1
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Armentrout PB. Perspective: intrinsic interactions of metal ions with biological molecules as studied by threshold collision-induced dissociation and infrared multiple photon dissociation. Phys Chem Chem Phys 2024. [PMID: 39042103 DOI: 10.1039/d4cp00897a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
In this perspective, gas-phase studies of group 1 monocations and group 12 dications with amino acids and small peptides are highlighted. Although the focus is on two experimental techniques, threshold collision-induced dissociation and infrared multiple photon dissociation action spectroscopy, these methods as well as complementary approaches are summarized. The synergistic interplay with theory, made particularly powerful by the small sizes of the systems explored and the absence of solvent and support, is also elucidated. Importantly, these gas-phase methods permit quantitative insight into the structures and thermodynamics of metal cations interacting with biological molecules. Periodic trends in how these interactions vary as the metal cations get heavier are discussed as are quantitative trends with changes in the amino acid side chain and effects of hydration. Such trends allow these results to transcend the limitations associated with the biomimetic model systems.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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2
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Wang Z, Ding R, Li X, Zhang J, Yang L, Wang Y, Liu J, Zhou Z. Blocking Accretion Enables Dimension Reduction of Metal-Organic Framework for Photocatalytic Performance. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2305308. [PMID: 37635096 DOI: 10.1002/smll.202305308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/07/2023] [Indexed: 08/29/2023]
Abstract
The evolution and formation process of two-dimensional metal-organic frameworks (MOFs) primarily arise from the anisotropic growth of crystals, leading to variations in photocatalytic performance. It is crucial to achieve a synergistic combination of anisotropic electron transfer direction and dimension reduction strategies. In this study, a novel approach that effectively blocks crystal growth accretion through the coordination of solvent molecules is presented, achieving the successful synthesis of impurity-free two-dimensional nanosheet Zn-PTC with exceptional hydrogen evolution reaction (HER) performance (15.4 mmol g-1 h-1 ). The structural and photophysical characterizations validate the successful prevention of crystal accretion, while establishing correlation between structural anisotropy and intrinsic charge transfer mode through transient spectroscopy. These findings unequivocally demonstrate that electron transfer along the [001] direction plays a pivotal role in the redox performance of nano-Zn-PTC. Subsequently, by coupling the photocatalytic performance and density functional theory (DFT) simulation calculations, the carrier diffusion kinetics is explored, revealing that effective dimension reduction along the ligand-to-metal charge transfer (LMCT) direction is the key to achieving superior photocatalytic performance.
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Affiliation(s)
- Zejin Wang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210033, P. R. China
| | - Rui Ding
- College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210033, P. R. China
| | - Xiaoke Li
- College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210033, P. R. China
| | - Jie Zhang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210033, P. R. China
| | - Le Yang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210033, P. R. China
| | - Ying Wang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210033, P. R. China
- Eco-Materials and Renewable Energy Research Center (ERERC), Jiangsu Key Laboratory for Nano Technology, National Laboratory of Solid State Microstructures, School of Physics, Nanjing University, Nanjing, Jiangsu, 210093, P. R. China
| | - Jianguo Liu
- Institute of Energy Power Innovation, North China Electric Power University, Beijing, 102206, P. R. China
| | - Zhigang Zhou
- College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210033, P. R. China
- Eco-Materials and Renewable Energy Research Center (ERERC), Jiangsu Key Laboratory for Nano Technology, National Laboratory of Solid State Microstructures, School of Physics, Nanjing University, Nanjing, Jiangsu, 210093, P. R. China
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3
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Cao W, Yuan Q, Zhang H, Zhou X, Kass SR, Wang XB. How generic is iodide-tagging photoelectron spectroscopy: An extended investigation on the Gly·X- (Gly = glycine, X = Cl or Br) complexes. J Chem Phys 2023; 159:034305. [PMID: 37466228 DOI: 10.1063/5.0159326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
We report a joint negative ion photoelectron spectroscopy (NIPES) and quantum chemical computational study on glycine-chloride/bromide complexes (denoted Gly·X-, X = Cl/Br) in close comparison to the previously studied Gly·I- cluster ion. Combining experimental NIPE spectra and theoretical calculations, various Gly·X- complexes were found to adopt the same types of low-lying isomers, albeit with different relative energies. Despite more congested spectral profiles for Gly·Cl- and Gly·Br-, spectral assignments were accomplished with the guidance of the knowledge learned from Gly·I-, where a larger spin-orbit splitting of iodine afforded well-resolved, recognizable spectral peaks. Three canonical plus one zwitterionic isomer for Gly·Cl- and four canonical conformers for Gly·Br- were experimentally identified and characterized in contrast to the five canonical ones observed for Gly·I- under similar experimental conditions. Taken together, this study investigates both genericity and variations in binding patterns for the complexes composed of glycine and various halides, demonstrating that iodide-tagging is an effective spectroscopic means to unravel diverse ion-molecule binding motifs for cluster anions with congested spectral bands by substituting the respective ion with iodide.
