101
|
Csizi KS, Eckert L, Brunken C, Hofstetter TB, Reiher M. The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases. Chemistry 2022; 28:e202103937. [PMID: 35072969 PMCID: PMC9306888 DOI: 10.1002/chem.202103937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/29/2022]
Abstract
Rieske dioxygenases belong to the non‐heme iron family of oxygenases and catalyze important cis‐dihydroxylation as well as O‐/N‐dealkylation and oxidative cyclization reactions for a wide range of substrates. The lack of substrate coordination at the non‐heme ferrous iron center, however, makes it particularly challenging to delineate the role of the substrate for productive O2
activation. Here, we studied the role of the substrate in the key elementary reaction leading to O2
activation from a theoretical perspective by systematically considering (i) the 6‐coordinate to 5‐coordinate conversion of the non‐heme FeII upon abstraction of a water ligand, (ii) binding of O2
, and (iii) transfer of an electron from the Rieske cluster. We systematically evaluated the spin‐state‐dependent reaction energies and structural effects at the active site for all combinations of the three elementary processes in the presence and absence of substrate using naphthalene dioxygenase as a prototypical Rieske dioxygenase. We find that reaction energies for the generation of a coordination vacancy at the non‐heme FeII
center through thermoneutral H2O reorientation and exothermic O2
binding prior to Rieske cluster oxidation are largely insensitive to the presence of naphthalene and do not lead to formation of any of the known reactive Fe‐oxygen species. By contrast, the role of the substrate becomes evident after Rieske cluster oxidation and exclusively for the 6‐coordinate non‐heme FeII
sites in that the additional electron is found at the substrate instead of at the iron and oxygen atoms. Our results imply an allosteric control of the substrate on Rieske dioxygenase reactivity to happen prior to changes at the non‐heme FeII
in agreement with a strategy that avoids unproductive O2
activation.
Collapse
Affiliation(s)
- Katja-Sophia Csizi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Lina Eckert
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Christoph Brunken
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| |
Collapse
|
102
|
Zhou A, Cao X, Chen H, Sun D, Zhao Y, Nam W, Wang Y. The chameleon-like nature of elusive cobalt-oxygen intermediates in C-H bond activation reactions. Dalton Trans 2022; 51:4317-4323. [PMID: 35212349 DOI: 10.1039/d2dt00224h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High-valence metal-oxo (M-O, M = Fe, Mn, etc.) species are well-known reaction intermediates that are responsible for a wide range of pivotal oxygenation reactions and water oxidation reactions in metalloenzymes. Although extensive efforts have been devoted to synthesizing and identifying such complexes in biomimetic studies, the structure-function relationship and related reaction mechanisms of these reaction intermediates remain elusive, especially for the cobalt-oxygen species. In the present manuscript, the calculated results demonstrate that the tetraamido macrocycle ligated cobalt complex, Co(O)(TAML) (1), behaves like a chameleon: the electronic structure varies from a cobalt(III)-oxyl species to a cobalt(IV)-oxo species when a Lewis acid Sc3+ salt coordinates or an acidic hydrocarbon attacks 1. The dichotomous correlation between the reaction rates of C-H bond activation by 1 and the bond dissociation energy (BDE) vs. the acidity (pKa) was rationalized for the first time by different reaction mechanisms: for normal C-H bond activation, the Co(III)-oxyl species directly activates the C-H bond via a hydrogen atom transfer (HAT) mechanism, whereas for acidic C-H bond activation, the Co(III)-oxyl species evolves to a Co(IV)-oxo species to increase the basicity of the oxygen to activate the acidic C-H bond, via a novel PCET(PT) mechanism (proton-coupled electron transfer with a PT(proton-transfer)-like transition state). These theoretical findings will enrich the knowledge of biomimetic metal-oxygen chemistry.
Collapse
Affiliation(s)
- Anran Zhou
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Xuanyu Cao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Huanhuan Chen
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea.
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| |
Collapse
|
103
|
Paik A, Paul S, Bhowmik S, Das R, Naveen T, Rana S. Recent Advances in First Row Transition Metal Mediated C‐H Halogenation of (Hetero)arenes and Alkanes. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202200060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Aniruddha Paik
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Sabarni Paul
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Sabyasachi Bhowmik
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Rahul Das
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Togati Naveen
- Sardar Vallabhbhai National Institute of Technology Department of Chemistry 395007 Surat INDIA
| | - Sujoy Rana
- University of North Bengal Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India, 734013 734013 Siliguri INDIA
| |
Collapse
|
104
|
Dagar S, Sarkar S, Rajamani S. Porphyrin in prebiotic catalysis: Ascertaining a route for the emergence of early metalloporphyrins. Chembiochem 2022; 23:e202200013. [PMID: 35233914 DOI: 10.1002/cbic.202200013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/15/2022] [Indexed: 11/09/2022]
Abstract
Metal ions are known to catalyze certain prebiotic reactions. However, the transition from metal ions to extant metalloenzymes remains unclear. Porphyrins are found ubiquitously in the catalytic core of many ancient metalloenzymes. In this study, we evaluated the influence of porphyrin-based organic scaffold, on the catalysis, emergence and putative molecular evolution of prebiotic metalloporphyrins. We studied the effect of porphyrins on the transition metal ion-mediated oxidation of hydroquinone (HQ). We report a change in the catalytic activity of the metal ions in the presence of porphyrin. This was observed to be facilitated by the coordination between metal ions and porphyrins or by the formation of non-coordinated complexes. The metal-porphyrin complexes also oxidized NADH, underscoring its versatility at oxidizing more than one substrate. Our study highlights the selective advantage that some of the metal ions would have had in the presence of porphyrin, underscoring their role in shaping the evolution of protometalloenzymes.
Collapse
Affiliation(s)
- Shikha Dagar
- IISER Pune: Indian Institute of Science Education Research Pune, Biology, IISER Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Pune, INDIA
| | - Susovan Sarkar
- IISER Pune: Indian Institute of Science Education Research Pune, Biology, Iiser Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Pune, INDIA
| | - Sudha Rajamani
- IISER Pune: Indian Institute of Science Education Research Pune, Biology, Dr. Homi Bhaba Rd, Pashan, Near NCL, 411008, Pune, INDIA
| |
Collapse
|
105
|
Bhattacharjee S, Isegawa M, Garcia-Ratés M, Neese F, Pantazis DA. Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches. J Chem Theory Comput 2022; 18:1619-1632. [PMID: 35191695 PMCID: PMC8908766 DOI: 10.1021/acs.jctc.1c01267] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Hydrated transition
metal ions are prototypical systems that can
be used to model properties of transition metals in complex chemical
environments. These seemingly simple systems present challenges for
computational chemistry and are thus crucial in evaluations of quantum
chemical methods for spin-state and redox energetics. In this work,
we explore the applicability of the domain-based pair natural orbital
implementation of coupled cluster (DLPNO-CC) theory to the calculation
of ionization energies and redox potentials for hydrated ions of all
first transition row (3d) metals in the 2+/3+ oxidation states, in
connection with various solvation approaches. In terms of model definition,
we investigate the construction of a minimally explicitly hydrated
quantum cluster with a first and second hydration layer. We report
on the convergence with respect to the coupled cluster expansion and
the PNO space, as well as on the role of perturbative triple excitations.
A recent implementation of the conductor-like polarizable continuum
model (CPCM) for the DLPNO-CC approach is employed to determine self-consistent
redox potentials at the coupled cluster level. Our results establish
conditions for the convergence of DLPNO-CCSD(T) energetics and stress
the absolute necessity to explicitly consider the second solvation
sphere even when CPCM is used. The achievable accuracy for redox potentials
of a practical DLPNO-based approach is, on average, 0.13 V. Furthermore,
multilayer approaches that combine a higher-level DLPNO-CCSD(T) description
of the first solvation sphere with a lower-level description of the
second solvation layer are investigated. The present work establishes
optimal and transferable methodological choices for employing DLPNO-based
coupled cluster theory, the associated CPCM implementation, and cost-efficient
multilayer derivatives of the approach for open-shell transition metal
systems in complex environments.
