Fold versus sequence effects on the driving force for protein-mediated electron transfer

Area of Science:

• Biochemistry and Molecular Biophysics
• Bioinorganic Chemistry
• Computational Biology

Background:

• Electron transport chains (ETCs) facilitate rapid energy flow via protein-based electron transfer reactions in metabolic pathways.
• Protein reduction potentials dictate the driving force for electron transfer, influenced by both amino acid sequence and protein fold.
• Experimentally determining the impact of protein fold on reduction potentials is challenging compared to analyzing specific sequences.

Purpose of the Study:

• To computationally analyze the contributions of protein fold and sequence to reduction potentials in [4Fe-4S] proteins.
• To compare reduction potentials across homologous proteins with distinct folds: high potential iron-sulfur proteins, bacterial ferredoxins, and nitrogenase iron proteins.

Main Methods:

• Utilized continuum electrostatics and density functional theory (DFT) calculations to model reduction potentials.
• Analyzed multiple homologous [4Fe-4S] proteins belonging to three different structural folds.

Main Results:

• Calculated absolute reduction potentials showed quantitative agreement with experimental electrochemical data.
• The protein backbone's contribution to reduction potential was found to be larger than that of side chains.
• Protein fold emerged as the primary determinant of reduction potential, with amino acid sequence fine-tuning this potential.

Conclusions:

• Protein fold, rather than specific amino acid sequence, is the major factor governing reduction potentials in [4Fe-4S] proteins.
• The electrostatic environment, particularly the redox site's proximity to the protein surface and backbone dipole orientation, dictates fold contribution.
• Computational methods provide accurate insights into the determinants of redox potentials in metalloproteins.