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Affiliation(s)
- Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Ministry of Education), Department of Chemistry, Anhui University, Hefei 230601, China
| | - Hanhui Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Steven R Kass
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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4
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Stevenson BC, Berden G, Martens J, Oomens J, Armentrout PB. Spectroscopic Investigation of the Metal Coordination of the Aromatic Amino Acids with Zinc and Cadmium. J Phys Chem A 2023; 127:3560-3569. [PMID: 37053556 DOI: 10.1021/acs.jpca.2c08940] [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: 06/19/2023]
Abstract
The aromatic amino acids (AAA), phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), were cationized with ZnCl+ and CdCl+, and the complexes were evaluated using infrared multiple photon dissociation (IRMPD) action spectroscopy. Specifically, the ZnCl+(Phe), CdCl+(Phe), ZnCl+(Tyr), CdCl+(Tyr), and ZnCl+(Trp) species were examined because the CdCl+(Trp) IRMPD spectrum is available in the literature. Several low-energy conformers for all complexes were found using quantum chemical calculations, and their simulated vibrational spectra were compared to the experimental IRMPD spectra to identify dominant isomers formed. In the case of MCl+(Phe) and MCl+(Tyr), these comparisons indicated the dominant binding motif is a tridentate structure, where the metal atom coordinates with the backbone amino nitrogen and carbonyl oxygen, as well as the aryl ring. These observations are consistent with the predicted ground states at the B3LYP, B3P86, B3LYP-GD3BJ, and MP2 levels of theory. For the ZnCl+(Trp) system, the experimental spectrum indicates a similar binding motif, with the zinc atom coordinating with the backbone nitrogen and carbonyl oxygen and either the pyrrole ring or the benzene ring of the indole side chain. These observations are consistent with the predicted low-lying conformers identified by the aforementioned levels of theory, with the B3LYP and B3P86 levels predicting the metal-pyrrole ring interaction is more favorable than the metal-benzene ring interactions and the opposite at the B3LYP-GD3BJ and MP2 levels.
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Affiliation(s)
- Brandon C Stevenson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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5
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Combs LR, Combs J, McKenna R, Toth Z. Protein Degradation by Gammaherpesvirus RTAs: More Than Just Viral Transactivators. Viruses 2023; 15:730. [PMID: 36992439 PMCID: PMC10055789 DOI: 10.3390/v15030730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a member of the Gammaherpesvirus subfamily that encodes several viral proteins with intrinsic E3 ubiquitin ligase activity or the ability to hijack host E3 ubiquitin ligases to modulate the host's immune response and to support the viral life cycle. This review focuses specifically on how the immediate-early KSHV protein RTA (replication and transcription activator) hijacks the host's ubiquitin-proteasome pathway (UPP) to target cellular and viral factors for protein degradation to allow for robust lytic reactivation. Notably, RTA's targets are either potent transcription repressors or they are activators of the innate and adaptive immune response, which block the lytic cycle of the virus. This review mainly focuses on what is currently known about the role of the E3 ubiquitin ligase activity of KSHV RTA in the regulation of the KSHV life cycle, but we will also discuss the potential role of other gammaherpesviral RTA homologs in UPP-mediated protein degradation.
