Iron-Histidine Coordination in Cytochrome b5: A Local Vibrational Mode Study

Area of Science:

• Biochemistry and Biophysics
• Computational Chemistry
• Protein Science

Background:

• Cytochrome b5 proteins are heme-containing proteins involved in various biological redox reactions.
• Understanding the intrinsic properties of heme coordination is crucial for predicting protein function and designing artificial variants.
• Previous studies often rely on geometric data and qualitative descriptions, limiting predictive accuracy for redox potentials.

Purpose of the Study:

• To analyze the intrinsic strength of Fe-N bonds and stiffness of N-Fe-N bond angles in diverse cytochrome b5 proteins.
• To investigate the impact of heme iron redox state (ferric vs. ferrous) on these intrinsic properties.
• To explore the utility of local mode force constants as features for machine learning models predicting redox potentials.

Main Methods:

• Utilized Quantum Mechanics/Molecular Mechanics (QM/MM) methodology for all calculations.
• Employed local vibrational stretching force constants k(FeN) and bending force constants k(NFeN) derived from local mode theory.
• Considered both ferric and ferrous oxidation states of the heme iron.

Main Results:

• Reduction of heme iron from ferric to ferrous state weakens, lengthens, and reduces covalency/polarity of Fe-N axial bonds.
• The axial N-Fe-N bond angle becomes stiffer and less flexible upon reduction.
• Local mode force constants are more sensitive to protein environment and redox changes than geometric parameters.

Conclusions:

• Local mode force constants provide sensitive, quantitative data for characterizing the heme coordination sphere in cytochrome b5 proteins.
• These force constants are valuable features for developing machine learning models to predict cytochrome b5 redox potentials.
• Findings offer guidance for the rational design and engineering of novel artificial cytochrome b5 variants.