Geometry Optimization Calculations of Dinuclear Fe Active Sites in Bacterial Metalloproteins

Alana Calello,1 Alexander Hanneman,1 Matthew Porowski,1 Ryan Salerno,1 Ruhi Shah,1 Zachary Ziolkowski,1 and Levi Ekanger*

Department of Chemistry, The College of New Jersey, Ewing, NJ 08628; 1These authors contributed equally to this work.

Introduction & motivation Bacterial Metalloproteins Optimization Results Summary ➢ Computational chemistry methods Fe1-O Bond Fe2-O Bond Fe1-O Bond Fe2-O Bond Ytfe boosts virulence of Protein Length (Å) Length (Å) Length (Å) Length (Å) produced models of bacterial Experimental Experimental pathogenic bacteria by Calculated Calculated metalloprotein active sites. repairing FeS clusters. MkA HLP 1.71 2.48 1.74 (1.88) 1.73 (1.86) ➢ Differences between experimental Ytfe PDB ID 5FNN Hemerythrin 2.16 1.78 1.73 (1.90) 1.70 (1.78) and calculated bond lengths Ytfe 1.89 1.98 1.71 (1.80) 1.68 (1.79) indicate the models need further MkA boosts optimization. Representative results (B3LYP, 6-31G(d)) comparing bond lengths virulence of within dinuclear Fe active sites. Experimental values are for Fe(III)- ➢ Molecular orbitals suggest unique Pathogenic bacterial infections are a Fe(II) states. Calculated values are for Fe(III)-Fe(III) states and pathogenic bacteria values in parentheses are for Fe(II)-Fe(II) states. electron densities in Ytfe and MkA significant cause of human disease and through a currently 1 relative to Hr. death. unknown pathway.3 Geometry calculations reproduced some MkA PDB ID 6Q09 general features of bacterial ➢ Collectively these results form a metalloprotein active sites. There are proof-of-concept for modelling and Hemerythrin (Hr) some discrepancies between calculated investigating structural differences is an oxygen- and experimental values. between Ytfe, MkA, and Hr. 4 6 transport protein found in marine Molecular Orbitals invertebrate phyla. Future Directions Hr PDB ID 1HMD ➢ Calculations presented here ignored Bacteria rely on FeS cluster metalloproteins antiferromagnetic coupling (AFC) to survive. The image above reveals an between iron centers. FeS cluster found within a bacterial DNA What about the structures of Ytfe and repair enzyme (PDB 2ABK). MkA enables such different function ➢ To improve the quality of our compared to Hr? 2 calculations, we will use a broken symmetry approach to account for Computational Methods AFC in bacterial metalloprotein active sites. 7 ➢ Density functional theory (DFT) is a quantum mechanical modelling method. Acknowledgments ➢ In DFT, the energy and associated ➢ TCNJ Chemistry & SoS properties of a system are calculable from the electron density of the system. ➢ Dr. Joe Baker for helpful discussions

Representative lowest unoccupied molecular orbital (LUMO) ➢ Shawn Sivy for ELSA support Functionals used: B3LYP and BPW91 and highest occupied molecular orbital (HOMO) for Hr, Ytfe, Basis sets: 6-31G(d) and 6-311G(d) and MkA (B3LYP, 6-31G(d)). ➢ You for your time! 8 LUMOs are similar across the series. Ytfe is a bacterial metalloprotein that helps ➢ We performed DFT calculations to References pathogenic bacteria survive the immune optimize the geometry of metalloprotein Ytfe HOMO has less electron density on active sites by minimizing the energy of 1. Antibiotic Resistance Threats in the United States, 2019. system by repairing FeS clusters.2 its bridging oxide relative to Hr. U.S. Centers for Disease Control and Prevention. the system on a potential energy surface. MkA HOMO is unique with significant 2. Justino, MC; Almeida, CC; Saraiva, LM. J. Biol. Chem. We want to study Ytfe to understand the 2007, 282, 10352-10359. mechanism of repairing FeS clusters. ➢ Calculations were performed on the electron density delocalized onto its Fe- 3. Ma, Z; Abendroth, J; Buchko, GW; Rohde, KH; Davidson, TCNJ ELSA high performance cluster. bound tyrosine residue. VL. Biochem. J. 2020, 477, 567-581. 1 53 5 109