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Grover K, Koblova A, Pezacki AT, Chang CJ, New EJ. Small-Molecule Fluorescent Probes for Binding- and Activity-Based Sensing of Redox-Active Biological Metals. Chem Rev 2024; 124:5846-5929. [PMID: 38657175 DOI: 10.1021/acs.chemrev.3c00819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Although transition metals constitute less than 0.1% of the total mass within a human body, they have a substantial impact on fundamental biological processes across all kingdoms of life. Indeed, these nutrients play crucial roles in the physiological functions of enzymes, with the redox properties of many of these metals being essential to their activity. At the same time, imbalances in transition metal pools can be detrimental to health. Modern analytical techniques are helping to illuminate the workings of metal homeostasis at a molecular and atomic level, their spatial localization in real time, and the implications of metal dysregulation in disease pathogenesis. Fluorescence microscopy has proven to be one of the most promising non-invasive methods for studying metal pools in biological samples. The accuracy and sensitivity of bioimaging experiments are predominantly determined by the fluorescent metal-responsive sensor, highlighting the importance of rational probe design for such measurements. This review covers activity- and binding-based fluorescent metal sensors that have been applied to cellular studies. We focus on the essential redox-active metals: iron, copper, manganese, cobalt, chromium, and nickel. We aim to encourage further targeted efforts in developing innovative approaches to understanding the biological chemistry of redox-active metals.
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Affiliation(s)
- Karandeep Grover
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alla Koblova
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Aidan T Pezacki
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Elizabeth J New
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Nano Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
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Daly MJ. The scientific revolution that unraveled the astonishing DNA repair capacity of the Deinococcaceae: 40 years on. Can J Microbiol 2023; 69:369-386. [PMID: 37267626 DOI: 10.1139/cjm-2023-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The family Deinococcaceae exhibits exceptional radiation resistance and possesses all the necessary traits for surviving in radiation-exposed environments. Their survival strategy involves the coupling of metabolic and DNA repair functions, resulting in an extraordinarily efficient homologous repair of DNA double-strand breaks (DSBs) caused by radiation or desiccation. The keys to their survival lie in the hyperaccumulation of manganous (Mn2+)-metabolite antioxidants that protect their DNA repair proteins under extreme oxidative stress and the persistent structural linkage by Holliday junctions of their multiple genome copies per cell that facilitates DSB repair. This coupling of metabolic and DNA repair functions has made polyploid Deinococcus bacteria a useful tool in environmental biotechnology, radiobiology, aging, and planetary protection. The review highlights the groundbreaking contributions of the late Robert G.E. Murray to the field of Deinococcus research and the emergent paradigm-shifting discoveries that revolutionized our understanding of radiation survivability and oxidative stress defense, demonstrating that the proteome, rather than the genome, is the primary target responsible for survivability. These discoveries have led to the commercial development of irradiated vaccines using Deinococcus Mn-peptide antioxidants and have significant implications for various fields.
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Affiliation(s)
- Michael J Daly
- Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Department of Pathology, Bethesda, MD 20814-4799, USA
- Committee on Planetary Protection (CoPP), National Academies of Sciences, Washington, DC 20001, USA
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Borg RE, Ozbakir HF, Xu B, Li E, Fang X, Peng H, Chen IA, Mukherjee A. Genetically engineered filamentous phage for bacterial detection using magnetic resonance imaging. SENSORS & DIAGNOSTICS 2023; 2:948-955. [PMID: 38405385 PMCID: PMC10888512 DOI: 10.1039/d3sd00026e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Detecting bacterial cells with high specificity in deep tissues is challenging. Optical probes provide specificity, but are limited by the scattering and absorption of light in biological tissues. Conversely, magnetic resonance imaging (MRI) allows unfettered access to deep tissues, but lacks contrast agents for detecting specific bacterial strains. Here, we introduce a biomolecular platform that combines both capabilities by exploiting the modularity of M13 phage to target bacteria with tunable specificity and allow deep-tissue imaging using T1-weighted MRI. We engineered two types of phage probes: one for detecting the phage's natural host, viz., F-pilus expressing E. coli; and the other for detecting a different (F-negative) bacterial target, V. cholerae. We show that these phage sensors generate 3-9-fold stronger T1 relaxation upon recognizing target cells relative to non-target bacteria. We further establish a preliminary proof-of-concept for in vivo applications, by demonstrating that phage-labeled bacteria can be detected in mice using MRI. The framework developed in this study may have potential utility in a broad range of applications, from basic biomedical research to in situ diagnostics, which require methods to detect and track specific bacteria in the context of intact living systems.
