Quinone reductase acts as a redox switch of the 20 S yeast proteasome

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102111/1/embr2008218.pd

Structural and spectroscopic characterization of a HdrA-like subunit from Hyphomicrobium denitrificans

Funding Information: We thank Laurenz Heidrich for help with statistical analyses. This work was supported by grant Da 351/8‐1 (to CD) from the Deutsche Forschungsgemeinschaft and Fundação para a Ciência e Tecnologia (Portugal) (grant PTDC/BIA‐BQM/29118 and R&D units MOSTMICRO‐ITQB (UIDB/04612/2020 and UIDP/04612/2020), and European Union's Horizon 2020 research and innovation program (grant agreement No 810856). Open access funding enabled and organized by Projekt DEAL. Publisher Copyright: © 2020 The Authors. The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies Copyright: Copyright 2021 Elsevier B.V., All rights reserved.Many bacteria and archaea employ a novel pathway of sulfur oxidation involving an enzyme complex that is related to the heterodisulfide reductase (Hdr or HdrABC) of methanogens. As a first step in the biochemical characterization of Hdr-like proteins from sulfur oxidizers (sHdr), we structurally analyzed the recombinant sHdrA protein from the Alphaproteobacterium Hyphomicrobium denitrificans at 1.4 Å resolution. The sHdrA core structure is similar to that of methanogenic HdrA (mHdrA) which binds the electron-bifurcating flavin adenine dinucleotide (FAD), the heart of the HdrABC-[NiFe]-hydrogenase catalyzed reaction. Each sHdrA homodimer carries two FADs and two [4Fe–4S] clusters being linked by electron conductivity. Redox titrations monitored by electron paramagnetic resonance and visible spectroscopy revealed a redox potential between −203 and −188 mV for the [4Fe–4S] center. The potentials for the FADH•/FADH− and FAD/FADH• pairs reside between −174 and −156 mV and between −81 and −19 mV, respectively. The resulting stable semiquinone FADH• species already detectable in the visible and electron paramagnetic resonance spectra of the as-isolated state of sHdrA is incompatible with basic principles of flavin-based electron bifurcation such that the sHdr complex does not apply this new mode of energy coupling. The inverted one-electron FAD redox potentials of sHdr and mHdr are clearly reflected in the different FAD-polypeptide interactions. According to this finding and the assumption that the sHdr complex forms an asymmetric HdrAA′B1C1B2C2 hexamer, we tentatively propose a mechanism that links protein-bound sulfane oxidation to sulfite on HdrB1 with NAD+ reduction via lipoamide disulfide reduction on HdrB2. The FAD of HdrA thereby serves as an electron storage unit. Database: Structural data are available in PDB database under the accession number 6TJR.publishe

Kinetic studies on the oxidation of semiquinone and hydroquinone forms of Arabidopsis cryptochrome by molecular oxygen

Cryptochromes (crys) are flavoprotein photoreceptors present throughout the biological kingdom that play important roles in plant development and entrainment of the circadian clock in several organisms. Crys non-covalently bind flavin adenine dinucleotide (FAD) which undergoes photoreduction from the oxidised state to a radical form suggested to be active in signalling in vivo. Although the photoreduction reactions have been well characterised by a number of approaches, little is known of the oxidation reactions of crys and their mechanisms. In this work, a stopped-flow kinetics approach is used to investigate the mechanism of cry oxidation in the presence and absence of an external electron donor. This in vitro study extends earlier investigations of the oxidation of Arabidopsis cryptochrome1 by molecular oxygen and demonstrates that, under some conditions, a more complex model for oxidation of the flavin than was previously proposed is required to accommodate the spectral evidence. In the absence of an electron donor, photoreduction leads predominantly to the formation of the radical FADHradical dot. Dark recovery most likely forms flavin hydroperoxide (FADHOOH) requiring superoxide. In the presence of reductant (DTT), illumination yields the fully reduced flavin species (FADH?). Reaction of this with dioxygen leads to transient radical (FADHradical dot) and simultaneous accumulation of oxidised species (FAD), possibly governed by interplay between different cryptochrome molecules or cooperativity effects within the cry homodimer

Methylene Homologues of Artemisone: An Unexpected Structure-Activity Relationship and a Possible Implication for the Design of C10-Substituted Artemisinins.

