REFERENCES
1. Jelen, B.I., D. Giovannelli, and P.G. Falkowski, The role of microbial electron transfer in the coevolution of the biosphere and geosphere. Annual review of microbiology, 2016. 70 : p. 45-62.
2. Moore, E.K., B.I. Jelen, D. Giovannelli, H. Raanan, and P.G. Falkowski, Metal availability and the expanding network of microbial metabolisms in the Archaean eon. Nature Geoscience, 2017.10 (9): p. 629-636.
3. Falkowski, P.G., T. Fenchel, and E.F. Delong, The microbial engines that drive Earth’s biogeochemical cycles. science, 2008.320 (5879): p. 1034-1039.
4. Marcus, R.A. and N. Sutin, Electron transfers in chemistry and biology. Biochimica et Biophysica Acta (BBA)-Reviews on Bioenergetics, 1985. 811 (3): p. 265-322.
5. Gray, H.B. and J.R. Winkler, Electron tunneling through proteins. Quarterly reviews of biophysics, 2003. 36 (3): p. 341-372.
6. Moser, C.C., J.M. Keske, K. Warncke, R.S. Farid, and P.L. Dutton,Nature of biological electron transfer. Nature, 1992.355 (6363): p. 796-802.
7. Page, C.C., C.C. Moser, X. Chen, and P.L. Dutton, Natural engineering principles of electron tunnelling in biological oxidation–reduction. Nature, 1999. 402 (6757): p. 47-52.
8. Atkinson, J.T., I. Campbell, G.N. Bennett, and J.J. Silberg,Cellular assays for ferredoxins: a strategy for understanding electron flow through protein carriers that link metabolic pathways.Biochemistry, 2016. 55 (51): p. 7047-7064.
9. Rogers, N.K., G.R. Moore, and M.J. Sternberg, Electrostatic interactions in globular proteins: calculation of the pH dependence of the redox potential of cytochrome C551. Journal of molecular biology, 1985. 182 (4): p. 613-616.
10. Sternberg, M.J., F.R. Hayes, A.J. Russell, P.G. Thomas, and A.R. Fersht, Prediction of electrostatic effects of engineering of protein charges. Nature, 1987. 330 (6143): p. 86-88.
11. Karlin, S., Z.-Y. Zhu, and K.D. Karlin, The extended environment of mononuclear metal centers in protein structures.Proceedings of the National Academy of Sciences, 1997. 94 (26): p. 14225-14230.
12. Adman, E., K.D. Watenpaugh, and L.H. Jensen, NH—S hydrogen bonds in Peptococcus aerogenes ferredoxin, Clostridium pasteurianum rubredoxin, and Chromatium high potential iron protein.Proceedings of the National Academy of Sciences, 1975. 72 (12): p. 4854-4858.
13. Dey, A., F.E. Jenney Jr, M.W. Adams, E. Babini, Y. Takahashi, K. Fukuyama, K.O. Hodgson, B. Hedman, and E.I. Solomon, Solvent tuning of electrochemical potentials in the active sites of HiPIP versus ferredoxin. Science, 2007. 318 (5855): p. 1464-1468.
14. Beratan, D.N., C. Liu, A. Migliore, N.F. Polizzi, S.S. Skourtis, P. Zhang, and Y. Zhang, Charge transfer in dynamical biosystems, or the treachery of (static) images. Accounts of chemical research, 2015.48 (2): p. 474-481.
15. Teo, J.J. and R. Sarpeshkar, The merging of biological and electronic circuits. Iscience, 2020. 23 (11): p. 101688.
16. Raanan, H., D.H. Pike, E.K. Moore, P.G. Falkowski, and V. Nanda,Modular origins of biological electron transfer chains. Proc Natl Acad Sci U S A, 2018. 115 (6): p. 1280-1285.
17. Raanan, H., S. Poudel, D.H. Pike, V. Nanda, and P.G. Falkowski,Small protein folds at the root of an ancient metabolic network.Proc Natl Acad Sci U S A, 2020. 117 (13): p. 7193-7199.
18. Timm, J., D.H. Pike, J.A. Mancini, A.M. Tyryshkin, S. Poudel, J.A. Siess, P.M. Molinaro, J.J. McCann, K.M. Waldie, R.L. Koder, P.G. Falkowski, and V. Nanda, Design of a minimal di-nickel hydrogenase peptide. Sci Adv, 2023. 9 (10): p. eabq1990.