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Affiliation(s)
- Lauren R. Combs
- Department of Oral Biology, University of Florida College of Dentistry, 1395 Center Drive, Gainesville, FL 32610, USA
| | - Jacob Combs
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 1200 Newell Drive, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 1200 Newell Drive, Gainesville, FL 32610, USA
| | - Zsolt Toth
- Department of Oral Biology, University of Florida College of Dentistry, 1395 Center Drive, Gainesville, FL 32610, USA
- UF Genetics Institute, Gainesville, FL 32610, USA
- UF Health Cancer Center, Gainesville, FL 32610, USA
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6
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Merx J, van Outersterp RE, Engelke UFH, Hendriks V, Wevers RA, Huigen MCDG, Waterval HWAH, Körver-Keularts IMLW, Mecinović J, Rutjes FPJT, Oomens J, Coene KLM, Martens J, Boltje TJ. Identification of Δ-1-pyrroline-5-carboxylate derived biomarkers for hyperprolinemia type II. Commun Biol 2022; 5:997. [PMID: 36131087 PMCID: PMC9492674 DOI: 10.1038/s42003-022-03960-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/07/2022] [Indexed: 11/10/2022] Open
Abstract
Hyperprolinemia type II (HPII) is an inborn error of metabolism due to genetic variants in ALDH4A1, leading to a deficiency in Δ-1-pyrroline-5-carboxylate (P5C) dehydrogenase. This leads to an accumulation of toxic levels of P5C, an intermediate in proline catabolism. The accumulating P5C spontaneously reacts with, and inactivates, pyridoxal 5’-phosphate, a crucial cofactor for many enzymatic processes, which is thought to be the pathophysiological mechanism for HPII. Here, we describe the use of a combination of LC-QTOF untargeted metabolomics, NMR spectroscopy and infrared ion spectroscopy (IRIS) to identify and characterize biomarkers for HPII that result of the spontaneous reaction of P5C with malonic acid and acetoacetic acid. We show that these biomarkers can differentiate between HPI, caused by a deficiency of proline oxidase activity, and HPII. The elucidation of their molecular structures yields insights into the disease pathophysiology of HPII. Combined metabolomics, NMR, and, IRIS identify biomarkers of hyperprolinemia type II (HPII) distinct from HPI and similar metabolic signatures as in patients with pyridoxine-dependent epilepsy.
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Affiliation(s)
- Jona Merx
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Rianne E van Outersterp
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Udo F H Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands
| | - Veronique Hendriks
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands.,United for Metabolic Disease, UMD, Amsterdam, The Netherlands
| | - Marleen C D G Huigen
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands.,United for Metabolic Disease, UMD, Amsterdam, The Netherlands
| | - Huub W A H Waterval
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Irene M L W Körver-Keularts
- United for Metabolic Disease, UMD, Amsterdam, The Netherlands.,Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Floris P J T Rutjes
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands.,United for Metabolic Disease, UMD, Amsterdam, The Netherlands.,Department of Clinical Chemistry and Hematology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED, Nijmegen, the Netherlands.
| | - Thomas J Boltje
- Radboud University, Institute for Molecules and Materials, Synthetic Organic Chemistry, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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7
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Paciotti R, Chiavarino B, Coletti C, Scuderi D, Re N, Corinti D, Rotari L, Fornarini S, Crestoni ME. IRMPD Spectroscopy of Bare Monodeprotonated Genistein, an Antioxidant Flavonoid. ACS OMEGA 2022; 7:19535-19544. [PMID: 35721943 PMCID: PMC9202291 DOI: 10.1021/acsomega.2c01236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/17/2022] [Indexed: 05/11/2023]
Abstract
Genistein is a naturally occurring polyphenol belonging to the family of flavonoids with estrogenic properties and proven antioxidant, anti-inflammatory, and hormonal effects. Genistein and its derivatives are involved in radical scavenging activity by way of mechanisms based on sequential proton-loss electron transfer. In view of this role, a detailed structural characterization of its bare deprotonated form, [geni-H]-, generated by electrospray ionization, has been performed by tandem mass spectrometry and infrared multiple photon dissociation (IRMPD) spectroscopy in the 800-1800 cm-1 spectral range. Quantum chemical calculations at the B3LYP/6-311+G(d,p) level of theory were carried out to determine geometries, thermochemical data, and anharmonic vibrational properties of low-lying isomers, enabling to interpret the experimental spectrum. Evidence is gathered that the conjugate base of genistein exists as a single isomeric form, which is deprotonated at the most acidic site (7-OH) and benefits from a strong intramolecular H-bond interaction between 5-OH and the adjacent carbonyl oxygen in the most stable arrangement.
