Calculation of redox properties: Understanding short- and long-range effects in rubredoxin

Autoren

Marialore Sulpizi
Simone Raugei
Joost VandeVondele
Paolo Carloni
Michiel Sprik

DOI

10.1021/jp067387y

eISSN

1520-5207

ISSN

1520-6106

Ausgabe der Veröffentlichung

15

Zeitschrift

The Journal of Physical Chemistry B

Sprache

en

Online publication date

2007

Paginierung

3969 - 3976

Datum der Veröffentlichung

2007

Status

Published

Herausgeber

American Chemical Society (ACS)

Herausgeber URL

http://dx.doi.org/10.1021/jp067387y

Datum der Datenerfassung

2023

Titel

Calculation of Redox Properties: Understanding Short- and Long-Range Effects in Rubredoxin

Ausgabe der Zeitschrift

111

Datenquelle: Crossref

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.

Addresses

Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom. ms647@cam.ac.uk

Autoren

Marialore Sulpizi
Simone Raugei
Joost VandeVondele
Paolo Carloni
Michiel Sprik

DOI

10.1021/jp067387y

eISSN

1520-5207

Externe Identifier

PubMed Identifier: 17388622

Open access

false

ISSN

1520-6106

Ausgabe der Veröffentlichung

15

Zeitschrift

The journal of physical chemistry. B

Schlüsselwörter

Rubredoxins
Protein Conformation
Oxidation-Reduction
Hydrogen Bonding
Thermodynamics
Models, Chemical
Models, Molecular
Time Factors
Computer Simulation

Sprache

eng

Medium

Print-Electronic

Online publication date

2007

Paginierung

3969 - 3976

Datum der Veröffentlichung

2007

Status

Published

Datum der Datenerfassung

2007

Titel

Calculation of redox properties: understanding short- and long-range effects in rubredoxin.

Sub types

Research Support, Non-U.S. Gov't
Journal Article

Ausgabe der Zeitschrift

111

Datenquelle: Europe PubMed Central

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.

Autoren

Marialore Sulpizi
Simone Raugei
Joost VandeVondele
Paolo Carloni
Michiel Sprik

Autoren-URL

https://www.ncbi.nlm.nih.gov/pubmed/17388622

DOI

10.1021/jp067387y

ISSN

1520-6106

Ausgabe der Veröffentlichung

15

Zeitschrift

J Phys Chem B

Schlüsselwörter

Computer Simulation
Hydrogen Bonding
Models, Chemical
Models, Molecular
Oxidation-Reduction
Protein Conformation
Rubredoxins
Thermodynamics
Time Factors

Sprache

eng

Country

United States

Paginierung

3969 - 3976

Datum der Veröffentlichung

2007

Status

Published

Datum, an dem der Datensatz öffentlich gemacht wurde

2007

Titel

Calculation of redox properties: understanding short- and long-range effects in rubredoxin.

Sub types

Journal Article
Research Support, Non-U.S. Gov't

Ausgabe der Zeitschrift

111

Datenquelle: PubMed

Calculation of redox properties: Understanding short- and long-range effects in rubredoxin

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