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A molecular dynamics simulation study of the solvent isotope effect on copper plastocyanin

TitoloA molecular dynamics simulation study of the solvent isotope effect on copper plastocyanin
Tipo di pubblicazioneArticolo su Rivista peer-reviewed
Anno di Pubblicazione1999
AutoriGuzzi, R., Arcangeli Caterina, and Bizzarri A.R.
RivistaBiophysical Chemistry
Volume82
Paginazione9-22
ISSN03014622
Parole chiavearticle, Chemical analysis, chemical structure, Copper, hydrogen bond, isotope, molecular dynamics, molecular interaction, plastocyanin, priority journal, simulation, solvent
Abstract

The effect of heavy water on the structure and dynamics of copper plastocyanin as well as on some aspects of the solvent dynamics at the protein-solvent interfacial region have been investigated by molecular dynamics simulation. The simulated system has been analyzed in terms of the atomic root mean square deviation and fluctuations, intraprotein H-bond pattern, dynamical cross-correlation map and the results have been compared with those previously obtained for plastocyanin in H2O (Ciocchetti et al. Biophys. Chem. 69 (1997), 185-198). The simulated plastocyanin structure in the two solvents, averaging 1 ns, is very similar along the β-structure regions, while the most significant differences are registered, analogous to the turns and the regions likely involved in the electron transfer pathway. Moreover, plastocyanin in D2O shows an increase in the number of both the intraprotein H-bonds and the residues involved in correlated motions. An analysis of the protein-solvent coupling evidenced that D2O makes the H-bond formation more difficult with the solvent molecules for positively charged and polar residues, while an opposite trend is observed for negatively charged residues. On the other hand, the frequency of exchange of the solvent molecules involved in the protein-solvent H-bond formation is significantly depressed in D2O. The results are discussed also in connection with protein functionality and briefly with some experimental results connected with the thermostability of proteins in D2O.

Note

cited By 13

URLhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-0032715218&doi=10.1016%2fS0301-4622%2899%2900097-6&partnerID=40&md5=60e3f9289bd65a33284e312bfa68f6ca
DOI10.1016/S0301-4622(99)00097-6
Citation KeyGuzzi19999