| 1. |
|
|
| 2. |
- Perche-Letuvée, Phanélie, et al.
(författare)
-
4-Demethylwyosine Synthase from Pyrococcus abyssi Is a Radical-S-adenosyl-l-methionine Enzyme with an Additional [4Fe-4S]+2 Cluster That Interacts with the Pyruvate Co-substrate
- 2012
-
Ingår i: Journal of Biological Chemistry. ; 287:49, s. 41174-41185
-
Tidskriftsartikel (refereegranskat)abstract
- Wybutosine and its derivatives are found in position 37 of tRNA encoding Phe in eukaryotes and archaea. They are believed to play a key role in the decoding function of the ribosome. The second step in the biosynthesis of wybutosine is catalyzed by TYW1 protein, which is a member of the well established class of metalloenzymes called “Radical-SAM.” These enzymes use a [4Fe-4S] cluster, chelated by three cysteines in a CX3CX2C motif, and S-adenosyl-l-methionine (SAM) to generate a 5′-deoxyadenosyl radical that initiates various chemically challenging reactions. Sequence analysis of TYW1 proteins revealed, in the N-terminal half of the enzyme beside the Radical-SAM cysteine triad, an additional highly conserved cysteine motif. In this study we show by combining analytical and spectroscopic methods including UV-visible absorption, Mössbauer, EPR, and HYSCORE spectroscopies that these additional cysteines are involved in the coordination of a second [4Fe-4S] cluster displaying a free coordination site that interacts with pyruvate, the second substrate of the reaction. The presence of two distinct iron-sulfur clusters on TYW1 is reminiscent of MiaB, another tRNA-modifying metalloenzyme whose active form was shown to bind two iron-sulfur clusters. A possible role for the second [4Fe-4S] cluster in the enzyme activity is discussed.
|
|
| 3. |
- Artero, Vincent, et al.
(författare)
-
From Enzyme Maturation to Synthetic Chemistry : The Case of Hydrogenases
- 2015
-
Ingår i: Accounts of Chemical Research. - : American Chemical Society (ACS). - 0001-4842 .- 1520-4898. ; 48:8, s. 2380-2387
-
Forskningsöversikt (refereegranskat)abstract
- CONSPECTUS: Water splitting into oxygen and hydrogen is one of the most attractive strategies for storing solar energy and electricity. Because the processes at work are multielectronic, there is a crucial need for efficient and stable catalysts, which in addition have to be cheap for future industrial developments (electrolyzers, photoelectrochemicals, and fuel cells). Specifically for the water/hydrogen interconversion, Nature is an exquisite source of inspiration since this chemistry contributes to the bioenergetic metabolism of a number of living organisms via the activity of fascinating metalloenzymes, the hydrogenases. In this Account, we first briefly describe the structure of the unique dinuclear organometallic active sites of the two classes of hydrogenases as well as the complex protein machineries involved in their biosynthesis, their so-called maturation processes. This knowledge allows for the development of a fruitful bioinspired chemistry approach, which has already led to a number of interesting and original catalysts mimicking the natural active sites. More specifically, we describe our own attempts to prepare artificial hydrogenases. This can be achieved via the standard bioinspired approach using the combination of a synthetic bioinspired catalyst and a polypeptide scaffold. Such hybrid complexes provide the opportunity to optimize the system by manipulating both the catalyst through chemical synthesis and the protein component through mutagenesis. We also raise the possibility to reach such artificial systems via an original strategy based on mimicking the enzyme maturation pathways. This is illustrated in this Account by two examples developed in our laboratory. First, we show how the preparation of a lysozyme-{Mn-I(CO)(3)} hybrid and its clean reaction with a nickel complex led us to generate a new class of binuclear Ni-Mn H-2-evolving catalysts mimicking the active site of [NiFe]-hydrogenases. Then we describe how we were able to rationally design and prepare a hybrid system, displaying remarkable structural similarities to an [FeFe]-hydrogenase, and we show here for the first time that it is catalytically active for proton reduction. This system is based on the combination of HydF, a protein involved in the maturation of [FeFe]-hydrogenase (HydA), and a close mimic of the active site of this class of enzymes. Moreover, the synthetic [Fe-2(adt)(CO)(4)(CN)(2)](2-) (adt(2-) = aza-propanedithiol) mimic, alone or within a HydF hybrid system, was shown to be able to maturate and activate a form of HydA itself lacking its diiron active site. We discuss the exciting perspectives this "synthetic maturation" opens regarding the "invention" of novel hydrogenases by the chemists.
|
|
| 4. |
- Bacchi, Marine, et al.