We sought to establish if methylene homologues of artemisone are biologically more active and more stable than artemisone. The analogy is drawn with the conversion of natural O- and N-glycosides into more stable C-glycosides that may possess enhanced biological activities and stabilities. Dihydroartemisinin was converted into 10β-cyano-10-deoxyartemisinin that was hydrolyzed to the α-primary amide. Reduction of the β-cyanide and the α-amide provided the respective methylamine epimers that upon treatment with divinyl sulfone gave the β- and α-methylene homologues, respectively, of artemisone. Surprisingly, the compounds were less active in vitro than artemisone against P. falciparum and displayed no appreciable activity against A549, HCT116, and MCF7 tumor cell lines. This loss in activity may be rationalized in terms of one model for the mechanism of action of artemisinins, namely the cofactor model, wherein the presence of a leaving group at C10 assists in driving hydride transfer from reduced flavin cofactors to the peroxide during perturbation of intracellular redox homeostasis by artemisinins. It is noted that the carba analogue of artemether is less active in vitro than the O-glycoside parent toward P. falciparum, although extrapolation of such activity differences to other artemisinins at this stage is not possible. However, literature data coupled with the leaving group rationale suggest that artemisinins bearing an amino group attached directly to C10 are optimal compounds. A brief critique is made of proteomic studies purporting to demonstrate the alkylation of intraparasitic proteins by alkyne- and azide-tagged artemisinins and synthetic peroxides in relation to mechanism of action

Biosynthetic Gene Cluster for the Cladoniamides, Bis-Indoles with a Rearranged Scaffold

The cladoniamides are bis-indole alkaloids isolated from Streptomyces uncialis, a lichen-associated actinomycete strain. The cladoniamides have an unusual, indenotryptoline structure rarely observed among bis-indole alkaloids. I report here the isolation, sequencing, and annotation of the cladoniamide biosynthetic gene cluster and compare it to the recently published gene cluster for BE-54017, a closely related indenotryptoline natural product. The cladoniamide gene cluster differs from the BE-54017 gene cluster in gene organization and in the absence of one N-methyltransferase gene but otherwise contains close homologs to all genes in the BE-54017 cluster. Both gene clusters encode enzymes needed for the construction of an indolocarbazole core, as well as flavin-dependent enzymes putatively involved in generating the indenotryptoline scaffold from an indolocarbazole. These two bis-indolic gene clusters exemplify the diversity of biosynthetic routes that begin from the oxidative dimerization of two molecules of l-tryptophan, highlight enzymes for further study, and provide new opportunities for combinatorial engineering

Crystallographic Evidence of Drastic Conformational Changes in the Active Site of a Flavin-Dependent

The soil actinomycete Kutzneria sp. 744 produces a class of highly decorated hexadepsipeptides, which represent a new chemical scaffold that has both antimicrobial and antifungal properties. These natural products, known as kutznerides, are created via nonribosomal peptide synthesis using various derivatized amino acids. The piperazic acid moiety contained in the kutzneride scaffold, which is vital for its antibiotic activity, has been shown to derive from the hydroxylated product of l-ornithine, l-N5-hydroxyornithine. The production of this hydroxylated species is catalyzed by the action of an FAD- and NAD(P)H-dependent N-hydroxylase known as KtzI. We have been able to structurally characterize KtzI in several states along its catalytic trajectory, and by pairing these snapshots with the biochemical and structural data already available for this enzyme class, we propose a structurally based reaction mechanism that includes novel conformational changes of both the protein backbone and the flavin cofactor. Further, we were able to recapitulate these conformational changes in the protein crystal, displaying their chemical competence. Our series of structures, with corroborating biochemical and spectroscopic data collected by us and others, affords mechanistic insight into this relatively new class of flavin-dependent hydroxylases and adds another layer to the complexity of flavoenzymes.National Center for Research Resources (U.S.) (P41RR012408)National Institute of General Medical Sciences (U.S.) (P41GM103473

Temperature and force dependence of nanoscale electron transport via the Cu protein Azurin

