Poster Presentation 21st International Conference on Biological Inorganic Chemistry 2025

Predicting metalloprotein redox potentials with machine learning: A focus on iron-sulfur systems (#480)

Federica Arrigoni 1 , Francesca Persico 1 , Luca De Gioia 1 , Chiara Damiani 1 , Bruno G Galuzzi 2
  1. Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
  2. Institute of Bioimaging and Molecular Physiology, National Research Council of Italy, Milan, Italy

The redox potential of protein-bound metallocofactors is a key determinant of their function, with broad implications across fundamental research and applied fields, including bioengineering, biosensing, biocatalysis, energy conversion, and life sciences.1 Beyond its determination, a major challenge lies in understanding how the protein matrix modulates redox properties, particularly in metallocofactors, where multiple structural and electronic factors interplay. Experimental methods for measuring protein redox potentials are labor-intensive, while standard computational approaches are highly demanding, making them impractical for large-scale studies. However, high-throughput predictive models are essential to guide the rational design of metalloproteins with tailored redox properties.2 Here, we present a data-driven approach for predicting the redox potential of metalloproteins, using iron-sulfur (FeS) proteins as a case study. We developed a machine learning (ML)-based model trained on a curated dataset of experimentally characterized FeS proteins. Ad hoc descriptors, capturing the physicochemical properties of the protein environment, are automatically extracted from protein structures, incorporating short-, medium-, and long-range effects. As an initial step, we focused on simple FeS cofactors, including FeS ferredoxins, Rieske-type proteins, mitoNEET, and rubredoxins, which are well-characterized and biologically relevant.3 Our results demonstrate that this ML-based strategy enables highly accurate redox potential predictions, outperforming traditional computational methods. Specifically, this approach achieved an error below 1 kcal/mol (~37 mV), comparing favorably with QM-based approaches while being computationally more efficient.4 Moreover, this approach identifies key protein features that quantitatively modulate redox potential. Preliminary results also indicate that the model successfully predicts the redox potential of FeS clusters in more complex protein environments, laying the groundwork for a generalizable strategy applicable to larger FeS clusters and other metalloproteins. This paves the way for efficient computational screening tools in protein engineering and redox biology.

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  2. Galuzzi, B.G.; Mirarchi, A.; Viganò, E.L.; De Gioia, L.; Damiani, C.; Arrigoni, F. Journal of Chemical Information and Modeling, 2022, 19, 4748–4759
  3. Boncella, A.E.; Sabo, E.T.; Santore, R.M.; Carter, J; Whalen, J.; Hudspeth, J.D.; Morrison, C.N. Coordination Chemistry Review, 2022, 453, 214229
  4. Jafari, S.; Santos, T.; Bergmann, J.; Irani, M.; Ryde, U. Inorganic Chemistry, 2022, 16, 5991–6007