19. Baymann, F., E. Lebrun, M. Brugna, B. Schoepp-Cothenet, M.T. Giudici-Orticoni, and W. Nitschke, The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes. Philos Trans R Soc Lond B Biol Sci, 2003. 358 (1429): p. 267-74.
20. Hoarfrost, A., A. Aptekmann, G. Farfañuk, and Y. Bromberg,Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter.Nature communications, 2022. 13 (1): p. 2606.
21. Falkowski, P.G., T. Fenchel, and E.F. Delong, The microbial engines that drive Earth’s biogeochemical cycles. Science, 2008.320 (5879): p. 1034-9.
22. Margulis, L. and J.E. Lovelock, Biological modulation of the Earth’s atmosphere. Icarus, 1974. 21 (4): p. 471-489.
23. Eck, R.V. and M.O. Dayhoff, Evolution of the structure of ferredoxin based on living relics of primitive amino acid sequences.Science, 1966. 152 (3720): p. 363-366.
24. Romero Romero, M.L., A. Rabin, and D.S. Tawfik, Functional Proteins from Short Peptides: Dayhoff’s Hypothesis Turns 50. Angew. Chem. Int. Ed., 2016. 55 : p. 15966-15971.
25. Todd, A.E., C.A. Orengo, and J.M. Thornton, Evolution of function in protein superfamilies, from a structural perspective.Journal of molecular biology, 2001. 307 (4): p. 1113-1143.
26. Kolodny, R., S. Nepomnyachiy, D.S. Tawfik, and N. Ben-Tal,Bridging themes: short protein segments found in different architectures. Molecular biology and evolution, 2021. 38 (6): p. 2191-2208.
27. Ferruz, N., F. Lobos, D. Lemm, S. Toledo-Patino, J.A. Farías-Rico, S. Schmidt, and B. Höcker, Identification and analysis of natural building blocks for evolution-guided fragment-based protein design.Journal of molecular biology, 2020. 432 (13): p. 3898-3914.
28. Abeln, S. and C.M. Deane, Fold usage on genomes and protein fold evolution. PROTEINS: Structure, Function, and Bioinformatics, 2005. 60 (4): p. 690-700.
29. Alva, V., M. Remmert, A. Biegert, A.N. Lupas, and J. Söding, A galaxy of folds. Protein Science, 2010. 19 (1): p. 124-130.
30. Alva, V., J. Soding, and A.N. Lupas, A vocabulary of ancient peptides at the origin of folded proteins. Elife, 2015. 4 : p. e09410.
31. Dupont, C.L., A. Butcher, R.E. Valas, P.E. Bourne, and G. Caetano-Anolles, History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc Natl Acad Sci U S A, 2010. 107 (23): p. 10567-72.
32. Cheng, H., R.D. Schaeffer, Y. Liao, L.N. Kinch, J. Pei, S. Shi, B.-H. Kim, and N.V. Grishin, ECOD: an evolutionary classification of protein domains. PLoS computational biology, 2014. 10 (12): p. e1003926.
33. Bromberg, Y., A.A. Aptekmann, Y. Mahlich, L. Cook, S. Senn, M. Miller, V. Nanda, D.U. Ferreiro, and P.G. Falkowski, Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer. Sci Adv, 2022. 8 (2): p. eabj3984.
34. Lyons, T.W., C.T. Reinhard, and N.J. Planavsky, The rise of oxygen in Earth’s early ocean and atmosphere. Nature, 2014.506 (7488): p. 307-15.
35. Hummer, D.R., J.J. Golden, G. Hystad, R.T. Downs, A. Eleish, C. Liu, J. Ralph, S.M. Morrison, M.B. Meyer, and R.M. Hazen, Evidence for the oxidation of Earth’s crust from the evolution of manganese minerals. Nature Communications, 2022. 13 (1): p. 960.
36. Chen, C.G., A.N. Nardi, A. Amadei, and M. D’Abramo,Theoretical Modeling of Redox Potentials of Biomolecules.Molecules, 2022. 27 (3): p. 1077.
37. Galuzzi, B.G., A. Mirarchi, E.L. Vigano, L. De Gioia, C. Damiani, and F. Arrigoni, Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case. J Chem Inf Model, 2022. 62 (19): p. 4748-4759.
38. Mauk, A.G. and G.R. Moore, Control of metalloprotein redox potentials: what does site-directed mutagenesis of hemoproteins tell us? JBIC Journal of Biological Inorganic Chemistry, 1997. 2 : p. 119-125.