Collapse
Affiliation(s)
- Sinjini Bhattacharjee
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Miquel Garcia-Ratés
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
106
|
Tomić A, Tomić S. Demystifying DPP III Catalyzed Peptide Hydrolysis—Computational Study of the Complete Catalytic Cycle of Human DPP III Catalyzed Tynorphin Hydrolysis. Int J Mol Sci 2022; 23:ijms23031858. [PMID: 35163780 PMCID: PMC8836397 DOI: 10.3390/ijms23031858] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 12/04/2022] Open
Abstract
Dipeptidyl peptides III (DPP III) is a dual-domain zinc exopeptidase that hydrolyzes peptides of varying sequence and size. Despite attempts to elucidate and narrow down the broad substrate-specificity of DPP III, there is no explanation as to why some of them, such as tynorphin (VVYPW), the truncated form of the endogenous heptapeptide spinorphin, are the slow-reacting substrates of DPP III compared to others, such as Leu-enkephalin. Using quantum molecular mechanics calculations followed by various molecular dynamics techniques, we describe for the first time the entire catalytic cycle of human DPP III, providing theoretical insight into the inhibitory mechanism of tynorphin. The chemical step of peptide bond hydrolysis and the substrate binding to the active site of the enzyme and release of the product were described for DPP III in complex with tynorphin and Leu-enkephalin and their products. We found that tynorphin is cleaved by the same reaction mechanism determined for Leu-enkephalin. More importantly, we showed that the product stabilization and regeneration of the enzyme, but not the nucleophilic attack of the catalytic water molecule and inversion at the nitrogen atom of the cleavable peptide bond, correspond to the rate-determining steps of the overall catalytic cycle of the enzyme.
Collapse
|
107
|
Karbalaei S, Goldsmith CR. Recent advances in the preclinical development of responsive MRI contrast agents capable of detecting hydrogen peroxide. J Inorg Biochem 2022; 230:111763. [DOI: 10.1016/j.jinorgbio.2022.111763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 01/10/2023]
|
108
|
Rhoda HM, Heyer AJ, Snyder BER, Plessers D, Bols ML, Schoonheydt RA, Sels BF, Solomon EI. Second-Sphere Lattice Effects in Copper and Iron Zeolite Catalysis. Chem Rev 2022; 122:12207-12243. [PMID: 35077641 DOI: 10.1021/acs.chemrev.1c00915] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transition-metal-exchanged zeolites perform remarkable chemical reactions from low-temperature methane to methanol oxidation to selective reduction of NOx pollutants. As with metalloenzymes, metallozeolites have impressive reactivities that are controlled in part by interactions outside the immediate coordination sphere. These second-sphere effects include activating a metal site through enforcing an "entatic" state, controlling binding and access to the metal site with pockets and channels, and directing radical rebound vs cage escape. This review explores these effects with emphasis placed on but not limited to the selective oxidation of methane to methanol with a focus on copper and iron active sites, although other transition-metal-ion zeolite reactions are also explored. While the actual active-site geometric and electronic structures are different in the copper and iron metallozeolites compared to the metalloenzymes, their second-sphere interactions with the lattice or the protein environments are found to have strong parallels that contribute to their high activity and selectivity.
Collapse
Affiliation(s)
- Hannah M Rhoda
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alexander J Heyer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Benjamin E R Snyder
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Dieter Plessers
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Max L Bols
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Robert A Schoonheydt
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Bert F Sels
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,Photon Science, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| |
Collapse
|
109
|
Banerjee S, Muderspach SJ, Tandrup T, Frandsen KEH, Singh RK, Ipsen JØ, Hernández-Rollán C, Nørholm MHH, Bjerrum MJ, Johansen KS, Lo Leggio L. Protonation State of an Important Histidine from High Resolution Structures of Lytic Polysaccharide Monooxygenases. Biomolecules 2022; 12:biom12020194. [PMID: 35204695 PMCID: PMC8961595 DOI: 10.3390/biom12020194] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/09/2022] [Accepted: 01/15/2022] [Indexed: 02/01/2023] Open
Abstract
Lytic Polysaccharide Monooxygenases (LPMOs) oxidatively cleave recalcitrant polysaccharides. The mechanism involves (i) reduction of the Cu, (ii) polysaccharide binding, (iii) binding of different oxygen species, and (iv) glycosidic bond cleavage. However, the complete mechanism is poorly understood and may vary across different families and even within the same family. Here, we have investigated the protonation state of a secondary co-ordination sphere histidine, conserved across AA9 family LPMOs that has previously been proposed to be a potential proton donor. Partial unrestrained refinement of newly obtained higher resolution data for two AA9 LPMOs and re-refinement of four additional data sets deposited in the PDB were carried out, where the His was refined without restraints, followed by measurements of the His ring geometrical parameters. This allowed reliable assignment of the protonation state, as also validated by following the same procedure for the His brace, for which the protonation state is predictable. The study shows that this histidine is generally singly protonated at the Nε2 atom, which is close to the oxygen species binding site. Our results indicate robustness of the method. In view of this and other emerging evidence, a role as proton donor during catalysis is unlikely for this His.
Collapse
Affiliation(s)
- Sanchari Banerjee
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark; (S.B.); (S.J.M.); (T.T.); (K.E.H.F.); (R.K.S.); (M.J.B.)
| | - Sebastian J. Muderspach
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark; (S.B.); (S.J.M.); (T.T.); (K.E.H.F.); (R.K.S.); (M.J.B.)
| | - Tobias Tandrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark; (S.B.); (S.J.M.); (T.T.); (K.E.H.F.); (R.K.S.); (M.J.B.)
| | - Kristian Erik Høpfner Frandsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark; (S.B.); (S.J.M.); (T.T.); (K.E.H.F.); (R.K.S.); (M.J.B.)
- Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, DK-1871 Copenhagen, Denmark;
| | - Raushan K. Singh
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark; (S.B.); (S.J.M.); (T.T.); (K.E.H.F.); (R.K.S.); (M.J.B.)
| | - Johan Ørskov Ipsen
- Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, DK-1871 Copenhagen, Denmark;
- Department of Geoscience & Natural Resource Management, University of Copenhagen, Frederiksberg 5, DK-1958 Copenhagen, Denmark;
| | - Cristina Hernández-Rollán
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kongens Lyngby, Denmark; (C.H.-R.); (M.H.H.N.)
| | - Morten H. H. Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kongens Lyngby, Denmark; (C.H.-R.); (M.H.H.N.)
| | - Morten J. Bjerrum
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark; (S.B.); (S.J.M.); (T.T.); (K.E.H.F.); (R.K.S.); (M.J.B.)
| | - Katja Salomon Johansen
- Department of Geoscience & Natural Resource Management, University of Copenhagen, Frederiksberg 5, DK-1958 Copenhagen, Denmark;
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark; (S.B.); (S.J.M.); (T.T.); (K.E.H.F.); (R.K.S.); (M.J.B.)
- Correspondence:
| |
Collapse
|
110
|
Mechanistic Insights of Chelator Complexes with Essential Transition Metals: Antioxidant/Pro-Oxidant Activity and Applications in Medicine. Int J Mol Sci 2022; 23:ijms23031247. [PMID: 35163169 PMCID: PMC8835618 DOI: 10.3390/ijms23031247] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/13/2022] [Accepted: 01/20/2022] [Indexed: 12/24/2022] Open
Abstract
The antioxidant/pro-oxidant activity of drugs and dietary molecules and their role in the maintenance of redox homeostasis, as well as the implications in health and different diseases, have not yet been fully evaluated. In particular, the redox activity and other interactions of drugs with essential redox metal ions, such as iron and copper, need further investigation. These metal ions are ubiquitous in human nutrition but also widely found in dietary supplements and appear to exert major effects on redox homeostasis in health, but also on many diseases of free radical pathology. In this context, the redox mechanistic insights of mainly three prototype groups of drugs, namely alpha-ketohydroxypyridines (alpha-hydroxypyridones), e.g., deferiprone, anthraquinones, e.g., doxorubicin and thiosemicarbazones, e.g., triapine and their metal complexes were examined; details of the mechanisms of their redox activity were reviewed, with emphasis on the biological implications and potential clinical applications, including anticancer activity. Furthermore, the redox properties of these three classes of chelators were compared to those of the iron chelating drugs and also to vitamin C, with an emphasis on their potential clinical interactions and future clinical application prospects in cancer, neurodegenerative and other diseases.
