jan 1, 1988·Annual Review of Biophysics and Biophysical Chemistry·H FrauenfelderR D Young
Jan 1, 1983·Biopolymers·R Huber, W S Bennett
Apr 11, 1995·Proceedings of the National Academy of Sciences of the United States of America·J B ClarageG N Phillips
Feb 1, 1994·Journal of Bioenergetics and Biomembranes·M R RedinboS Merchant
Dec 1, 1993·Proteins·A AmadeiH J Berendsen
Oct 1, 1996·Biophysical Journal·B L de GrootH J Berendsen
Feb 1, 1996·Journal of Biomolecular Structure & Dynamics·A AmadeiH J Berendsen
Dec 23, 1998·Protein Engineering·D M van AaltenK J Hellingwerf
Apr 27, 1992·Physical Review Letters·A E García
Oct 13, 2006·Biophysical Chemistry·A CiocchettiS Cannistraro

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Citations

Jan 25, 2005·Journal of Computer-aided Molecular Design·John Mongan
Oct 15, 2003·Biophysical Chemistry·Anna Rita BizzarriSalvatore Cannistraro
Jan 28, 2003·Current Opinion in Chemical Biology·Lucia Banci
Feb 25, 2009·Journal of Biomolecular Structure & Dynamics·Malkaram S Achary, Hampapathalu A Nagarajaram
Feb 22, 2003·Nucleic Acids Research·Giovanni ChillemiAlessandro Desideri
Nov 17, 2009·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Francisco J Muñoz-LópezPaolo Carloni
Jul 11, 2013·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Stefania EvoliBruno Rizzuti
Sep 3, 2011·Biophysical Chemistry·Edi GabellieriPatrizia Cioni
Apr 20, 2010·FEBS Letters·Francisco J Muñoz-LópezAntonio Díaz-Quintana
Mar 29, 2005·Biophysical Journal·Patrizia CioniGiovanni B Strambini
Jan 30, 2004·Biophysical Journal·Patrizia CioniGiovanni B Strambini
May 26, 2017·Protein Science : a Publication of the Protein Society·Ariel R LevySharon Ruthstein
Mar 5, 2005·Chembiochem : a European Journal of Chemical Biology·Marieke van den BoschGerard W Canters
Dec 18, 2015·Physical Chemistry Chemical Physics : PCCP·Debodyuti Dutta, Sabyashachi Mishra
Apr 12, 2005·Protein Engineering, Design & Selection : PEDS·A Pandini, L Bonati
Jun 24, 2009·ACS Nano·Mattia FalconiAlessandro Desideri
Mar 15, 2013·The Journal of Physical Chemistry. B·Martin McCullagh, Gregory A Voth
Sep 2, 2009·Journal of Molecular Graphics & Modelling·Sarkkarai Raja SinghChandran Karunakaran

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