39. Iismaa, S.E., A. Vazquez, G. Jensen, P. Stephens, J. Butt, F. Armstrong, and B. Burgess, Site-directed mutagenesis of Azotobacter vinelandii ferredoxin I. Changes in [4Fe-4S] cluster reduction potential and reactivity. Journal of Biological Chemistry, 1991. 266 (32): p. 21563-21571.
40. Clark, K.M., Y. Yu, N.M. Marshall, N.A. Sieracki, M.J. Nilges, N.J. Blackburn, W.A. Van Der Donk, and Y. Lu, Transforming a blue copper into a red copper protein: engineering cysteine and homocysteine into the axial position of azurin using site-directed mutagenesis and expressed protein ligation. Journal of the American Chemical Society, 2010. 132 (29): p. 10093-10101.
41. Campbell, I.J., D. Kahanda, J.T. Atkinson, O.N. Sparks, J. Kim, C.-P. Tseng, R. Verduzco, G.N. Bennett, and J.J. Silberg,Recombination of 2Fe-2S ferredoxins reveals differences in the inheritance of thermostability and midpoint potential. ACS Synthetic Biology, 2020. 9 (12): p. 3245-3253.
42. Mutter, A.C., A.M. Tyryshkin, I.J. Campbell, S. Poudel, G.N. Bennett, J.J. Silberg, V. Nanda, and P.G. Falkowski, De novo design of symmetric ferredoxins that shuttle electrons in vivo.Proceedings of the National Academy of Sciences, 2019. 116 (29): p. 14557-14562.
43. Hosseinzadeh, P., N.M. Marshall, K.N. Chacón, Y. Yu, M.J. Nilges, S.Y. New, S.A. Tashkov, N.J. Blackburn, and Y. Lu, Design of a single protein that spans the entire 2-V range of physiological redox potentials. Proceedings of the National Academy of Sciences, 2016.113 (2): p. 262-267.
44. Prabhulkar, S., H. Tian, X. Wang, J.J. Zhu, and C.Z. Li,Engineered proteins: redox properties and their applications.Antioxid Redox Signal, 2012. 17 (12): p. 1796-822.
45. Campbell, I.J., G.N. Bennett, and J.J. Silberg, Evolutionary relationships between low potential ferredoxin and flavodoxin electron carriers. Frontiers in energy research, 2019. 7 : p. 79.
46. Jumper, J., R. Evans, A. Pritzel, T. Green, M. Figurnov, O. Ronneberger, K. Tunyasuvunakool, R. Bates, A. Žídek, and A. Potapenko,Highly accurate protein structure prediction with AlphaFold.Nature, 2021. 596 (7873): p. 583-589.
47. Baek, M., F. DiMaio, I. Anishchenko, J. Dauparas, S. Ovchinnikov, G.R. Lee, J. Wang, Q. Cong, L.N. Kinch, and R.D. Schaeffer,Accurate prediction of protein structures and interactions using a three-track neural network. Science, 2021. 373 (6557): p. 871-876.
48. Lin, Z., H. Akin, R. Rao, B. Hie, Z. Zhu, W. Lu, N. Smetanin, R. Verkuil, O. Kabeli, and Y. Shmueli, Evolutionary-scale prediction of atomic-level protein structure with a language model. Science, 2023.379 (6637): p. 1123-1130.
49. Hekkelman, M.L., I. de Vries, R.P. Joosten, and A. Perrakis,AlphaFill: enriching AlphaFold models with ligands and cofactors.Nature Methods, 2023. 20 (2): p. 205-213.
50. Atkinson, J.T., I.J. Campbell, E.E. Thomas, S.C. Bonitatibus, S.J. Elliott, G.N. Bennett, and J.J. Silberg, Metalloprotein switches that display chemical-dependent electron transfer in cells. Nature chemical biology, 2019. 15 (2): p. 189-195.
51. Berman, H.M., J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne, The Protein Data Bank.Nucleic Acids Res, 2000. 28 (1): p. 235-42.
52. 03/14/2023]; Available from: https://firebase.google.com/docs/firestore.
53. Feehan, R., M.W. Franklin, and J.S.G. Slusky, Machine learning differentiates enzymatic and non-enzymatic metals in proteins. Nat Commun, 2021. 12 (1): p. 3712.