Collapse
|
111
|
Mejuto-Zaera C, Tzeli D, Williams-Young D, Tubman NM, Matoušek M, Brabec J, Veis L, Xantheas SS, de Jong WA. The Effect of Geometry, Spin, and Orbital Optimization in Achieving Accurate, Correlated Results for Iron-Sulfur Cubanes. J Chem Theory Comput 2022; 18:687-702. [PMID: 35034448 DOI: 10.1021/acs.jctc.1c00830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Iron-sulfur clusters comprise an important functional motif in the catalytic centers of biological systems, capable of enabling important chemical transformations at ambient conditions. This remarkable capability derives from a notoriously complex electronic structure that is characterized by a high density of states that is sensitive to geometric changes. The spectral sensitivity to subtle geometric changes has received little attention from correlated, large active space calculations, owing partly to the exceptional computational complexity for treating these large and correlated systems accurately. To provide insight into this aspect, we report the first Complete Active Space Self Consistent Field (CASSCF) calculations for different geometries of the [Fe(II/III)4S4(SMe)4]-2 clusters using two complementary, correlated solvers: spin-pure Adaptive Sampling Configuration Interaction (ASCI) and Density Matrix Renormalization Group (DMRG). We find that the previously established picture of a double-exchange driven magnetic structure, with minute energy gaps (<1 mHa) between consecutive spin states, has a weak dependence on the underlying geometry. However, the spin gap between the singlet and the spin state 2S + 1 = 19, corresponding to a maximal number of Fe-d electrons being unpaired and of parallel spin, is strongly geometry dependent, changing by a factor of 3 upon slight deformations that are still within biologically relevant parameters. The CASSCF orbital optimization procedure, using active spaces as large as 86 electrons in 52 orbitals, was found to reduce this gap compared to typical mean-field orbital approaches. Our results show the need for performing large active space calculations to unveil the challenging electronic structure of these complex catalytic centers and should serve as accurate starting points for fully correlated treatments upon inclusion of dynamical correlation outside the active space.
Collapse
Affiliation(s)
- Carlos Mejuto-Zaera
- University of California, Berkeley, California 94720, United States.,Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Demeter Tzeli
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 15784, Greece.,Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
| | - David Williams-Young
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Norm M Tubman
- Quantum Artificial Intelligence Lab. (QuAIL), Exploration Technology Directorate, NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Mikuláš Matoušek
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Jiri Brabec
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Libor Veis
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Sotiris S Xantheas
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98185, United States
| | - Wibe A de Jong
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
112
|
Affiliation(s)
- Xin‐Xin Peng
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
| | - Song Gao
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
- Spin-X Institute, School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510641 P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials Guangzhou 510641 P. R. China
| | - Jun‐Long Zhang
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
| |
Collapse
|
113
|
Molecular Docking, Synthesis, and Tyrosinase Inhibition Activity of Acetophenone Amide: Potential Inhibitor of Melanogenesis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1040693. [PMID: 35059457 PMCID: PMC8766184 DOI: 10.1155/2022/1040693] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/17/2021] [Indexed: 11/18/2022]
Abstract
Tyrosinase and its related proteins are responsible for pigmentation disorders, and inhibiting tyrosinase is an established strategy to treat hyperpigmentation. The carbonyl scaffolds can be effective inhibitors of tyrosinase activity, and the fact that both benzoic and cinnamic acids are safe natural substances with such a scaffolded structure, it was speculated that hydroxyl-substituted benzoic and cinnamic acid derivatives may exhibit potent tyrosinase inhibitory activity. These moieties were incorporated into new chemotypes that displayed in vitro inhibitory effect against mushroom tyrosinase with a view to explore antimelanogenic ingredients. The most active compound, 2-((3-acetylphenyl)amino)-2-oxoethyl(E)-3-(2,4-dihydroxyphenyl)acrylate (5c), inhibited mushroom tyrosinase with an IC50 of
, while 2-((3-acetylphenyl)amino)-2-oxoethyl 2,4-dihydroxybenzoate (3c) had an IC50 of
in comparison to the positive control arbutin and kojic acid with a tyrosinase inhibitory activity of IC50 of
and IC50 of
, respectively. Analysis of enzyme kinetics revealed that 5c is a competitive and reversible inhibitor with dissociation constant (Ki) value 0.0072 μM. In silico docking studies with mushroom tyrosinase (PDB ID 2Y9X) predicted possible binding modes in the enzymatic pocket for these compounds. The orthohydroxyl of the cinnamic acid moiety of 5c is predicted to form hydrogen bond with the active site side chain carbonyl of Asn 260 (2.16 Å) closer to the catalytic site Cu ions. The acetyl carbonyl is picking up another hydrogen bond with Asn 81 (1.90 Å). The inhibitor 5c passed the panassay interference (PAINS) alerts. This study presents the potential of hydroxyl-substituted benzoic and cinnamic acids and could be beneficial for various cosmetic formulations.
Collapse
|
114
|
Bouroumane N, El Kodadi M, Touzani R, El Boutaybi M, Oussaid A, Hammouti B, Nandiyanto ABD. New Pyrazole-Based Ligands: Synthesis, Characterization, and Catalytic Activity of Their Copper Complexes. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2022. [DOI: 10.1007/s13369-021-05343-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
115
|
Sarkar P, Sarmah A, Mukherjee C. Where is the unpaired electron density? A combined experimental and theoretical finding on the geometric and electronic structures of the Co( iii) and Mn( iv) complexes of the unsymmetrical non-innocent pincer ONS ligand. Dalton Trans 2022; 51:16723-16732. [DOI: 10.1039/d2dt01868c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The geometry and electronic structures of the Co and Mn complexes of the pincer H3LONS ligand composed of both hard and soft donor atoms at the coordinating sites are reported.
Collapse
Affiliation(s)
- Prasenjit Sarkar
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Amrit Sarmah
- Department of Molecular Modelling, Institute of Organic Chemistry and Biochemistry ASCR, v.v.i. Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Chandan Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| |
Collapse
|
116
|
Huang XL. What are the inorganic nanozymes? Artificial or inorganic enzymes! NEW J CHEM 2022. [DOI: 10.1039/d2nj02088b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The research on inorganic nanozymes remains very active since the first paper on the “intrinsic peroxidase-like properties of ferromagnetic nanoparticles” was published in Nature Nanotechnology in 2007. However, there is...
Collapse
|
117
|
Solomon EI, Jose A. Spiers Memorial Lecture: Activating Metal Sites for Biological Electron Transfer. Faraday Discuss 2022; 234:9-30. [DOI: 10.1039/d2fd00001f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal sites in biology often exhibit unique spectroscopic features that reflect novel geometric and electronic structures imposed by the protein that are key to reactivity. The Blue copper active site...