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Affiliation(s)
- Raymond E Borg
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Harun F Ozbakir
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Binzhi Xu
- Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Eugene Li
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Xiwen Fang
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Huan Peng
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Arnab Mukherjee
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
- Biological Engineering, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
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Pelucelli A, Peana M, Orzeł B, Piasta K, Gumienna-Kontecka E, Medici S, Zoroddu MA. Zn 2+ and Cu 2+ Interaction with the Recognition Interface of ACE2 for SARS-CoV-2 Spike Protein. Int J Mol Sci 2023; 24:ijms24119202. [PMID: 37298154 DOI: 10.3390/ijms24119202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
The spike protein (S) of SARS-CoV-2 is able to bind to the human angiotensin-converting enzyme 2 (ACE2) receptor with a much higher affinity compared to other coronaviruses. The binding interface between the ACE2 receptor and the spike protein plays a critical role in the entry mechanism of the SARS-CoV-2 virus. There are specific amino acids involved in the interaction between the S protein and the ACE2 receptor. This specificity is critical for the virus to establish a systemic infection and cause COVID-19 disease. In the ACE2 receptor, the largest number of amino acids playing a crucial role in the mechanism of interaction and recognition with the S protein is located in the C-terminal part, which represents the main binding region between ACE2 and S. This fragment is abundant in coordination residues such as aspartates, glutamates, and histidine that could be targeted by metal ions. Zn2+ ions bind to the ACE2 receptor in its catalytic site and modulate its activity, but it could also contribute to the structural stability of the entire protein. The ability of the human ACE2 receptor to coordinate metal ions, such as Zn2+, in the same region where it binds to the S protein could have a crucial impact on the mechanism of recognition and interaction of ACE2-S, with consequences on their binding affinity that deserve to be investigated. To test this possibility, this study aims to characterize the coordination ability of Zn2+, and also Cu2+ for comparison, with selected peptide models of the ACE2 binding interface using spectroscopic and potentiometric techniques.
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Affiliation(s)
- Alessio Pelucelli
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Bartosz Orzeł
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Karolina Piasta
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | | | - Serenella Medici
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Maria Antonietta Zoroddu
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
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Monger LJ, Razinkov D, Bjornsson R, Suman SG. Synthesis, Characterization, and Reaction Studies of Pd(II) Tripeptide Complexes. Molecules 2021; 26:molecules26175169. [PMID: 34500604 PMCID: PMC8433849 DOI: 10.3390/molecules26175169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
The aqueous synthesis of Pd(II) complexes with alkylated tripeptides led to the hydrolysis of the peptides at low pH values and mixtures of complexed peptides were formed. A non-aqueous synthetic route allowed the formation and isolation of single products and their characterization. Pd(II) complexes with α-Asp(OR)AlaGly(OR), β-Asp(OR)AlaGly(OR), and TrpAlaGly(OR) (R = H or alkyl) as tri and tetradentate chelates were characterized. The tridentate coordination mode was accompanied by a fourth monodentate ligand that was shown to participate in both ligand exchange reactions and a direct removal to form the tetradentate coordination mode. The tetradentate coordination revealed a rare a hemi labile carbonyl goup coordination mode to Pd(II). Reactivity with small molecules such as ethylene, acids, formate, and episulfide was investigated. Under acidic conditions and in the presence of ethylene; acetaldehyde was formed. The Pd(II) is a soft Lewis acid and thiophilic and the complexes abstract sulfur from episulfide at apparent modest catalytic rates. The complexes adopt a square planar geometry according to a spectroscopic analysis and DFT calculations that were employed to evaluate the most energetically favorable coordination geometry and compared with the observed infrared and NMR data.
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Affiliation(s)
- Lindsey J. Monger
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland; (L.J.M.); (D.R.)
| | - Dmitrii Razinkov
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland; (L.J.M.); (D.R.)
| | - Ragnar Bjornsson
- Max Planck Institute Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany;
| | - Sigridur G. Suman
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland; (L.J.M.); (D.R.)