54. Virtanen, P., R. Gommers, T.E. Oliphant, M. Haberland, T. Reddy, D. Cournapeau, E. Burovski, P. Peterson, W. Weckesser, J. Bright, S.J. van der Walt, M. Brett, J. Wilson, K.J. Millman, N. Mayorov, A.R.J. Nelson, E. Jones, R. Kern, E. Larson, C.J. Carey, I. Polat, Y. Feng, E.W. Moore, J. VanderPlas, D. Laxalde, J. Perktold, R. Cimrman, I. Henriksen, E.A. Quintero, C.R. Harris, A.M. Archibald, A.H. Ribeiro, F. Pedregosa, P. van Mulbregt, and C. SciPy, SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat Methods, 2020. 17 (3): p. 261-272.
55. Saridakis, E., P. Giastas, G. Efthymiou, V. Thoma, J.M. Moulis, P. Kyritsis, and I.M. Mavridis, Insight into the protein and solvent contributions to the reduction potentials of [4Fe-4S]2+/+ clusters: crystal structures of the Allochromatium vinosum ferredoxin variants C57A and V13G and the homologous Escherichia coli ferredoxin. J Biol Inorg Chem, 2009. 14 (5): p. 783-99.
56. Ishikita, H., B. Loll, J. Biesiadka, W. Saenger, and E.W. Knapp,Redox potentials of chlorophylls in the photosystem II reaction center. Biochemistry, 2005. 44 (10): p. 4118-24.
57. Moore, G.R., G.W. Pettigrew, and N.K. Rogers, Factors influencing redox potentials of electron transfer proteins. Proc Natl Acad Sci U S A, 1986. 83 (14): p. 4998-9.
58. Essex, D.W., M. Li, R.D. Feinman, and A. Miller, Platelet surface glutathione reductase-like activity. Blood, 2004.104 (5): p. 1383-5.
59. Di Rocco, G., G. Battistuzzi, M. Borsari, C.A. Bortolotti, A. Ranieri, and M. Sola, The enthalpic and entropic terms of the reduction potential of metalloproteins: Determinants and interplay.Coordination Chemistry Reviews, 2021. 445 .
60. Hughes, T.F. and R.A. Friesner, Development of Accurate DFT Methods for Computing Redox Potentials of Transition Metal Complexes: Results for Model Complexes and Application to Cytochrome P450. J Chem Theory Comput, 2012. 8 (2): p. 442-59.
61. Jafari, S., Y.A. Tavares Santos, J. Bergmann, M. Irani, and U. Ryde,Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins. Inorg Chem, 2022. 61 (16): p. 5991-6007.
62. Krishtalik, L.I., pH-dependent redox potential: how to use it correctly in the activation energy analysis. Biochim Biophys Acta, 2003. 1604 (1): p. 13-21.
63. Jeuken, L.C., R. Camba, F.A. Armstrong, and G.W. Canters, The pH-dependent redox inactivation of amicyanin from Paracoccus versutus as studied by rapid protein-film voltammetry. J Biol Inorg Chem, 2002.7 (1-2): p. 94-100.
64. Battistuzzi, G., M. Borsari, G.W. Canters, E. de Waal, A. Leonardi, A. Ranieri, and M. Sola, Thermodynamics of the acid transition in blue copper proteins. Biochemistry, 2002. 41 (48): p. 14293-8.
65. Hulsker, R., A. Mery, E.A. Thomassen, A. Ranieri, M. Sola, M.P. Verbeet, T. Kohzuma, and M. Ubbink, Protonation of a histidine copper ligand in fern plastocyanin. J Am Chem Soc, 2007.129 (14): p. 4423-9.
66. Fell, D.A. and A. Wagner, The small world of metabolism.Nature biotechnology, 2000. 18 (11): p. 1121-1122.
67. Wagner, A., The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Molecular biology and evolution, 2001. 18 (7): p. 1283-1292.
68. Barabási, A.-L., The new science of networks. Cambridge: Perseus, 2002.
69. Williams, R.J.P., The bakerian lecture, 1981 natural selection of the chemical elements. Proceedings of the Royal Society of London. Series B. Biological Sciences, 1981. 213 (1193): p. 361-397.
70. Anbar, A.D., Elements and evolution. Science, 2008.322 (5907): p. 1481-1483.
71. Senn, S., V. Nanda, P. Falkowski, and Y. Bromberg,Function-based assessment of structural similarity measurements using metal co-factor orientation. Proteins, 2014. 82 (4): p. 648-56.