Collapse
|
118
|
Selvakumaran B, Murali M. Functional mimic for amine and catechol oxidases: Structural, spectral, electrochemical and catalytic properties of mononuclear copper(II) complex. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.120819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
119
|
Dastidar TG, Chattopadhyay S. Synthetic strategies, structures and properties of di and polynuclear cobalt complexes with H2salen type Schiff bases and their reduced analogues. Polyhedron 2022. [DOI: 10.1016/j.poly.2021.115511] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
120
|
Azadmanesh J, Lutz WE, Coates L, Weiss KL, Borgstahl GEO. Cryotrapping peroxide in the active site of human mitochondrial manganese superoxide dismutase crystals for neutron diffraction. Acta Crystallogr F Struct Biol Commun 2022; 78:8-16. [PMID: 34981770 PMCID: PMC8725007 DOI: 10.1107/s2053230x21012413] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/22/2021] [Indexed: 12/28/2022] Open
Abstract
Structurally identifying the enzymatic intermediates of redox proteins has been elusive due to difficulty in resolving the H atoms involved in catalysis and the susceptibility of ligand complexes to photoreduction from X-rays. Cryotrapping ligands for neutron protein crystallography combines two powerful tools that offer the advantage of directly identifying hydrogen positions in redox-enzyme intermediates without radiolytic perturbation of metal-containing active sites. However, translating cryogenic techniques from X-ray to neutron crystallography is not straightforward due to the large crystal volumes and long data-collection times. Here, methods have been developed to visualize the evasive peroxo complex of manganese superoxide dismutase (MnSOD) so that all atoms, including H atoms, could be visualized. The subsequent cryocooling and ligand-trapping methods resulted in neutron data collection to 2.30 Å resolution. The P6122 crystal form of MnSOD is challenging because it has some of the largest unit-cell dimensions (a = b = 77.8, c = 236.8 Å) ever studied using high-resolution cryo-neutron crystallography. The resulting neutron diffraction data permitted the visualization of a dioxygen species bound to the MnSOD active-site metal that was indicative of successful cryotrapping.
Collapse
Affiliation(s)
- Jahaun Azadmanesh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | - William E. Lutz
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
| |
Collapse
|
121
|
Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
Collapse
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| |
Collapse
|
122
|
Liu M, Nazemi A, Taylor MG, Nandy A, Duan C, Steeves AH, Kulik HJ. Large-Scale Screening Reveals That Geometric Structure Matters More Than Electronic Structure in the Bioinspired Catalyst Design of Formate Dehydrogenase Mimics. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Mingjie Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Azadeh Nazemi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael G. Taylor
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chenru Duan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Adam H. Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
123
|
Shiga T, Ito H, Mihara N, Nihei M. Syntheses, structures, and magnetic properties of a series of Mn-M-Mn trinuclear complexes with different spin configurations. Dalton Trans 2021; 51:562-569. [PMID: 34901982 DOI: 10.1039/d1dt03030b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of trinuclear complexes, [MnII2YIII(L)2(HL)2(NO3)3][YIII(NO3)5]·7H2O (1'), [MnII2GdIII(HL)4(NO3)4]2[MnII2GdIII(L)(HL)3(NO3)4][GdIII(NO3)5]4·2(o-Xy)·12H2O (2') and [MnII3(L)(HL)2(NO3)4](NO3)·1.25(p-Xy) (3'), were synthesized using a β-diketone ligand HL (HL = 1,3-bis(pyridin-2-yl)propane-1,3-dione). X-ray structural analyses revealed that each complex has a trinuclear core with an Mn(II)-M-Mn(II) arrangement (M = YIII (1), GdIII (2), and MnII (3)). In 1' with a diamagnetic Y(III) ion, negligible antiferromagnetic interactions between terminal Mn(II) ions are operative. On the other hand, 2' shows ferromagnetic interactions between Mn(II) and Gd(III) ions, affording a spin ground state of ST = 17/2. The homometallic Mn(II)3 complex of 3' has an ST = 5/2 spin ground state resulting from the antiferromagnetic interactions between neighboring Mn(II) ions. The maximum magnetic entropy change (-ΔSm) of 1'-3' was estimated to be 12.3, 24.8, and 8.0 J kg-1 K-1, respectively.
Collapse
Affiliation(s)
- Takuya Shiga
- Degree Programs in Pure and Applied Sciences, Graduate School of Science and Technology, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8571, Japan.
| | - Honami Ito
- Degree Programs in Pure and Applied Sciences, Graduate School of Science and Technology, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8571, Japan.
| | - Nozomi Mihara
- Degree Programs in Pure and Applied Sciences, Graduate School of Science and Technology, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8571, Japan.
| | - Masayuki Nihei
- Degree Programs in Pure and Applied Sciences, Graduate School of Science and Technology, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8571, Japan.
| |
Collapse
|
124
|
|
125
|
Kroneck PMH. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. J Biol Inorg Chem 2021; 27:1-21. [PMID: 34865208 PMCID: PMC8840924 DOI: 10.1007/s00775-021-01921-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2- is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2- to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
Collapse
Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
| |
Collapse
|
126
|
Gorinchoy V, Cuzan O, Melnic S, Petuhov O, Shova S. Synthesis and Characterisation of New {Fe2CrO} Heterotrinuclear Iron-chromium Clusters. CHEMISTRY JOURNAL OF MOLDOVA 2021. [DOI: 10.19261/cjm.2021.885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Two new μ3-oxo trinuclear heterometallic Fe2IIICrIII complexes with furan-2-carboxylic and salicylic acids with the composition: [Fe2CrO(C4H3OCOO)6(CH3OH)3]NO3·0.5CH3OH and [Fe2CrO(C6H4(OH)COO)7(CH3OH)2]·2DMA were synthesized starting from iron(III) and chromium(III) salts mixture. The complexes structures were confirmed by elemental analysis, IR, Mössbauer spectroscopies, and X-ray analysis. The atomic absorption spectroscopy confirmed that the iron: chromium ratio is 2:1. The thermal properties of both heteronuclear complexes have been investigated in oxidizing and inert atmospheres revealing the stability of the trinuclear core up to 170 and 220°C, respectively.
Collapse
|
127
|
Mandal SK, Kanaujia SP. Structural and thermodynamic insights into a novel Mg 2+-citrate-binding protein from the ABC transporter superfamily. Acta Crystallogr D Struct Biol 2021; 77:1516-1534. [PMID: 34866608 DOI: 10.1107/s2059798321010457] [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: 08/26/2021] [Accepted: 10/08/2021] [Indexed: 11/11/2022] Open
Abstract
More than one third of proteins require metal ions to accomplish their functions, making them obligatory for the growth and survival of microorganisms in varying environmental niches. In prokaryotes, besides their involvement in various cellular and physiological processes, metal ions stimulate the uptake of citrate molecules. Citrate is a source of carbon and energy and is reported to be transported by secondary transporters. In Gram-positive bacteria, citrate molecules are transported in complex with divalent metal ions, whereas in Gram-negative bacteria they are translocated by Na+/citrate symporters. In this study, the presence of a novel divalent-metal-ion-complexed citrate-uptake system that belongs to the primary active ABC transporter superfamily is reported. For uptake, the metal-ion-complexed citrate molecules are sequestered by substrate-binding proteins (SBPs) and transferred to transmembrane domains for their transport. This study reports crystal structures of an Mg2+-citrate-binding protein (MctA) from the Gram-negative thermophilic bacterium Thermus thermophilus HB8 in both apo and holo forms in the resolution range 1.63-2.50 Å. Despite binding various divalent metal ions, MctA possesses the coordination geometry to bind its physiological metal ion, Mg2+. The results also suggest an extended subclassification of cluster D SBPs, which are known to bind and transport divalent-metal-ion-complexed citrate molecules. Comparative assessment of the open and closed conformations of the wild-type and mutant MctA proteins suggests a gating mechanism of ligand entry following an `asymmetric domain movement' of the N-terminal domain for substrate binding.
Collapse
Affiliation(s)
- Suraj Kumar Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| |
Collapse
|
128
|
Mijošek T, Filipović Marijić V, Dragun Z, Krasnići N, Ivanković D, Redžović Z, Erk M. First insight in trace element distribution in the intestinal cytosol of two freshwater fish species challenged with moderate environmental contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149274. [PMID: 34375239 DOI: 10.1016/j.scitotenv.2021.149274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/09/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Cytosolic distribution of six essential elements and nonessential Cd among biomolecules of different molecular masses was investigated in the intestine of brown trout (Salmo trutta) from the karst Krka River and Prussian carp (Carassius gibelio) from the lowland Ilova River. Fish were sampled at two locations (reference and contaminated) and in two seasons (autumn and spring). Analyses were conducted by size exclusion high performance liquid chromatography and high resolution inductively coupled plasma mass spectrometry. Although studied salmonid and cyprinid fish have different biological characteristics, obtained profiles often showed mostly similar patterns in both species. Specifically, Cd and Cu were dominantly bound to metallothioneins in both species, but the same association was not observed for Zn, whereas Mo distribution was similar in the intestine of both fish species with two well shaped and clear peaks in HMM (100-400 kDa) and VLMM (2-8 kDa) range. In brown trout, Se was mostly associated with biomolecules of very low molecular masses (VLMM, <10 kDa), whereas significant additional elution in HMM region (30-303 kDa) was observed only in Prussian carp. Iron binding to VLMM biomolecules (1.8-14 kDa) was observed only in brown trouts, and of Zn in Prussian carps. Cobalt was mostly bound to HMM biomolecules (85-235 kDa) in brown trout and to VLMM biomolecules (0.7-18 kDa) in Prussian carp. Comparison of intestinal profiles with previously published data on liver and gills revealed some similarities in distribution, but also organ-specific differences due to the different function and composition of each organ. As so far there is no published data on intestinal trace metal distribution, the obtained results represent the novel findings, and the key point for the exact identification of specific metal-binding biomolecules which could eventually be used as biomarkers of metal exposure or effects.