- Correspondence:
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Dollery SJ, Zurawski DV, Gaidamakova EK, Matrosova VY, Tobin JK, Wiggins TJ, Bushnell RV, MacLeod DA, Alamneh YA, Abu-Taleb R, Escatte MG, Meeks HN, Daly MJ, Tobin GJ. Radiation-Inactivated Acinetobacter baumannii Vaccine Candidates. Vaccines (Basel) 2021; 9:vaccines9020096. [PMID: 33514059 PMCID: PMC7912630 DOI: 10.3390/vaccines9020096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 12/20/2022] Open
Abstract
Acinetobacter baumannii is a bacterial pathogen that is often multidrug-resistant (MDR) and causes a range of life-threatening illnesses, including pneumonia, septicemia, and wound infections. Some antibiotic treatments can reduce mortality if dosed early enough before an infection progresses, but there are few other treatment options when it comes to MDR-infection. Although several prophylactic strategies have been assessed, no vaccine candidates have advanced to clinical trials or have been approved. Herein, we rapidly produced protective whole-cell immunogens from planktonic and biofilm-like cultures of A. baumannii, strain AB5075 grown using a variety of methods. After selecting a panel of five cultures based on distinct protein profiles, replicative activity was extinguished by exposure to 10 kGy gamma radiation in the presence of a Deinococcus antioxidant complex composed of manganous (Mn2+) ions, a decapeptide, and orthophosphate. Mn2+ antioxidants prevent hydroxylation and carbonylation of irradiated proteins, but do not protect nucleic acids, yielding replication-deficient immunogenic A. baumannii vaccine candidates. Mice were immunized and boosted twice with 1.0 × 107 irradiated bacterial cells and then challenged intranasally with AB5075 using two mouse models. Planktonic cultures grown for 16 h in rich media and biofilm cultures grown in static cultures underneath minimal (M9) media stimulated immunity that led to 80–100% protection.
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Affiliation(s)
- Stephen J. Dollery
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
- Correspondence:
| | - Daniel V. Zurawski
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (D.V.Z.); (Y.A.A.); (R.A.-T.); (M.G.E.)
| | - Elena K. Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (E.K.G.); (V.Y.M.); (M.J.D.)
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Vera Y. Matrosova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (E.K.G.); (V.Y.M.); (M.J.D.)
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - John K. Tobin
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
| | - Taralyn J. Wiggins
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
| | - Ruth V. Bushnell
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
| | - David A. MacLeod
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
| | - Yonas A. Alamneh
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (D.V.Z.); (Y.A.A.); (R.A.-T.); (M.G.E.)
| | - Rania Abu-Taleb
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (D.V.Z.); (Y.A.A.); (R.A.-T.); (M.G.E.)
| | - Mariel G. Escatte
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (D.V.Z.); (Y.A.A.); (R.A.-T.); (M.G.E.)
| | | | - Michael J. Daly
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (E.K.G.); (V.Y.M.); (M.J.D.)
| | - Gregory J. Tobin
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA; (J.K.T.); (T.J.W.); (R.V.B.); (D.A.M.); (G.J.T.)
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Production of extracellular silver nanoparticles by radiation-resistant Deinococcus wulumuqiensis R12 and its mechanism perspective. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Monger LJ, Runarsdottir GR, Suman SG. Directed coordination study of [Pd(en)(H 2O) 2] 2+ with hetero-tripeptides containing C-terminus methyl esters employing NMR spectroscopy. J Biol Inorg Chem 2020; 25:811-825. [PMID: 32676770 DOI: 10.1007/s00775-020-01804-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/02/2020] [Indexed: 12/25/2022]
Abstract
Alkylation of the C-terminus acids in small peptides allows direction to amine and amide coordination, while changing the peptide composition to form tetradentate κ4[n,5,5], where n = 5-, 6-, 7-, or 8-membered ring coordination geometries, can be achieved. The alkylated tripeptide ligands, TrpAlaGly(OMe), β-Asp(OtBu)AlaGly(OMe), Asp(OtBu)AlaGly(OMe), and the fully methylated GSH, γ-Glu(OMe)Cys(SMe)Gly(OMe), were synthesized and their coordination properties to [Pd(en)(H2O)2]2+ were studied. pH-dependent coordination was analyzed by NMR spectroscopy and the coordination to the alkylated tripeptides at selected pH values inferred from their NMR spectra. If selective coordination of amine/amide donors results in metal complexation, allowing for flexible and adjustable ligand frameworks, then this strategy could potentially be extended to other metal ions and peptide system.
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Affiliation(s)
- Lindsey J Monger
- Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavik, Iceland
| | | | - Sigridur G Suman
- Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavik, Iceland.
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