Toward a DFT-based molecular dynamics description of Co(II) binding in sulfur-rich peptides

Physical Chemistry Chemical Physics : PCCP
Riccardo SpeziaMarie-Pierre Gaigeot

Abstract

In this paper, we investigated the reliability of a Car-Parrinello molecular dynamics (CPMD) approach to characterize the binding of Co(II) metal cation to peptide molecules containing cysteine. To this end, we compared pseudo-potentials and DFT plane wave expansion, which are used as key ingredients in the CPMD method, with standard all-electron Gaussian basis set DFT calculations. The simulations presented here are the first attempts to characterize interactions and dynamics of Co(II) metal with the building blocks of phytochelatin peptide molecules. Benchmark calculations are performed on [Co(Cys-H)]+ and [Co(Glutathione-H)]+ complexes, since they are the main fragments of the Co(II)-Cys and Co(II)-glutathione systems found in gas phase electrospray ionisation mass spectrometry (ESI-MS) experiments done in our laboratory. We also present benchmark calculations on the [Co(H2O)6)]2+ cluster with direct comparisons to highly correlated ab initio calculations and experiments. In particular, we investigated the dissociation path of one water molecule from the first hydration shell of Co(II) with CPMD. Overall, our molecular dynamics simulations shed some light on the nature of the Co(II) interaction and reactivity in Co(II)-phyto...Continue Reading

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Citations

Sep 24, 2013·Journal of Molecular Graphics & Modelling·Aravindhan GanesanJulen Larrucea
Aug 5, 2014·Journal of Molecular Modeling·Riccardo SpeziaRodolphe Vuilleumier
Dec 22, 2014·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·Md Elius HossainMohammad A Halim
Nov 15, 2014·Journal of Mass Spectrometry : JMS·Maria I H Schmied-TobiesThorsten Reemtsma
Apr 16, 2020·Environmental Microbiology·Todsapol TechoChoowong Auesukaree
Feb 27, 2007·Journal of Mass Spectrometry : JMS·William BuchmannJeanine Tortajada
Jan 15, 2014·Physical Chemistry Chemical Physics : PCCP·Fausto MartelliRiccardo Spezia
Apr 30, 2008·The Journal of Physical Chemistry. B·Riccardo SpeziaMarie-Pierre Gaigeot
Jul 14, 2009·The Journal of Physical Chemistry. a·Erika ConstantinoLuis Rodríguez-Santiago
Jun 16, 2009·The Journal of Physical Chemistry. a·Yannick Jeanvoine, Riccardo Spezia
Dec 1, 2006·The Journal of Physical Chemistry. a·Riccardo SpeziaMarie-Pierre Gaigeot
Aug 4, 2006·The Journal of Physical Chemistry. a·Riccardo SpeziaYannick Jeanvoine

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