Collapse
Affiliation(s)
- Tatjana Mijošek
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Vlatka Filipović Marijić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Zrinka Dragun
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Nesrete Krasnići
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Dušica Ivanković
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Zuzana Redžović
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Marijana Erk
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Laboratory for Biological Effects of Metals, Bijenička cesta 54, 10000 Zagreb, Croatia.
| |
Collapse
|
129
|
Immobilized Enzymes-Based Biosensing Cues for Strengthening Biocatalysis and Biorecognition. Catal Letters 2021. [DOI: 10.1007/s10562-021-03866-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
130
|
New insights into the formation and recovery of sublethally injured Escherichia coli O157:H7 induced by lactic acid. Food Microbiol 2021; 102:103918. [PMID: 34809944 DOI: 10.1016/j.fm.2021.103918] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 08/19/2021] [Accepted: 09/26/2021] [Indexed: 11/21/2022]
Abstract
Escherichia coli O157:H7 can be injured by the action of lactic acid (LA) and injured cells can be recovered under suitable condition. In this study, RNA sequencing analysis revealed the overall genes change of sublethally injured (4 mM LA, 60 min; SI) and initial recovered (minA, 20 min; R) cells. Compared with untreated samples, 53 up-regulated and 98 down-regulated differentially expressed genes (DEGs; Padj < 0.05, change fold ≥2) were found in SI. Meanwhile, Genes related to carbohydrate transport and metabolic were up-regulated and the addition of carbohydrate increased cells resistance to LA. Genes involved in osmotic stress response and cell membrane integrity were down-regulated and E. coli O157:H7 cells were sensitive to osmotic stress during sublethal injury. Genes related to iron stress response and cation transport were changed and cation may affect sublethal injury formation by influencing production of ROS and cellular processes. In R, 1370 up-regulated and 1110 down-regulated DEGs were subdivided into various GO terms and membrane, biological adhesion, cell projection, oxidation-reduction process and catalytic activity, etc., showed significant enrichment (corrected P < 0.05). Particularly, genes related to fimbrial, flagellum and type III secretion system were up-regulated, which may improve infection ability and virulence property during recovery of injured cells. These findings provide novel insights into formation and recovery of sublethally injured E. coli O157:H7 induced by LA.
Collapse
|
131
|
Maliszewska HK, Arnau Del Valle C, Xia Y, Marín MJ, Waller ZAE, Muñoz MP. Precious metal complexes of bis(pyridyl)allenes: synthesis and catalytic and medicinal applications. Dalton Trans 2021; 50:16739-16750. [PMID: 34761768 DOI: 10.1039/d1dt02929k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The incorporation of donor-type substituents on the allene core opens up the possibility of coordination complexes in which the metal is bonded to the donor groups, with or without interaction with the double bond system. Despite the challenges in the synthesis of such allene-containing metal complexes, their unique 3D environments and dual functionality (allene and metal) could facilitate catalysis and interaction with chemical and biological systems. Bis(pyridyl)allenes are presented here as robust ligands for novel Pd(II), Pt(IV) and Au(III) complexes. Their synthesis, characterisation and first application as catalysts of benchmark reactions for Pd, Pt and Au are presented with interesting reactivity and selectivities. The complexes have also been probed as antimicrobial and anticancer agents with promising activities, and the first studies on their unusual interaction with several DNA structures will open new avenues for research in the area of metallodrugs with new mechanisms of action.
Collapse
Affiliation(s)
- Hanna K Maliszewska
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Carla Arnau Del Valle
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Ying Xia
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - María J Marín
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - María Paz Muñoz
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| |
Collapse
|
132
|
Al-Attar S, Rendon J, Sidore M, Duneau JP, Seduk F, Biaso F, Grimaldi S, Guigliarelli B, Magalon A. Gating of Substrate Access and Long-Range Proton Transfer in Escherichia coli Nitrate Reductase A: The Essential Role of a Remote Glutamate Residue. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sinan Al-Attar
- Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Julia Rendon
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Marlon Sidore
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (UMR7255), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Jean-Pierre Duneau
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (UMR7255), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Farida Seduk
- Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Frédéric Biaso
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Stéphane Grimaldi
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Bruno Guigliarelli
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Axel Magalon
- Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| |
Collapse
|
133
|
Slope LN, Daubney OJ, Campbell H, White SA, Peacock AFA. Location-Dependent Lanthanide Selectivity Engineered into Structurally Characterized Designed Coiled Coils. Angew Chem Int Ed Engl 2021; 60:24473-24477. [PMID: 34495573 PMCID: PMC8597134 DOI: 10.1002/anie.202110500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Indexed: 11/08/2022]
Abstract
Herein we report unprecedented location-dependent, size-selective binding to designed lanthanide (Ln3+ ) sites within miniature protein coiled coil scaffolds. Not only do these engineered sites display unusual Ln3+ selectivity for moderately large Ln3+ ions (Nd to Tb), for the first time we demonstrate that selectivity can be location-dependent and can be programmed into the sequence. A 1 nm linear translation of the binding site towards the N-terminus can convert a selective site into a highly promiscuous one. An X-ray crystal structure, the first of a lanthanide binding site within a coiled coil to be reported, coupled with CD studies, reveal the existence of an optimal radius that likely stems from the structural constraints of the coiled coil scaffold. To the best of our knowledge this is the first report of location-dependent metal selectivity within a coiled coil scaffold, as well as the first report of location-dependent Ln3+ selectivity within a protein.
Collapse
Affiliation(s)
- Louise N. Slope
- School of ChemistryUniversity of BirminghamEdgbastonB15 2TTUK
| | | | - Hannah Campbell
- School of ChemistryUniversity of BirminghamEdgbastonB15 2TTUK
| | - Scott A. White
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
| | | |
Collapse
|
134
|
Slope LN, Daubney OJ, Campbell H, White SA, Peacock AFA. Location‐Dependent Lanthanide Selectivity Engineered into Structurally Characterized Designed Coiled Coils. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Louise N. Slope
- School of Chemistry University of Birmingham Edgbaston B15 2TT UK
| | | | - Hannah Campbell
- School of Chemistry University of Birmingham Edgbaston B15 2TT UK
| | - Scott A. White
- School of Biosciences University of Birmingham Edgbaston B15 2TT UK
| | | |
Collapse
|
135
|
Shahid M, I . M, Khan S, Mehtab M, Yadav O, Ansari A, Qasem KM, Ahmed A, Saniya M, Akhtar MN, AlDamen MA. Elucidating the contribution of solvent on the catecholase activity in a mononuclear Cu(II) system: An experimental and theoretical approach. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130878] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
136
|
SantaLucia DJ, Berry JF. Antiferromagnetic Exchange and Metal-Metal Bonding in Roussin's Black Sulfur and Selenium Salts. Inorg Chem 2021; 60:16241-16255. [PMID: 34662109 DOI: 10.1021/acs.inorgchem.1c02052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Atom-efficient syntheses of the tetraethylammonium Roussin black sulfur and selenium salts ((Et4N)[Fe4E3(NO)7], E = S, Se) as well as their 15N-labeled counterparts are described herein. Broken-symmetry DFT calculations were conducted on both complexes to model an antiferromagnetic interaction between the apical {FeNO}7 unit, Sap = 3/2, and the three basal {Fe(NO)2}9 units, Sbas = 1/2. The calculated J values are -1813 and -1467 cm-1 for the sulfur and selenium compounds, respectively. The mechanism for antiferromagnetic exchange in both compounds was deduced to be direct exchange on the basis of the partially overlapping magnetic orbitals with orbital density only residing on the Fe-centers. The obtained Mössbauer parameters are most consistent with the calculated MS = 0 broken-symmetry state for both complexes. The values for J have been determined with variable-temperature 15N NMR experiments. Values of -1660 and -1430 cm-1 for the sulfur and selenium compounds, respectively, were obtained by fits to the variable-temperature NMR data, further validating the broken-symmetry MS = 0 model of the electronic structure.
