Calculation of redox properties

Understanding short- and long-range effects in rubredoxin

Marialore Sulpizi, Simone Raugei, Joost VandeVondele, Paolo Carloni, Michiel Sprik

Research output: Contribution to journalArticle

77 Citations (Scopus)

Abstract

In this computational study we show that for rubredoxin, a small and comparatively simple iron-sulfur protein, it is possible to combine a full ab initio description of the electronic structure of the protein in explicit solvent with sampling of the relevant time scale of the protein dynamics by using a hybrid method based on a force field molecular dynamics/density functional theory scheme. Applying this scheme within the framework of Marcus theory we are able to reproduce the experimental redox potential difference of 60 mV between a mesophilic and thermophilic rubredoxin within an accuracy of 20 mV and explain it in terms of short-range contributions from a few residues close to the metal center. We also compute the reorganization free energy for oxidation of the protein obtaining 720 meV for the mesophilic and 590 meV for thermophilic variant. Decomposition of the reorganization energy by using the classical force field shows that this quantity is largely determined by the solvent, with both short-range (an oxidation induced change of coordination number) and long-range (dielectric) contributions. The 130 meV higher value for the mesophilic form is analyzed in terms of detailed differences in the solvent structure around the metal center and the dielectric response. These results underline the importance of a molecular description of the solvent and of a correct inclusion of the polarization effects.

Original languageEnglish
Pages (from-to)3969-3976
Number of pages8
JournalJournal of Physical Chemistry B
Volume111
Issue number15
DOIs
Publication statusPublished - Apr 19 2007

Fingerprint

Rubredoxins
proteins
Proteins
field theory (physics)
Metals
Electric insulation coordination
Iron-Sulfur Proteins
Oxidation
oxidation
coordination number
metals
Free energy
Electronic structure
Density functional theory
Molecular dynamics
sulfur
Sulfur
sampling
free energy
inclusions

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Calculation of redox properties : Understanding short- and long-range effects in rubredoxin. / Sulpizi, Marialore; Raugei, Simone; VandeVondele, Joost; Carloni, Paolo; Sprik, Michiel.

In: Journal of Physical Chemistry B, Vol. 111, No. 15, 19.04.2007, p. 3969-3976.

Research output: Contribution to journalArticle

Sulpizi, Marialore ; Raugei, Simone ; VandeVondele, Joost ; Carloni, Paolo ; Sprik, Michiel. / Calculation of redox properties : Understanding short- and long-range effects in rubredoxin. In: Journal of Physical Chemistry B. 2007 ; Vol. 111, No. 15. pp. 3969-3976.
@article{ca93ff9e459e4111b31d923e3f215f29,
title = "Calculation of redox properties: Understanding short- and long-range effects in rubredoxin",
abstract = "In this computational study we show that for rubredoxin, a small and comparatively simple iron-sulfur protein, it is possible to combine a full ab initio description of the electronic structure of the protein in explicit solvent with sampling of the relevant time scale of the protein dynamics by using a hybrid method based on a force field molecular dynamics/density functional theory scheme. Applying this scheme within the framework of Marcus theory we are able to reproduce the experimental redox potential difference of 60 mV between a mesophilic and thermophilic rubredoxin within an accuracy of 20 mV and explain it in terms of short-range contributions from a few residues close to the metal center. We also compute the reorganization free energy for oxidation of the protein obtaining 720 meV for the mesophilic and 590 meV for thermophilic variant. Decomposition of the reorganization energy by using the classical force field shows that this quantity is largely determined by the solvent, with both short-range (an oxidation induced change of coordination number) and long-range (dielectric) contributions. The 130 meV higher value for the mesophilic form is analyzed in terms of detailed differences in the solvent structure around the metal center and the dielectric response. These results underline the importance of a molecular description of the solvent and of a correct inclusion of the polarization effects.",
author = "Marialore Sulpizi and Simone Raugei and Joost VandeVondele and Paolo Carloni and Michiel Sprik",
year = "2007",
month = "4",
day = "19",
doi = "10.1021/jp067387y",
language = "English",
volume = "111",
pages = "3969--3976",
journal = "Journal of Physical Chemistry B Materials",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "15",

}

TY - JOUR

T1 - Calculation of redox properties

T2 - Understanding short- and long-range effects in rubredoxin

AU - Sulpizi, Marialore

AU - Raugei, Simone

AU - VandeVondele, Joost

AU - Carloni, Paolo

AU - Sprik, Michiel

PY - 2007/4/19

Y1 - 2007/4/19

N2 - In this computational study we show that for rubredoxin, a small and comparatively simple iron-sulfur protein, it is possible to combine a full ab initio description of the electronic structure of the protein in explicit solvent with sampling of the relevant time scale of the protein dynamics by using a hybrid method based on a force field molecular dynamics/density functional theory scheme. Applying this scheme within the framework of Marcus theory we are able to reproduce the experimental redox potential difference of 60 mV between a mesophilic and thermophilic rubredoxin within an accuracy of 20 mV and explain it in terms of short-range contributions from a few residues close to the metal center. We also compute the reorganization free energy for oxidation of the protein obtaining 720 meV for the mesophilic and 590 meV for thermophilic variant. Decomposition of the reorganization energy by using the classical force field shows that this quantity is largely determined by the solvent, with both short-range (an oxidation induced change of coordination number) and long-range (dielectric) contributions. The 130 meV higher value for the mesophilic form is analyzed in terms of detailed differences in the solvent structure around the metal center and the dielectric response. These results underline the importance of a molecular description of the solvent and of a correct inclusion of the polarization effects.

AB - In this computational study we show that for rubredoxin, a small and comparatively simple iron-sulfur protein, it is possible to combine a full ab initio description of the electronic structure of the protein in explicit solvent with sampling of the relevant time scale of the protein dynamics by using a hybrid method based on a force field molecular dynamics/density functional theory scheme. Applying this scheme within the framework of Marcus theory we are able to reproduce the experimental redox potential difference of 60 mV between a mesophilic and thermophilic rubredoxin within an accuracy of 20 mV and explain it in terms of short-range contributions from a few residues close to the metal center. We also compute the reorganization free energy for oxidation of the protein obtaining 720 meV for the mesophilic and 590 meV for thermophilic variant. Decomposition of the reorganization energy by using the classical force field shows that this quantity is largely determined by the solvent, with both short-range (an oxidation induced change of coordination number) and long-range (dielectric) contributions. The 130 meV higher value for the mesophilic form is analyzed in terms of detailed differences in the solvent structure around the metal center and the dielectric response. These results underline the importance of a molecular description of the solvent and of a correct inclusion of the polarization effects.

UR - http://www.scopus.com/inward/record.url?scp=34247868775&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34247868775&partnerID=8YFLogxK

U2 - 10.1021/jp067387y

DO - 10.1021/jp067387y

M3 - Article

VL - 111

SP - 3969

EP - 3976

JO - Journal of Physical Chemistry B Materials

JF - Journal of Physical Chemistry B Materials

SN - 1520-6106

IS - 15

ER -