The mechanisms of solid-state electron transport (ETp) via a monolayer of immobilized Azurin (Az) was examined by conducting probe atomic force microscopy (CP-AFM), both as function of temperature (248 - 373K) and of applied tip force (6-12 nN). By varying both temperature and force in CP-AFM, we find that the ETp mechanism can alter with a change in the force applied via the tip to the proteins. As the applied force increases, ETp via Az changes from temperature-independent to thermally activated at high temperatures. This is in contrast to the Cu-depleted form of Az (apo-Az), where increasing the applied force causes only small quantitative effects, that fit with a decrease in electrode spacing. At low force ETp via holo-Az is temperature-independent and thermally activated via apo-Az. This observation agrees with macroscopic-scale measurements, thus confirming that the difference in ETp dependence on temperature between holo- and apo-Az is an inherent one that may reflect a difference in rigidity between the two forms. An important implication of these results, which depend on CP-AFM measurements over a significant temperature range, is that for ETp measurements on floppy systems, such as proteins, the stress applied to the sample should be kept constant or, at least controlled during measurement.Comment: 24 pages, 6 figures, plus Supporting Information with 4 pages and 2 figure

FACTORS AFFECTING MIGRATION FROM THE CROATIAN RURAL AREA

U radu se daju rezultati istraživanja migracija u seoskom području Republike Hrvatske. Cilj je istražiti čimbenike koji utječu na iseljavanje seoskog stanovništva Republike Hrvatske. Istraživanje je provedeno 2007. godine na uzorku od 914 ispitanika dobi od 24 do 45 godina u seoskom području Republike Hrvatske. Odabir naselja i ispitanika bio je slučajan. Provedeno istraživanje pokazuje da su najveće poteškoće života u hrvatskom seoskom području gospodarske naravi, manjak zaposlenja, slaba mogućnost izbora zanimanja i niža zarada u odnosu na zaposlenje u gradu. Petina ispitanika nije zadovoljna uvjetima seoskog života i namjerava se iseliti. To je zabrinjavajući pokazatelj budući da se radi o populaciji koja je u pravilu završila proces obrazovanja i većinom osnovala obitelj. Najviše mogućih iseljenika, što je bilo i za očekivati, je iz gospodarski nerazvijenih područja Republike Hrvatske. Daljnja depopulacija hrvatskog sela bila bi pogubna, a njene najveće posljedice bile bi: prevelika urbanizacija, posebice velikih gradova, daljnji neravnomjerni razvitak Republike Hrvatske te nedovoljno iskorištenje prostornog, proizvodnog i ljudskog potencijala. S obzirom na strateški cilj ulaska Republike Hrvatske u Europsku uniju, navedeno predstavlja bitno ograničenje njene uspješne prilagodbe europskoj ekonomskoj integraciji. Iseljavanje seoskog pučanstva može se spriječiti prvenstveno povećanjem zaposlenosti i dohotka te stvaranjem takve fizičke i društvene infrastrukture u seoskom području koja će bitno poboljšati životne uvjete seoskog pučanstva. Seoska područja, poglavito gospodarski nerazvijena, nemaju dovoljno vlastitih mogućnosti za ubrzanje razvoja odnosno za nužno smanjivanje razlika u kakvoći življenja prema gradskim područjima. Zbog toga je nužno da njihov razvojni proces više nego dosada potpomogne Država osmišljenim mjerama regionalnog razvoja, uz svekoliku potporu lokalne uprave i samouprave. U tome bi svoj znatan obol trebalo dati novo-osnovano Ministarstvo za regionalni razvoj.The paper presents results of the research study on migrations in rural areas of the Republic of Croatia. The aim was to determine factors influencing migrations of rural population in Croatia. The research was carried out in 2007 on 914 respondents from 25 to 45 years of age. The rural communities and respondents were selected on a random basis. The study results indicate that the major difficulties in rural life in Croatia are of economic nature: lack of employment opportunities, inadequate choice of profession and lower income in comparison with employment in urban areas. One fifth of the respondents is not satisfied with conditions of rural life and intends to leave villages. This is a very disturbing indicator, since it refers to population, which in general, has finished education and started a family. As we expect, the largest number of potential migrants comes from economically underdeveloped Croatian areas. Further depopulation of Croatian villages would have dramatic effects, and the worst consequences would be excessive urbanization, especially of large cities, further uneven development of the Republic of Croatia, and insufficient utilization of spatial, production and human resources. Since the strategic Croatian goal is to become a member of the European Union, this is a major obstacle to its successful adjustment to the European economic integration. The migration of rural population could be prevented primarily by increase in employment and income opportunities and creation of such physical and social infrastructure in rural areas that would considerably improve living conditions for rural population. The rural areas, particularly underdeveloped, have no adequate capacities for intensification of its development and diminishing differences in their quality of life compared to urban areas. Thus, the state support is increasingly required by introducing measures of regional development with complementary support of the local government. The newly founded Ministry of Regional Development is therefore inevitable in this process