Collapse
Affiliation(s)
- Daniel J SantaLucia
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - John F Berry
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| |
Collapse
|
137
|
Structural Diversity of Di-Metalized Arginine Evidenced by Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy in the Gas Phase. Molecules 2021; 26:molecules26216546. [PMID: 34770955 PMCID: PMC8587954 DOI: 10.3390/molecules26216546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 12/18/2022] Open
Abstract
Although metal cations are prevalent in biological media, the species of multi-metal cationized biomolecules have received little attention so far. Studying these complexes in isolated state is important, since it provides intrinsic information about the interaction among them on the molecular level. Our investigation here demonstrates the unexpected structural diversity of such species generated by a matrix-assisted laser desorption ionization (MALDI) source in the gas phase. The photodissociation spectroscopic and theoretical study reflects that the co-existing isomers of [Arg+Rb+K−H]+ can have energies ≥95 kJ/mol higher than that of the most stable one. While the result can be rationalized by the great isomerization energy barrier due to the coordination, it strongly reminds us to pay more attention to their structural diversities for multi-metalized fundamental biological molecules, especially for the ones with the ubiquitous alkali metal ions.
Collapse
|
138
|
Kaya Z, Bentouhami E, Pelzer K, Armspach D. Cavity-shaped ligands for asymmetric metal catalysis. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214066] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
139
|
Brunetti E, Marcelis L, Zhurkin FE, Luhmer M, Jabin I, Reinaud O, Bartik K. A Water Molecule Triggers Guest Exchange at a Mono-Zinc Centre Confined in a Biomimetic Calixarene Pocket: a Model for Understanding Ligand Stability in Zn Proteins. Chemistry 2021; 27:13730-13738. [PMID: 34288166 DOI: 10.1002/chem.202102184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 11/12/2022]
Abstract
In this study, the ligand exchange mechanism at a biomimetic ZnII centre, embedded in a pocket mimicking the possible constrains induced by a proteic structure, is explored. The residence time of different guest ligands (dimethylformamide, acetonitrile and ethanol) inside the cavity of a calix[6]arene-based tris(imidazole) tetrahedral zinc complex was probed using 1D EXchange SpectroscopY NMR experiments. A strong dependence of residence time on water content was observed with no exchange occurring under anhydrous conditions, even in the presence of a large excess of guest ligand. These results advocate for an associative exchange mechanism involving the transient exo-coordination of a water molecule, giving rise to 5-coordinate ZnII intermediates, and inversion of the pyramid at the ZnII centre. Theoretical modelling by DFT confirmed that the associative mechanism is at stake. These results are particularly relevant in the context of the understanding of kinetic stability/lability in Zn proteins and highlight the key role that a single water molecule can play in catalysing ligand exchange and controlling the lability of ZnII in proteins.
Collapse
Affiliation(s)
- Emilio Brunetti
- Engineering of Molecular Nanosystems, Université libre de Bruxelles, Avenue F. D. Roosevelt 50, CP165/64, 1050, Brussels, Belgium.,Laboratory of Organic Chemistry, Université libre de Bruxelles, Avenue F. D. Roosevelt 50, CP165/64, 1050, Brussels, Belgium
| | - Lionel Marcelis
- Engineering of Molecular Nanosystems, Université libre de Bruxelles, Avenue F. D. Roosevelt 50, CP165/64, 1050, Brussels, Belgium
| | - Fedor E Zhurkin
- Laboratory of Pharmacological and Toxicological Chemistry and Biochemistry, Université Paris Descartes, 45, rue des Saints-Pères, 75006, Paris, France
| | - Michel Luhmer
- High-Resolution Nuclear Magnetic Resonance laboratory, Université libre de Bruxelles, Avenue F. D. Roosevelt 50, CP165/64, 1050, Brussels, Belgium
| | - Ivan Jabin
- Laboratory of Organic Chemistry, Université libre de Bruxelles, Avenue F. D. Roosevelt 50, CP165/64, 1050, Brussels, Belgium
| | - Olivia Reinaud
- Laboratory of Pharmacological and Toxicological Chemistry and Biochemistry, Université Paris Descartes, 45, rue des Saints-Pères, 75006, Paris, France
| | - Kristin Bartik
- Engineering of Molecular Nanosystems, Université libre de Bruxelles, Avenue F. D. Roosevelt 50, CP165/64, 1050, Brussels, Belgium
| |
Collapse
|
140
|
Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
Collapse
Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
141
|
Madjroh N, Mellou E, Æbelø L, Davies PA, Söderhielm PC, Jensen AA. Probing the molecular basis for signal transduction through the Zinc-Activated Channel (ZAC). Biochem Pharmacol 2021; 193:114781. [PMID: 34560053 DOI: 10.1016/j.bcp.2021.114781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 12/18/2022]
Abstract
The molecular basis for the signal transduction through the classical Cys-loop receptors (CLRs) has been delineated in great detail. The Zinc-Activated Channel (ZAC) constitutes a so far poorly elucidated fifth branch of the CLR superfamily, and in this study we explore the molecular mechanisms underlying ZAC signaling in Xenopus oocytes by two-electrode voltage clamp electrophysiology. In studies of chimeric receptors fusing either the extracellular domain (ECD) or the transmembrane/intracellular domain (TMD-ICD) of ZAC with the complementary domains of 5-HT3A serotonin or α1 glycine receptors, serotonin and Zn2+/H+ evoked robust concentration-dependent currents in 5-HT3A/ZAC- and ZAC/α1-Gly-expressing oocytes, respectively, suggesting that Zn2+ and protons activate ZAC predominantly through its ECD. The molecular basis for Zn2+-mediated ZAC signaling was probed further by introduction of mutations of His, Cys, Glu and Asp residues in this domain, but as none of the mutants tested displayed substantially impaired Zn2+ functionality compared to wild-type ZAC, the location of the putative Zn2+ binding site(s) in the ECD was not identified. Finally, the functional importance of Leu246 (Leu9') in the transmembrane M2 α-helix of ZAC was investigated by Ala, Val, Ile and Thr substitutions. In concordance with findings for this highly conserved residue in classical CLRs, the ZACL9'X mutants exhibited left-shifted agonist concentration-response relationships, markedly higher degrees of spontaneous activity and slower desensitization kinetics compared to wild-type ZAC. In conclusion, while ZAC is an atypical CLR in terms of its (identified) agonists and channel characteristics, its signal transduction seems to undergo similar conformational transitions as those in the classical CLR.
Collapse
Affiliation(s)
- Nawid Madjroh
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Eleni Mellou
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Laura Æbelø
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Paul A Davies
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Pella C Söderhielm
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø 2100, Denmark.
| |
Collapse
|
142
|
Abstract
Biopolymers are natural polymers sourced from plants and animals, which include a variety of polysaccharides and polypeptides. The inclusion of biopolymers into biomedical hydrogels is of great interest because of their inherent biochemical and biophysical properties, such as cellular adhesion, degradation, and viscoelasticity. The objective of this Review is to provide a detailed overview of the design and development of biopolymer hydrogels for biomedical applications, with an emphasis on biopolymer chemical modifications and cross-linking methods. First, the fundamentals of biopolymers and chemical conjugation methods to introduce cross-linking groups are described. Cross-linking methods to form biopolymer networks are then discussed in detail, including (i) covalent cross-linking (e.g., free radical chain polymerization, click cross-linking, cross-linking due to oxidation of phenolic groups), (ii) dynamic covalent cross-linking (e.g., Schiff base formation, disulfide formation, reversible Diels-Alder reactions), and (iii) physical cross-linking (e.g., guest-host interactions, hydrogen bonding, metal-ligand coordination, grafted biopolymers). Finally, recent advances in the use of chemically modified biopolymer hydrogels for the biofabrication of tissue scaffolds, therapeutic delivery, tissue adhesives and sealants, as well as the formation of interpenetrating network biopolymer hydrogels, are highlighted.
