Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2022 Feb 5;27(3):1077.
doi: 10.3390/molecules27031077.

Theoretical Modeling of Redox Potentials of Biomolecules

Cheng Giuseppe Chen  1 , Alessandro Nicola Nardi  1 , Andrea Amadei  2 , Marco D'Abramo  1
Affiliations
Review

Theoretical Modeling of Redox Potentials of Biomolecules

Cheng Giuseppe Chen et al. Molecules. .

Abstract

The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.

Keywords: DNA; proteins; redox potentials; theoretical-computational chemistry.

PubMed Disclaimer

Conflict of interest statement

The authors have no conflict of interest to declare.

Figures

Figure 1
Figure 1
Synthetic scheme of available computational approaches.
Figure 2
Figure 2
Cartoon representations of the Azurin protein (left) from Pseudomonas aeruginosa (PDB: 4AZU) and its copper binding site (right).
Figure 3
Figure 3
Fe4S4 cluster (right) found in high-potential iron–sulfur proteins I from E. Halophila (left).
Figure 4
Figure 4
FAD cofactor (right) found in cholesterol oxidase from Streptomyces (left).
Figure 5
Figure 5
Crystal structure of diheme cytochrome c (DHC) from Rhodobacter Sphaeroides (cartoons, left) and its active site (right).
Figure 6
Figure 6
Active site (right) of the oxygen-evolving complex in PSII (left).
Figure 7
Figure 7
Active site (right) of nitric-oxide reductase (left) obtained from Pseudomonas aeruginosa (PDB: 3WFB).
Figure 8
Figure 8
Solvated DNA double strand. The four DNA nitrogenous bases are highlighted.
Figure 9
Figure 9
Schematic representation of the redox reaction of the neutral guanosine in aqueous solution.
Figure 10
Figure 10
Double-stranded oligonucleotide ds-(5′-GGG-3′) studied by Kumar et al. [154]. DFT calculations were performed on the atoms represented in stick, whereas the environment (indicated by the the light blue region) was modeled by means of the IEF-PCM implicit solvent model.
Figure 11
Figure 11
Representation of the solvated ds-(3′-TCGCGTTGCGCT-5′) DNA double strand studied by Cauet et al. [158]. The highlighted atoms represent the two different QCs chosen in that work.
See this image and copyright information in PMC

References

    1. Meunier B., De Visser S.P., Shaik S. Mechanism of Oxidation Reactions Catalyzed by Cytochrome P450 Enzymes. Chem. Rev. 2004;104:3947–3980. doi: 10.1021/cr020443g. - DOI - PubMed
    1. Bertini I., Cavallaro G., Rosato A. Cytochrome c: Occurrence and Functions. Chem. Rev. 2005;106:90–115. doi: 10.1021/cr050241v. - DOI - PubMed
    1. Vandenberghe I., Leys D., Demol H., Van Driessche G., Meyer T.E., Cusanovich M.A., Van Beeumen J. The Primary Structures of the Low-Redox Potential Diheme Cytochromescfrom the Phototrophic BacteriaRhodobacter sphaeroidesandRhodobacter adriaticusReveal a New Structural Family ofc-Type Cytochromes. Biochemistry. 1998;37:13075–13081. doi: 10.1021/bi981076z. - DOI - PubMed
    1. Frey M. ChemInform Abstract: Hydrogenases: Hydrogen-Activating Enzymes. ChemInform. 2010;33:153–160. doi: 10.1002/chin.200221294. - DOI - PubMed
    1. Sykes A.G. Advances in Inorganic Chemistry. Elsevier; Amsterdam, The Netherlands: 1991. Active-Site Properties Of The Blue Copper Proteins; pp. 377–408. - DOI

LinkOut - more resources