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Affiliation(s)
- Roberto Paciotti
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Barbara Chiavarino
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Cecilia Coletti
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Debora Scuderi
- Institut
de Chimie Physique (UMR8000), CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Nazzareno Re
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Davide Corinti
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Lucretia Rotari
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
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8
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Chetry N, Gomti Devi T, Karlo T. Synthesis and characterization of metal complex amino acid using spectroscopic methods and theoretical calculation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131670] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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9
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van Outersterp R, Engelke UF, Merx J, Berden G, Paul M, Thomulka T, Berkessel A, Huigen MC, Kluijtmans LA, Mecinović J, Rutjes FP, van Karnebeek CD, Wevers RA, Boltje TJ, Coene KL, Martens J, Oomens J. Metabolite Identification Using Infrared Ion Spectroscopy─Novel Biomarkers for Pyridoxine-Dependent Epilepsy. Anal Chem 2021; 93:15340-15348. [PMID: 34756024 PMCID: PMC8613736 DOI: 10.1021/acs.analchem.1c02896] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/25/2021] [Indexed: 11/30/2022]
Abstract
Untargeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics strategies are being increasingly applied in metabolite screening for a wide variety of medical conditions. The long-standing "grand challenge" in the utilization of this approach is metabolite identification─confidently determining the chemical structures of m/z-detected unknowns. Here, we use a novel workflow based on the detection of molecular features of interest by high-throughput untargeted LC-MS analysis of patient body fluids combined with targeted molecular identification of those features using infrared ion spectroscopy (IRIS), effectively providing diagnostic IR fingerprints for mass-isolated targets. A significant advantage of this approach is that in silico-predicted IR spectra of candidate chemical structures can be used to suggest the molecular structure of unknown features, thus mitigating the need for the synthesis of a broad range of physical reference standards. Pyridoxine-dependent epilepsy (PDE-ALDH7A1) is an inborn error of lysine metabolism, resulting from a mutation in the ALDH7A1 gene that leads to an accumulation of toxic levels of α-aminoadipic semialdehyde (α-AASA), piperideine-6-carboxylate (P6C), and pipecolic acid in body fluids. While α-AASA and P6C are known biomarkers for PDE in urine, their instability makes them poor candidates for diagnostic analysis from blood, which would be required for application in newborn screening protocols. Here, we use combined untargeted metabolomics-IRIS to identify several new biomarkers for PDE-ALDH7A1 that can be used for diagnostic analysis in urine, plasma, and cerebrospinal fluids and that are compatible with analysis in dried blood spots for newborn screening. The identification of these novel metabolites has directly provided novel insights into the pathophysiology of PDE-ALDH7A1.
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Affiliation(s)
- Rianne
E. van Outersterp
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Udo F.H. Engelke
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jona Merx
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Mathias Paul
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Thomas Thomulka
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Albrecht Berkessel
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Marleen C.D.G. Huigen
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Leo A.J. Kluijtmans
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jasmin Mecinović
- University
of Southern Denmark, Department of Physics,
Chemistry and Pharmacy, Campusvej 55, 5230 Odense, Denmark
| | - Floris P.J.T. Rutjes
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Clara D.M. van Karnebeek
- Department
of Pediatrics-Metabolic Diseases, Radboud Center for Mitochondrial
Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Ron A. Wevers
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Thomas J. Boltje
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Karlien L.M. Coene
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 908, 1098XH Amsterdam, The Netherlands
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10
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Cao W, Zhang H, Yuan Q, Zhou X, Kass SR, Wang XB. Observation of Conformational Simplification upon N-Methylation on Amino Acid Iodide Clusters. J Phys Chem Lett 2021; 12:2780-2787. [PMID: 33710892 DOI: 10.1021/acs.jpclett.1c00125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This Letter reports a counterintuitive observation that methylation of the glycine-iodide cluster leads to fewer conformations and spectroscopic simplicity. Cryogenic "iodide-tagging" negative ion photoelectron spectroscopy (NIPES) is used to probe specific binding sites of three N-methylated glycine derivatives, i.e., N-methylglycine (sarcosine), N,N-dimethylglycine, and N,N,N-trimethylglycine (glycine betaine). NIPES reveals a progressive spectral simplification of the iodide clusters with increasing methylation due to fewer contributing structures. Low energy conformers and tautomers of each cluster are computationally identified, and those observed in the experiments are assigned based on excellent agreement between the NIPE spectra and theoretical simulations. Zwitterionic cluster structures are found to be less stable than their canonical forms and do not contribute to the observed spectra. This work demonstrates the power of iodide-tagging NIPES in probing conformations of amino acid-iodide clusters and provides a molecular level understanding on the effect of methyl substitution on amino acid binding sites.