(författare)
-
Cobaloxime-Based Artificial Hydrogenases
- 2014
-
Ingår i: Inorganic Chemistry. - : American Chemical Society. - 0020-1669 .- 1520-510X. ; 53:15, s. 8071-8082
-
Tidskriftsartikel (refereegranskat)abstract
- Cobaloximes are popular H2 evolution molecular catalysts but have so far mainly been studied in nonaqueous conditions. We show here that they are also valuable for the design of artificial hydrogenases for application in neutral aqueous solutions and report on the preparation of two well-defined biohybrid species via the binding of two cobaloxime moieties, {Co(dmgH)2} and {Co(dmgBF2)2} (dmgH2 = dimethylglyoxime), to apo Sperm-whale myoglobin (SwMb). All spectroscopic data confirm that the cobaloxime moieties are inserted within the binding pocket of the SwMb protein and are coordinated to a histidine residue in the axial position of the cobalt complex, resulting in thermodynamically stable complexes. Quantum chemical/molecular mechanical docking calculations indicated a coordination preference for His93 over the other histidine residue (His64) present in the vicinity. Interestingly, the redox activity of the cobalt centers is retained in both biohybrids, which provides them with the catalytic activity for H2 evolution in near-neutral aqueous conditions.
|
|
| 5. |
- Davydov, Albert, 1969-
(författare)
-
Electron paramagnetic resonance and biochemical studies of red-ox properties of the diferric/radical center in mouse and Mycobacterium tuberculosis ribonucleotide reductase R2 proteins
- 1999
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Ribonucleotide reductase (RNR) catalyses the reduction of all four ribonucleotides to the corresponding deoxyribonucleotides that are used by the cells for DNA synthesis. The active enzyme from mouse, Mycobacterium tuberculosis (M. tuberculosis) and aerobically grown E. coli consists of two nonidentical subunits, proteins R1 and R2, both required for enzymatic activity. The R1 protein contains the regulatory sites and the binding site for the ribonucleotide substrates whereas the R2 subunit contains a stable tyrosyl radical and an antiferromagnetically coupled _-oxo-bridged diferric center. According to the proposed reaction mechanism the radical properties of the R2 protein are transferred to the active site of the R1 protein upon binding of the substrate molecule to the R1. This transfer is proposed to propagate via a conserved chain of hydrogen-bonded amino acids within the R1 and R2 proteins. Once generated the diferric/radical center may exist in different red-ox states: active (with Fe(III)Fe(III) center and tyrosyl radical), met (Fe(III)Fe(III) center without tyrosyl radical), mixed-valent (Fe(II)Fe(III) center) and fully reduced (Fe(II)Fe(II) center). Admission of oxygen to the fully reduced form of an R2 protein (a so-called regeneration reaction) results in a spontaneous formation of the active form. The regeneration reaction may be one of the possible ways employed by the cell for the generation of the active enzyme and therefore the study of this reaction is important for understanding the enzyme functionality.The aim of this thesis is to study the red-ox transitions of the diferric/radical center in mouse and Mycobacterium tuberculosis R2 proteins. Despite the significant similarities in the structure, the red-ox properties of the diferric/radical centers in mouse and M. tuberculosis R2 proteins are significantly different. The diferric/radical center in mouse R2 was found to be much more accessible for the external reductants than the centers of E. coli and M. tuberculosis R2 proteins. A higher accessibility of the diferric/radical center in mouse R2 protein can be explained by the presence of an open channel from the surface of the protein to the diferric/radical center. The tyrosyl radical in mouse R2 protein strongly interacts with the diferric center. Removing the tyrosyl radical in the active mouse R2 protein results in irreversible structural changes of the diferric cluster leading to an inactivation of the protein. Therefore the met form of mouse R2 protein can not be stabilized. Unlike mouse R2, the tyrosyl radical of M. tuberculosis R2 protein exhibits extremely weak magnetic interaction with the diferric center. The met form of M. tuberculosis R2 can be easily obtained and stabilized by the treatment of the active enzyme with hydroxyurea. The results of the chemical reduction of the diferric/radical center in the native mouse R2 protein as well as in two mutants (D266A and Y370W) in a proposed electron transfer pathway indicate that in all cases the second order rate constants in the mutants are comparable or faster than in native protein suggesting that the proposed radical transfer pathway is not important for the chemical reduction to proceed.Studying the oxidation of the fully reduced mouse R2 protein by different non-oxygen oxidants, we have demonstrated that the transitions between Fe(III)Fe(III), Fe(II)Fe(II) and Fe(II)Fe(III) states of this protein are fully reversible. The possibility to form a proper binuclear iron center without using molecular oxygen as an oxidant suggests that the _-oxo-bridge in mouse R2 protein does not necessary need molecular oxygen to be formed. Application of the low temperature reduction to mouse and M. tuberculosis R2 proteins demonstrated a presence of two structurally different diferric clusters giving rise to two distinct mixed-valent EPR signals. Whereas the shape of the mixed-valent EPR signal generated by _-irradiation at 77 K in mouse R2 protein is significantly affected by the presence of the tyrosyl radical, we did not observe any effect of the tyrosyl radical presence on the shape of mixed - valent signal generated in M. tuberculosis R2.