Collapse
Affiliation(s)
- Victoria G. Muir
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason A. Burdick
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
143
|
Chattopadhyay S, Mukherjee M, Kandemir B, Bowman SEJ, Bren KL, Dey A. Contributions to cytochrome c inner- and outer-sphere reorganization energy. Chem Sci 2021; 12:11894-11913. [PMID: 34659730 PMCID: PMC8442690 DOI: 10.1039/d1sc02865k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/05/2021] [Indexed: 11/21/2022] Open
Abstract
Cytochromes c are small water-soluble proteins that catalyze electron transfer in metabolism and energy conversion processes. Hydrogenobacter thermophilus cytochrome c552 presents a curious case in displaying fluxionality of its heme axial methionine ligand; this behavior is altered by single point mutation of the Q64 residue to N64 or V64, which fixes the ligand in a single configuration. The reorganization energy (λ) of these cytochrome c552 variants is experimentally determined using a combination of rotating disc electrochemistry, chronoamperometry and cyclic voltammetry. The differences between the λ determined from these complementary techniques helps to deconvolute the contribution of the active site and its immediate environment to the overall λ (λTotal). The experimentally determined λ values in conjunction with DFT calculations indicate that the differences in λ among the protein variants are mainly due to the differences in contributions from the protein environment and not just inner-sphere λ. DFT calculations indicate that the position of residue 64, responsible for the orientation of the axial methionine, determines the geometric relaxation of the redox active molecular orbital (RAMO). The orientation of the RAMO with respect to the heme is key to determining electron transfer coupling (HAB) which results in higher ET rates in the wild-type protein relative to the Q64V mutant despite a 150 mV higher λTotal in the former. Efficient delocalization of the redox-active molecular orbital (RAMO) in HtWT results in an increase in HAB value which in turn accelerates the electron transfer (ET) rate in spite of the higher reorganization energy (λ) than the HtQ64V mutant.![]()
Collapse
Affiliation(s)
- Samir Chattopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A Raja SC Mullick Road Kolkata WB 700032 India
| | - Manjistha Mukherjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A Raja SC Mullick Road Kolkata WB 700032 India
| | - Banu Kandemir
- Department of Chemistry, University of Rochester Rochester NY 14627-0216 USA
| | - Sarah E J Bowman
- Department of Chemistry, University of Rochester Rochester NY 14627-0216 USA
| | - Kara L Bren
- Department of Chemistry, University of Rochester Rochester NY 14627-0216 USA
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A Raja SC Mullick Road Kolkata WB 700032 India
| |
Collapse
|
144
|
Bím D, Alexandrova AN. Electrostatic regulation of blue copper sites. Chem Sci 2021; 12:11406-11413. [PMID: 34667549 PMCID: PMC8447924 DOI: 10.1039/d1sc02233d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/26/2021] [Indexed: 01/06/2023] Open
Abstract
In the last 50 years, the blue copper proteins became central targets of investigation. Extensive experiments focused on the Cu coordination to probe the effect of local perturbations on its properties. We found that local electric fields, generated by charged residues evolutionarily placed throughout the protein edifice, mainly second sphere, but also more remotely, constitute an additional significant factor regulating blue copper proteins. These fields are not random, but exhibit a highly specific directionality, negative with respect to the and vectors in the Cu first shell. The field magnitude contributes to fine-tuning of the geometric and electronic properties of Cu sites in individual blue copper proteins. Specifically, the local electric fields evidently control the Cu–SMet bond distance, Cu(ii)–SCys bond covalency, and the energies of the frontier molecular orbitals, which, in turn, govern the Cu(ii/i) reduction potential and the relative absorption intensities at 450 nm and 600 nm. Intramolecular electric fields in blue copper proteins are oriented in a fixed way to modulate properties of their copper sites: they control the first-shell copper interactions to influence geometric, spectroscopic, and redox behavior.![]()
Collapse
Affiliation(s)
- Daniel Bím
- Department of Chemistry and Biochemistry, University of California, Los Angeles 607 Charles E. Young Drive East Los Angeles CA 90095-1569 USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles 607 Charles E. Young Drive East Los Angeles CA 90095-1569 USA .,California NanoSystems Institute, University of California, Los Angeles 570 Westwood Plaza Los Angeles California 90095-1569 USA
| |
Collapse
|
145
|
Flieger J, Dolar-Szczasny J, Rejdak R, Majerek D, Tatarczak-Michalewska M, Proch J, Blicharska E, Flieger W, Baj J, Niedzielski P. The Multi-Elemental Composition of the Aqueous Humor of Patients Undergoing Cataract Surgery, Suffering from Coexisting Diabetes, Hypertension, or Diabetic Retinopathy. Int J Mol Sci 2021; 22:ijms22179413. [PMID: 34502323 PMCID: PMC8430749 DOI: 10.3390/ijms22179413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/25/2022] Open
Abstract
The aim of the study was the multi-elemental analysis of aqueous humor (AH) collected from patients undergoing cataract surgery. The study included: 16 patients with age-related macular degeneration AMD (99 controls), 10 patients with retinopathy (105 controls), 61 patients with hypertension (54 controls), and 33 patients with coexisting diabetes (82 controls). The control groups were recruited from patients with a lack of co-existing disease characterizing the specified studied group. The measurements were performed by the use of inductively coupled plasma optical emission spectrometry (ICP-OES). The statistical analysis was carried out using non-parametric testing (Mann–Whitney U). The level of significance was set at p = 0.05. The data obtained revealed substantial variations in elemental composition between the test groups in comparison to the controls. However, the significant variations concerned only a few elements. The phosphorous (P) level and the ratio of P/Ca were significant in retinopathy and diabetes, whereas cobalt (0.091 ± 0.107 mg/L vs. 0.031 ± 0.075 mg/L; p = 0.004) was significant in AMD. In co-existing hypertension, the levels of tin (0.293 ± 0.409 mg/L vs. 0.152 ± 0.3 mg/L; p = 0.031), titanium (0.096 ± 0.059 mg/L vs. 0.152 ± 0.192 mg/L; p = 0.045), and ruthenium (0.035 ± 0.109 mg/L vs. 0.002 ± 0.007 mg/L; p = 0.006) varied in comparison to the controls. The study revealed inter-elemental interactions. The correlation matrices demonstrated the domination of the positive correlations, whereas negative correlations mainly concerned sodium.
Collapse
Affiliation(s)
- Jolanta Flieger
- Department of Analytical Chemistry, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland; (M.T.-M.); (E.B.)
