Our research is part of the Department of Chemistry and Biochemistry at the University of Maryland, Baltimore County. We are also part of the Metallotherapeutics Research Center based out of the University of Maryland School of Pharmacy.
There are three current research areas in the lab:
1) The mechanism and regulation of post-translational arginylation
2) Pathogenic ferrous iron uptake and delivery
3) Bacterial ferrous iron sensing and generation
ATE1-catalyzed post-translational arginylation. Top panel: ATE1 is a global regulator of eukaryotic cellular homeostasis. Bottom panel: the first 3-D structure of a eukaryotic ATE1 ever determined.
Proteins are a versatile group of biological macromolecules that are responsible for undertaking many indispensable functions within the cell. However, when constrained to only the 20 canonical amino acids, not every necessary cellular function may be fulfilled. Thus, the encoding capacity of the genome must be expanded, and such augmentation is achieved by the ability of proteins to be co- and/or post-translationally modified. A lesser-studied but essential eukaryotic PTM is arginylation, which is the covalent addition of the amino acid arginine (Arg) to an acceptor protein, catalyzed by the enzyme arginyltransferase 1 (ATE1). Arginylation is emerging as a global regulator of eukaryotic cellular homeostasis through its degradative and non-degradative effects on the proteome. Arginylation has a major role within the N-degron pathway, a hierarchal determinant of intracellular protein half-life. However, degradation is not the only fate for proteins and enzymes that have be post-translationally arginylated and recent and important research has shown that proteins may also be stabilized and oligomerize differently once arginylated. Examples of some proteins that change their oligomeric state in response to arginylation include β-actin and calreticulin, while recent studies have even shown that arginylation even affects viruses such as the human immunodeficiency virus (HIV) and SARS-CoV-2, the causitive agent of the COVID-19 pandemic. Despite its physiological importance, the structural and the biophysical properties of ATE1 are poorly understood, and research in the Smith laboratory is attempting to answer these pressing questions.
This research project aims to understand how the mechanism and regulation of ATE1-catalyzed post-translational arginylation, which affects normal eukaryotic development and is linked to cardiovascular disease, development disease, and some forms of cancers.
Our recent publications in this area include:
Cartwright, M.; Parakra, R.; Oduwole, A.#; Zhang, F.; Deredge, D. J.; and Smith, A. T. Identification of an intrinsically disordered region (IDR) in arginyltransferase 1 (ATE1). Biochemistry. 2024, 63, 3236-3249.
Van, V.; Brown, J. B.; O'Shea, C. R.; Rosenbach, H.; Mohamed, I.; Ejimogu, N.-E.; Bui, T. S#; Szalai, V. A.; Chacón, K. N.; Span, I.; Zhang, F.; and Smith, A. T. Iron-sulfur clusters are involved in post-translational arginylation. Nature Communications. 2023, 14, 458, DOI: https://doi.org/0.1038/s41467-023-36158-z
Van, V.; Ejimogu, N.-E.; Bui, T. S.; and Smith, A. T. The structure of Saccharomyces cerevisiae arginyltransferase 1 (ATE1). J. Mol. Biol. 2022, 434, 167816 and bioRxiv, 2022, DOI: 10.1101/2022.07.20.500667
Iron is an essential element for virtually every living organism and has been adopted to serve in major biological processes such as nitrogen fixation, methane oxidation, hydrogen production, aerobic cellular respiration, oxygen transport, DNA biosynthesis, and even gene regulation. However, iron-based life represents a double-edged sword, as Fe(II) is bioavailable but highly reactive, whereas Fe(III) is intractable but fairly chemically inert. Every organism that utilizes iron employs biological pathways to obtain this element from the environment, to regulate its bioavailable concentration, and to sequester its excess. In order to establish infection in humans, pathogenic bacteria have evolved several responses to manage iron acquisition and utilization. The ability to acquire and utilize iron aids in the proliferation of numerous infectious bacteria. One important route for the uptake of Fe(II) for bacteria is via the ferrous iron uptake (Feo) system However, the mechanism of iron uptake through this pathway is poorly understood by comparison to Fe(III) and heme uptake pathways. In an era of increasing antibacterial resistance, understanding and targeting the routes of bacterial nutrient uptake are crucial to stem bacterial virulence. We are using a multifaceted approach to understand the structure and function of proteins involved in bacterial Fe(II) uptake.
This research project aims to understand how pathogenic bacteria acquire ferrous iron, with the goal of targeting this system for novel antibiotic developments.
The bacterial ferrous iron acquistion system, Feo. The multicomponent Feo system, canonically comprising the proteins FeoA, FeoB, and FeoC, function in concert to supply pathogenic organisms with iron under anaerobic and/or acidic conditions. There is a paucity of understanding of the structure and function of this system, which could be the target for novel antibiotic developments in the future.