|
|
| 6. |
|
|
| 7. |
|
|
| 8. |
- Grammatico, Domenico, et al.
(författare)
-
Heterogenised Molecular Catalysts for Sustainable Electrochemical CO 2 Reduction
- 2022
-
Ingår i: Angewandte Chemie International Edition. - : John Wiley & Sons. - 1433-7851 .- 1521-3773. ; 61:38
-
Forskningsöversikt (refereegranskat)abstract
- There has been a rapid rise in interest regarding the advantages of support materials to protect and immobilise molecular catalysts for the carbon dioxide reduction reaction (CO2RR) in order to overcome the weaknesses of many well-known catalysts in terms of their stability and selectivity. In this Review, the state of the art of different catalyst-support systems for the CO2RR is discussed with the intention of leading towards standard benchmarking for comparison of such systems across the most relevant supports and immobilisation strategies, taking into account these multiple pertinent metrics, and also enabling clearer consideration of the necessary steps for further progress. The most promising support systems are described, along with a final note on the need for developing more advanced experimental and computational techniques to aid the rational design principles that are prerequisite to prospective industrial upscaling.
|
|
| 9. |
- Logan, Derek, et al.
(författare)
-
A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase.
- 2003
-
Ingår i: Proc Natl Acad Sci U S A. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 100:7, s. 3826-31
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- A Zn(Cys)(4) center has been found in the C-terminal region of the crystal structure of the anaerobic class III ribonucleotide reductase (RNR) from bacteriophage T4. The metal center is structurally related to the zinc ribbon motif and to rubredoxin and rubrerythrin. Mutant enzymes of the homologous RNR from Escherichia coli, in which the coordinating cysteines, conserved in almost all known class III RNR sequences, have been mutated into alanines, are shown to be inactive as the result of their inability to generate the catalytically essential glycyl radical. The possible roles of the metal center are discussed in relationship to the currently proposed reaction mechanism for generation of the glycyl radical in class III RNRs.
|
|
| 10. |
- Persson, Annika, 1964-
(författare)
-
Essential conserved active site residues in class Ia ribonucleotide reductase from Escherichia coli : identification of radical reaction intermediates and radical transfer intermediates
- 1999
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The enzyme ribonucleotide reductase catalyzes the reduction of ribonucleotides to the corresponding deoxyribonucleotides, the building blocks of DNA. The class Ia enzyme from Escherichia coli consists of two homodimeric subunits denoted protein R1 and protein R2, each inactive alone. Protein R1 contains the active site and allosteric effector sites. Protein R2 contains a stable tyrosyl radical and a dinuclear iron-oxo site essential for catalysis. A radical based reaction mechanism and a radical transfer pathway between R1 and R2 has been proposed.The three conserved active site residues Glu441, Asn437 and Ser224 were studied. Their functions in catalysis were adressed with site-directed mutagenesis. The mutant proteins were characterized with biochemical, biophysical and structural methods. A carboxylate at position 441 is the minimum requirement for catalysis. Glu441 contributes to substrate binding. Its role as a general base in the first part of the reaction mechanism and as a general acid in the second part of the reaction mechanism is corroborated. The residues Asn437 and Ser224 are essential for catalysis and participate in the first part of the reaction.E441Q is a suicidal protein converting the normal substrate into a mechanism-based inhibitor. Consecutive reactions with at least three intermediates were identified. The intermediates are free radical species, a cysteine-localized radical, a nucleotide-localized radical and a tyrosyl radical in the radical transfer pathway were identified. This is the first direct evidence for kinetically coupled radical transfer and reaction intermediates in ribonucleotide reductase.