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Affiliation(s)
- Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Hanhui Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Steven R Kass
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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11
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Huang L, Fang Z, Gao J, Wang J, Li Y, Sun L, Wang Y, Liao J, Gooneratne R. Protective role of l-threonine against cadmium toxicity in Saccharomyces cerevisiae. J Basic Microbiol 2021; 61:339-350. [PMID: 33570201 DOI: 10.1002/jobm.202100012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022]
Abstract
Environment and food contamination with cadmium (Cd) can cause serious toxicity, posing a severe threat to agricultural production and human health. However, how amino acids contribute to defenses against oxidative stress caused by Cd in cells is not fully understood. As a model eukaryote with a relatively clear genetic background, Saccharomyces cerevisiae has been commonly used in Cd toxicity research. To gain insight into Cd toxicity and cell defenses against it, 20 amino acids were screened for protective roles against Cd stress in S. cerevisiae. The results showed that threonine (Thr, T) had the strongest protective effect against Cd-induced mortality and membrane damage in the cells. Compared to the antioxidant vitamin C (VC), Thr exhibited a higher efficacy in restoring the superoxide dismutase (SOD) activity that was inhibited by Cd but not by H2 O2 in vivo. Thr exhibited evident DPPH (2,2-diphenyl-1-picrylhydrazyl) activity but weak ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-9 sulfonic acid)) scavenging activity, giving it a weaker effect against Cd-induced lipid peroxidation and superoxide radical O2- , compared to VC. More importantly, compared to the chelating agent EDTA, Thr showed stronger chelation of Cd, giving it a stronger protective effect on SOD against Cd than VC in vitro. The results of the in vivo and in vitro experiments revealed that the role Thr plays in cell defenses against Cd may be attributed to its protection of the SOD enzyme, predominantly through the preferential chelation of Cd. Our results provide insights into the protective mechanisms of amino acid Thr that ameliorate Cd toxicity and suggest that a supplement of Thr might help to reduce Cd-induced oxidative damage.
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Affiliation(s)
- Linru Huang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology, Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Cunjin College, Guangdong Ocean University, Zhanjiang, China
| | - Zhijia Fang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology, Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Cunjin College, Guangdong Ocean University, Zhanjiang, China
| | - Jian Gao
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology, Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Cunjin College, Guangdong Ocean University, Zhanjiang, China
| | - Jingwen Wang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology, Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Cunjin College, Guangdong Ocean University, Zhanjiang, China
| | - Yongbin Li
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology, Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Cunjin College, Guangdong Ocean University, Zhanjiang, China
| | - Lijun Sun
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology, Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Cunjin College, Guangdong Ocean University, Zhanjiang, China
| | - Yaling Wang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology, Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Cunjin College, Guangdong Ocean University, Zhanjiang, China
| | - Jianmeng Liao
- Institute for Food and Drug Control, Zhanjiang, China
| | - Ravi Gooneratne
- Department of Wine, Food, and Molecular Biosciences, Lincoln University, Lincoln, Canterbury, New Zealand
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Corinti D, Chiavarino B, Scuderi D, Fraschetti C, Filippi A, Fornarini S, Crestoni ME. Molecular Properties of Bare and Microhydrated Vitamin B5-Calcium Complexes. Int J Mol Sci 2021; 22:E692. [PMID: 33445631 PMCID: PMC7826572 DOI: 10.3390/ijms22020692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
Pantothenic acid, also called vitamin B5, is an essential nutrient involved in several metabolic pathways. It shows a characteristic preference for interacting with Ca(II) ions, which are abundant in the extracellular media and act as secondary mediators in the activation of numerous biological functions. The bare deprotonated form of pantothenic acid, [panto-H]-, its complex with Ca(II) ion, [Ca(panto-H)]+, and singly charged micro-hydrated calcium pantothenate [Ca(panto-H)(H2O)]+ adduct have been obtained in the gas phase by electrospray ionization and assayed by mass spectrometry and IR multiple photon dissociation spectroscopy in the fingerprint spectral range. Quantum chemical calculations at the B3LYP(-D3) and MP2 levels of theory were performed to simulate geometries, thermochemical data, and linear absorption spectra of low-lying isomers, allowing us to assign the experimental absorptions to particular structural motifs. Pantothenate was found to exist in the gas phase as a single isomeric form showing deprotonation on the carboxylic moiety. On the contrary, free and monohydrated calcium complexes of deprotonated pantothenic acid both present at least two isomers participating in the gas-phase population, sharing the deprotonation of pantothenate on the carboxylic group and either a fourfold or fivefold coordination with calcium, thus justifying the strong affinity of pantothenate for the metal.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Debora Scuderi