Our recent publications in this area include:
Lee, M.; Armstrong, C. M.; and Smith, A. T. Characterization of intact FeoB in a lipid bilayer using styrene-maleic acid (SMA) copolymers. BBA-Biomembranes. 2025, 1867, 184404.
Lee, M.; Magante, K.; Gómez-Garzón, C.; Payne, S. M.; and Smith, A. T. Structural determinants of Vibrio cholerae FeoB nucleotide promiscuity. J. Biol. Chem. 2024, 300, 107663.
Sestok, A. E.; Brown, J. B.; Obi, J. O.; O'Sullivan, S. M.; Garcin, E. D.; Deredge, D. J.; and Smith A. T. A fusion of the Bacteroides fragilis ferrous iron import proteins reveals a role for FeoA in stabilizing GTP-bound FeoB. J. Biol. Chem. 2022, 298, 101808.
Proposed interplay of the bacterial ferrous iron acquistion system (Feo, blue), the bacterial ferrous iron sensing two-component system (BqsRS, purple), and ferrous iron-generating membrane ferric reductases (mFRs, teal). Research in the lab aims to decipher the complex interplay of these membrane proteins in maintaining Fe(II) homeostasis in both pathogenic prokaryotes as well as magnetactic bacteria that synthesize complex iron oxide nanoparticles.
There is an emerging connection between Feo and additional membrane-bound proteins that function more broadly in bacterial Fe(II) homeostasis through: 1) sensing Fe(II) as part of a mechanism to control biofilm formation in antibiotic-resistant pathogens and 2) using Fe(III)-siderophores to supply Fe(II) to the Feo system for hyper iron accumulation in select bacteria. For example, studies have identified a two-component signal transduction system, BqsR-BqsS, that regulates biofilm formation and quorum sensing in Pseudomonas aeruginosa through the sensing of periplasmic Fe(II), and these proteins appear to be conserved in many bacteria. Moreover, there is an increasing consensus that a family of small membrane proteins known as membrane ferric reductases (mFRs) contribute to the Fe(II) pool in bacteria through the reductive dissociation of iron from Fe(III)-siderophores, which could explain why the Feo system is expressed even under O2-replete conditions. We hypothesize that mFRs are heme b-containing proteins of the enigmatic cytb561 family that couple Fe(III) reduction to Feo-mediated Fe(II) transport in bacteria. Using structural, biochemical, and biophysical methods coupled with in vivo approaches, we are working to uncover the complex interplay of these membrane proteins in maintaining Fe(II) homeostasis in both pathogenic prokaryotes as well as magnetotactic bacteria that are capable of synthesizing complex iron nanoparticles.
This research project aims to understand how pathogenic bacteria acquire sense and generate ferrous iron, with the goal of targeting this system for attenuating bacterial virulence and for new material developments aided by hyper iron accumulating bacteria.
Our recent publications in this area include:
Paredes, A.; Iheacho, C.; and Smith, A. T. Metal messengers: communication in the bacterial world through transition-metal-sensing two-component systems. Biochemistry. 2023, 62, 2339-2357.
Sestok, A. E.; Lee, M.; and Smith, A. T. Prokaryotic ferrous iron uptake: exploiting pools of reduced iron across multiple microbial environments. In: Hurst, C.J. (ed) Microbial Metabolism of Metals and Metalloids. Advances in Environmental Microbiology. 2022, 10, 299-357. Springer, Cham. DOI: 10.1007/978-3-030-97185-4_12
Cain, T. J. and Smith, A. T. Ferric iron reductases and their contribution to unicellular ferrous iron uptake. J. Inorg. Biochem. 2021, 218, 11407, 1-9.
We are interested in understanding the structure (both electronic and three-dimensional) and function of metalloproteins. In order to interrogate these proteins, we utilize numerous strategies. Members of the Smith laboratory learn to manipulate proteins from the gene upwards by executing techniques in molecular biology, cell culture, protein expression, protein purification, and anaerobic/anoxic manipulation. Once isolated and purified, we employ a wide variety of methods to interrogate protein and nucleic acid structure and function, including spectroscopy, crystallography, small-angle X-ray scattering, mass photometry, and enzyme assays. At UMBC, we have an array of equipment and instrumentation for protein purification, protein crystallography, anaerobic techniques, metal analysis, and spectroscopy. For more specialized techniques, such as electron paramagnetic resonance (EPR), X-ray absorption (XAS) etc., we have dedicated instrumentation support at other institutions. Students interested in these techniques are encouraged to learn to prepare their own samples and to travel to these institutions or to collect data remotely. Training in these techniques will equip students with a broad toolbox to study protein and nucleic acid structure and function independently.