- Correspondence: ; Tel.: +48-81448-7182
| | - Joanna Dolar-Szczasny
- Department of General and Pediatric Ophthalmology, Medical University of Lublin, Chmielna 1, 20-079 Lublin, Poland; (J.D.-S.); (R.R.)
| | - Robert Rejdak
- Department of General and Pediatric Ophthalmology, Medical University of Lublin, Chmielna 1, 20-079 Lublin, Poland; (J.D.-S.); (R.R.)
| | - Dariusz Majerek
- Department of Applied Mathematics, University of Technology, Nadbystrzycka 38D, 20-618 Lublin, Poland;
| | | | - Jędrzej Proch
- Faculty of Chemistry, Department of Analytical Chemistry, Adam Mickiewicz University in Poznań, 89B Umultowska Street, 61-614 Poznań, Poland; (J.P.); (P.N.)
| | - Eliza Blicharska
- Department of Analytical Chemistry, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland; (M.T.-M.); (E.B.)
| | - Wojciech Flieger
- Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland; (W.F.); (J.B.)
| | - Jacek Baj
- Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland; (W.F.); (J.B.)
| | - Przemysław Niedzielski
- Faculty of Chemistry, Department of Analytical Chemistry, Adam Mickiewicz University in Poznań, 89B Umultowska Street, 61-614 Poznań, Poland; (J.P.); (P.N.)
| |
Collapse
|
146
|
Dobbelaar E, Rauber C, Bonck T, Kelm H, Schmitz M, de Waal Malefijt ME, Klein JEMN, Krüger HJ. Combining Structural with Functional Model Properties in Iron Synthetic Analogue Complexes for the Active Site in Rabbit Lipoxygenase. J Am Chem Soc 2021; 143:13145-13155. [PMID: 34383499 DOI: 10.1021/jacs.1c04422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Iron complexes that model the structural and functional properties of the active iron site in rabbit lipoxygenase are described. The ligand sphere of the mononuclear pseudo-octahedral cis-(carboxylato)(hydroxo)iron(III) complex, which is completed by a tetraazamacrocyclic ligand, reproduces the first coordination shell of the active site in the enzyme. In addition, two corresponding iron(II) complexes are presented that differ in the coordination of a water molecule. In their structural and electronic properties, both the (hydroxo)iron(III) and the (aqua)iron(II) complex reflect well the only two essential states found in the enzymatic mechanism of peroxidation of polyunsaturated fatty acids. Furthermore, the ferric complex is shown to undergo hydrogen atom abstraction reactions with O-H and C-H bonds of suitable substrates, and the bond dissociation free energy of the coordinated water ligand of the ferrous complex is determined to be 72.4 kcal·mol-1. Theoretical investigations of the reactivity support a concerted proton-coupled electron transfer mechanism in close analogy to the initial step in the enzymatic mechanism. The propensity of the (hydroxo)iron(III) complex to undergo H atom abstraction reactions is the basis for its catalytic function in the aerobic peroxidation of 2,4,6-tri(tert-butyl)phenol and its role as a radical initiator in the reaction of dihydroanthracene with oxygen.
Collapse
Affiliation(s)
- Emiel Dobbelaar
- Department of Chemistry, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Christian Rauber
- Department of Chemistry, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Thorsten Bonck
- Department of Chemistry, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Harald Kelm
- Department of Chemistry, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Markus Schmitz
- Department of Chemistry, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Matina Eloïse de Waal Malefijt
- Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, Faculty of Science and Engineering, University of Groningen, Nijenborgh 9, 9747 AG Groningen, The Netherlands
| | - Johannes E M N Klein
- Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, Faculty of Science and Engineering, University of Groningen, Nijenborgh 9, 9747 AG Groningen, The Netherlands
| | - Hans-Jörg Krüger
- Department of Chemistry, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| |
Collapse
|
147
|
Wang CH, DeBeer S. Structure, reactivity, and spectroscopy of nitrogenase-related synthetic and biological clusters. Chem Soc Rev 2021; 50:8743-8761. [PMID: 34159992 DOI: 10.1039/d1cs00381j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The reduction of dinitrogen (N2) is essential for its incorporation into nucleic acids and amino acids, which are vital to life on earth. Nitrogenases convert atmospheric dinitrogen to two ammonia molecules (NH3) under ambient conditions. The catalytic active sites of these enzymes (known as FeM-cofactor clusters, where M = Mo, V, Fe) are the sites of N2 binding and activation and have been a source of great interest for chemists for decades. In this review, recent studies on nitrogenase-related synthetic molecular complexes and biological clusters are discussed, with a focus on their reactivity and spectroscopic characterization. The molecular models that are discussed span from simple mononuclear iron complexes to multinuclear iron complexes and heterometallic iron complexes. In addition, recent work on the extracted biological cofactors is discussed. An emphasis is placed on how these studies have contributed towards our understanding of the electronic structure and mechanism of nitrogenases.
Collapse
Affiliation(s)
- Chen-Hao Wang
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
| |
Collapse
|
148
|
Vallée Y, Youssef-Saliba S. Sulfur Amino Acids: From Prebiotic Chemistry to Biology and Vice Versa. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/a-1472-7914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractTwo sulfur-containing amino acids are included in the list of the 20 classical protein amino acids. A methionine residue is introduced at the start of the synthesis of all current proteins. Cysteine, thanks to its thiol function, plays an essential role in a very large number of catalytic sites. Here we present what is known about the prebiotic synthesis of these two amino acids and homocysteine, and we discuss their introduction into primitive peptides and more elaborate proteins.1 Introduction2 Sulfur Sources3 Prebiotic Synthesis of Cysteine4 Prebiotic Synthesis of Methionine5 Homocysteine and Its Thiolactone6 Methionine and Cystine in Proteins7 Prebiotic Scenarios Using Sulfur Amino Acids8 Introduction of Cys and Met in the Genetic Code9 Conclusion
Collapse
|
149
|
Shteinman AA, Mitra M. Nonheme mono- and dinuclear iron complexes in bio-inspired C H and C C bond hydroxylation reactions: Mechanistic insight. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
150
|
Kawase O, Iwaya H, Asano Y, Inoue H, Kudo S, Sasahira M, Azuma N, Kondoh D, Ichikawa-Seki M, Xuan X, Sakamoto K, Okamoto H, Nakadate H, Inoue W, Saito I, Narita M, Sekii K, Kobayashi K. Identification of novel yolk ferritins unique to planarians: planarians supply aluminum rather than iron to vitellaria in egg capsules. Cell Tissue Res 2021; 386:391-413. [PMID: 34319433 DOI: 10.1007/s00441-021-03506-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 07/07/2021] [Indexed: 11/29/2022]
Abstract
All animals, other than Platyhelminthes, produce eggs containing yolk, referred to as "entolecithal" eggs. However, only Neoophora, in the phylum Platyhelminthes, produce "ectolecithal" eggs (egg capsules), in which yolk is stored in the vitelline cells surrounding oocytes. Vitelline cells are derived from vitellaria (yolk glands). Vitellaria are important reproductive organs that may be studied to elucidate unique mechanisms that have been evolutionarily conserved within Platyhelminthes. Currently, only limited molecular level information is available on vitellaria. The current study identified major vitellaria-specific proteins in a freshwater planarian, Dugesia ryukyuensis, using peptide mass fingerprinting (PMF) and expression analyses. Amino acid sequence analysis and orthology analysis via OrthoFinder ver.2.3.8 indicated that the identified major vitellaria-specific novel yolk ferritins were conserved in planarians (Tricladida). Because ferritins play an important role in Fe (iron) storage, we examined the metal elements contained in vitellaria and ectolecithal eggs, using non-heme iron histochemistry, elemental analysis based on inductively coupled plasma mass spectrometry and transmission electron microscopy- energy-dispersive X-ray spectroscopy analysis. Interestingly, vitellaria and egg capsules contained large amounts of aluminum (Al), but not Fe. The knockdown of the yolk ferritin genes caused a decrease in the volume of egg capsules, abnormality in juveniles, and increase in Al content in vitellaria. Yolk ferritins of D. ryukyuensis may regulate Al concentration in vitellaria via their pooling function of Al and protect the egg capsule production and normal embryogenesis from Al toxicity.
Collapse
Affiliation(s)
- Osamu Kawase
- Department of Biology, Premedical Sciences, Dokkyo Medical University, Mibu-machi, Shimotsuga-gun, Tochigi, 321-0293, Japan
| | - Hisashi Iwaya
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Yoshiya Asano
- Department of Neuroanatomy, Cell Biology and Histology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Hiromoto Inoue
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Seiya Kudo
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Motoki Sasahira
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Nobuyuki Azuma
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Daisuke Kondoh
- Department of Basic Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Inaba-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Madoka Ichikawa-Seki
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan
| | - Xuenan Xuan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inaba-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Kimitoshi Sakamoto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Hikaru Okamoto
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Hinaki Nakadate
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Wataru Inoue
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Ikuma Saito
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Miyu Narita
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Kiyono Sekii
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Kazuya Kobayashi
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan.
| |
Collapse
|