- Institut de Chimie Physique (UMR8000), CNRS, Université Paris-Saclay, 91405 Orsay, France;
| | - Caterina Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
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13
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Stevenson BC, Martens J, Berden G, Oomens J, Schäfer M, Armentrout PB. IRMPD Spectroscopic and Theoretical Structural Investigations of Zinc and Cadmium Dications Bound to Histidine Dimers. J Phys Chem A 2020; 124:10266-10276. [PMID: 33241937 DOI: 10.1021/acs.jpca.0c08861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallated gas-phase structures consisting of a deprotonated and an intact histidine (His) ligand, yielding M(His-H)(His)+, where M = Zn and Cd, were examined with infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light from a free-electron laser (FEL). In parallel, quantum chemical calculations identified several low-energy isomers for each complex. Experimental action spectra were compared to linear spectra calculated at the B3LYP level of theory using the 6-311+G(d,p) and def2-TZVP basis sets for the zinc and cadmium complexes, respectively. For both Zn and Cd species, the definitive assignment is complicated by conflicting relative energetics, which were calculated at B3LYP, B3LYP-GD3BJ, B3P86, and MP2(full) levels. Spectral comparison for both species indicates that the dominant conformation, [Nα,Nπ,CO-][CO2-](NπH+), has the deprotonated His chelating the metal at the amine nitrogen, π nitrogen of the imidazole ring, and the deprotonated carbonyl oxygen and that the intact His ligand adopts a salt-bridge bidentate binding motif, coordinating the metal with both carboxylate oxygens. There is also evidence for a conformation where the deprotonated His coordination is maintained, but the intact His ligand adopts a more canonical structure, coordinating with the metal atom at the amine nitrogen and π nitrogen, [Nα,Nπ,CO-][Nα,Nπ]gtgg. For both metallated species, B3LYP, B3P86, and B3LYP-GD3BJ levels of theory appear to describe the relative stability of the dominant zwitterionic species more accurately than the MP2(full) level.
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Affiliation(s)
- Brandon C Stevenson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL, 1098 XH Amsterdam, The Netherlands
| | - Mathias Schäfer
- Department of Chemistry, University of Cologne, 50939 Cologne, Germany
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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14
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Boles GC, Stevenson BC, Hightower RL, Berden G, Oomens J, Armentrout PB. Zinc and cadmium complexation of L-methionine: An infrared multiple photon dissociation spectroscopy and theoretical study. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 56:e4580. [PMID: 32677757 DOI: 10.1002/jms.4580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Methionine (Met) cationized with Zn2+ , forming Zn (Met-H)+ (ACN) where ACN = acetonitrile, Zn (Met-H)+ , and ZnCl+ (Met), as well as Cd2+ , forming CdCl+ (Met), were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from the FELIX free electron laser. A series of low-energy conformers for each complex was found using quantum-chemical calculations in order to identify the structures formed experimentally. For all four complexes, spectral comparison indicated that the main binding motif observed is a charge solvated, tridentate structure where the metal center binds to the backbone amino group nitrogen, backbone carbonyl oxygen (where the carboxylic acid is deprotonated in two of the Zn2+ complexes), and side-chain sulfur. For all species, the predicted ground structures reproduce the experimental spectra well, although low-lying conformers characterized by similar binding motifs may also contribute in each system. The current work provides valuable information regarding the binding interaction between Met and biologically relevant metals. Further, the comparison between the current work and previous analyses involving alkali metal cationized Met as well as cysteine (the other sulfur containing amino acid) cationized with Zn2+ and Cd2+ allows for the elucidation of important metal dependent trends associated with physiologically important metal-sulfur binding.
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Affiliation(s)
- Georgia C Boles
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | | | - Randy L Hightower
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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