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Long-term molecular dynamics simulation of copper azurin: Structure, dynamics and functionality

TitleLong-term molecular dynamics simulation of copper azurin: Structure, dynamics and functionality
Publication TypeArticolo su Rivista peer-reviewed
Year of Publication1999
AuthorsArcangeli, Caterina, Bizzarri A.R., and Cannistraro S.
JournalBiophysical Chemistry
Volume78
Pagination247-257
ISSN03014622
Keywordsarticle, azurin, Computer simulation, Copper, Crystallography, electron transport, molecular dynamics, plastocyanin, priority journal, protein secondary structure, simulation
Abstract

A long-term molecular dynamics simulation (1.1 ns), at 300 K, of fully hydrated azurin has been performed to put into relationship the protein dynamics to functional properties with particular attention to those structural elements involved in the electron transfer process. A detailed analysis of the root mean square deviations and fluctuations and of the intraprotein H-bonding pattern has allowed us to demonstrate that a rigid arrangement of the β-stranded protein skeleton is maintained during the simulation run, while a large mobility is registered in the solvent-exposed connecting regions (turns) and in the α-helix. Moreover, the structural elements, likely involved in the electron transfer path, show a stable H-bonding arrangement and low fluctuations. Analysis of the dynamical cross-correlation map has revealed the existence of correlated motions among residues connected by hydrogen bonds and of correlated and anti-correlated motions between regions which are supposed to be involved in the functional process, namely the hydrophobic patch and the regions close to the copper reaction center. The results are briefly discussed also in connection to the current through-bond tunneling model for the electron transfer process. Finally, a comparison with the structural and the dynamical behaviour of plastocyanin, whose structure and functional role are very similar to those of azurin, has been performed. Copyright (C) 1999 Elsevier Science B.V. All rights reserved.

Notes

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URLhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-0032896949&doi=10.1016%2fS0301-4622%2899%2900029-0&partnerID=40&md5=bcadb11dae9f33fb165fe981c82edae8
DOI10.1016/S0301-4622(99)00029-0
Citation KeyArcangeli1999247