|
|
| 11. |
- Simmons, Trevor R., et al.
(författare)
-
Mimicking hydrogenases : From biomimetics to artificial enzymes
- 2014
-
Ingår i: Coordination chemistry reviews. - : Elsevier BV. - 0010-8545 .- 1873-3840. ; 270–271:0, s. 127-150
-
Tidskriftsartikel (refereegranskat)abstract
- Over the last 15 years, a plethora of research has provided major insights into the structure and function of hydrogenase enzymes. This has led to the important development of chemical models that mimic the inorganic enzymatic co-factors, which in turn has further contributed to the understanding of the specific molecular features of these natural systems that facilitate such large and robust enzyme activities. More recently, efforts have been made to generate guest–host models and artificial hydrogenases, through the incorporation of transition metal-catalysts (guests) into various hosts. This adds a new layer of complexity to hydrogenase-like catalytic systems that allows for better tuning of their activity through manipulation of both the first (the guest) and the second (the host) coordination spheres. Herein we review the aforementioned advances achieved during the last 15 years, in the field of inorganic biomimetic hydrogenase chemistry. After a brief presentation of the enzymes themselves, as well as the early bioinspired catalysts, we review the more recent systems constructed as models for the hydrogenase enzymes, with a specific focus on the various strategies employed for incorporating of synthetic models into supramolecular frameworks and polypeptidic/protein scaffolds, and critically discuss the advantages of such an elaborate approach, with regard to the catalytic performances.
|
|
| 12. |
- Valencia-Gallardo, Cesar, et al.
(författare)
-
Shigella IpaA mediates actin bundling through diffusible vinculin oligomers with activation imprint
- 2023
-
Ingår i: Cell Reports. - 2211-1247. ; 42:4
-
Tidskriftsartikel (refereegranskat)abstract
- Upon activation, vinculin reinforces cytoskeletal anchorage during cell adhesion. Activating ligands classically disrupt intramolecular interactions between the vinculin head and tail domains that bind to actin filaments. Here, we show that Shigella IpaA triggers major allosteric changes in the head domain, leading to vinculin homo-oligomerization. Through the cooperative binding of its three vinculin-binding sites (VBSs), IpaA induces a striking reorientation of the D1 and D2 head subdomains associated with vinculin oligomerization. IpaA thus acts as a catalyst producing vinculin clusters that bundle actin at a distance from the activation site and trigger the formation of highly stable adhesions resisting the action of actin relaxing drugs. Unlike canonical activation, vinculin homo-oligomers induced by IpaA appear to keep a persistent imprint of the activated state in addition to their bundling activity, accounting for stable cell adhesion independent of force transduction and relevant to bacterial invasion.
|
|
| 13. |
- Zhang, Pan, et al.
(författare)
-
Phosphine Coordination to a Cobalt Diimine-Dioxime Catalyst Increases Stability during Light-Driven H-2 Production
- 2012
-
Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 51:4, s. 2115-2120
-
Tidskriftsartikel (refereegranskat)abstract
- The combination of cobalt diimine-dioxime complexes with a cyclometalated iridium photosensitizer gives efficient systems for hydrogen generation under visible-light irradiation using triethylamine as a sacrificial electron donor. Interestingly, the addition of triphenylphosphine (PPh3) to the medium results in a significant improvement of the stability of the system, with up to similar to 700 turnovers achieved within 10 h. UV-visible spectroscopic monitoring of the reaction allows identification of a PPh3-coordinated Co-I intermediate as the active species. Mechanistic issues regarding (i) the photogeneration of the Co-I species, (ii) the nature of the active species, and (iii) the influence of PPh3 on the H-2-evolution mechanism are discussed.
|
|
