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1.
Extremophiles ; 25(5-6): 413-424, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34480656

RESUMO

Acetogenic bacteria are a polyphyletic group of organisms that fix carbon dioxide under anaerobic, non-phototrophic conditions by reduction of two mol of CO2 to acetyl-CoA via the Wood-Ljungdahl pathway. This pathway also allows for lithotrophic growth with H2 as electron donor and this pathway is considered to be one of the oldest, if not the oldest metabolic pathway on Earth for CO2 reduction, since it is coupled to the synthesis of ATP. How ATP is synthesized has been an enigma for decades, but in the last decade two ferredoxin-dependent respiratory chains were discovered. Those respiratory chains comprise of a cytochrome-free, ferredoxin-dependent respiratory enzyme complex, which is either the Rnf or Ech complex. However, it was discovered already 50 years ago that some acetogens contain cytochromes and quinones, but their role had only a shadowy existence. Here, we review the literature on the characterization of cytochromes and quinones in acetogens and present a hypothesis that they may function in electron transport chains in addition to Rnf and Ech.


Assuntos
Ferredoxinas , Quinonas , Bactérias/metabolismo , Citocromos , Transporte de Elétrons , Ferredoxinas/metabolismo
2.
Proc Natl Acad Sci U S A ; 118(39)2021 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-34556577

RESUMO

Proteins achieve efficient energy storage and conversion through electron transfer along a series of redox cofactors. Multiheme cytochromes are notable examples. These proteins transfer electrons over distance scales of several nanometers to >10 µm and in so doing they couple cellular metabolism with extracellular redox partners including electrodes. Here, we report pump-probe spectroscopy that provides a direct measure of the intrinsic rates of heme-heme electron transfer in this fascinating class of proteins. Our study took advantage of a spectrally unique His/Met-ligated heme introduced at a defined site within the decaheme extracellular MtrC protein of Shewanella oneidensis We observed rates of heme-to-heme electron transfer on the order of 109 s-1 (3.7 to 4.3 Å edge-to-edge distance), in good agreement with predictions based on density functional and molecular dynamics calculations. These rates are among the highest reported for ground-state electron transfer in biology. Yet, some fall 2 to 3 orders of magnitude below the Moser-Dutton ruler because electron transfer at these short distances is through space and therefore associated with a higher tunneling barrier than the through-protein tunneling scenario that is usual at longer distances. Moreover, we show that the His/Met-ligated heme creates an electron sink that stabilizes the charge separated state on the 100-µs time scale. This feature could be exploited in future designs of multiheme cytochromes as components of versatile photosynthetic biohybrid assemblies.


Assuntos
Grupo dos Citocromos c/metabolismo , Citocromos/metabolismo , Elétrons , Heme/metabolismo , Histidina/metabolismo , Metionina/metabolismo , Shewanella/metabolismo , Grupo dos Citocromos c/química , Citocromos/química , Transporte de Elétrons , Heme/química , Histidina/química , Metionina/química , Simulação de Dinâmica Molecular , Nanofios , Oxirredução
3.
J Cell Sci ; 134(9)2021 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-34550353

RESUMO

Cytochrome c6 is a redox carrier in the thylakoid lumen of cyanobacteria and some eukaryotic algae. Although the isofunctional plastocyanin is present in land plants and the green alga Chlamydomonas reinhardtii, these organisms also possess a cytochrome c6-like protein designated as cytochrome c6A. Two other cytochrome c6-like groups, c6B and c6C, have been identified in cyanobacteria. In this study, we have identified a novel c6-like cytochrome called PetJ2, which is encoded in the nuclear genome of Cyanophora paradoxa, a member of the glaucophytes - the basal branch of the Archaeplastida. We propose that glaucophyte PetJ2 protein is related to cyanobacterial c6B and c6C cytochromes, and that cryptic green algal and land plant cytochromes c6A evolved from an ancestral archaeplastidial PetJ2 protein. In vitro import experiments with isolated muroplasts revealed that PetJ2 is imported into plastids. Although it harbors a twin-arginine motif in its thylakoid-targeting peptide, which is generally indicative of thylakoid import via the Tat import pathway, our import experiments with isolated muroplasts and the heterologous pea thylakoid import system revealed that PetJ2 uses the Sec pathway instead of the Tat import pathway.


Assuntos
Cyanophora , Sequência de Aminoácidos , Cyanophora/metabolismo , Citocromos/metabolismo , Eucariotos/metabolismo , Plastídeos/metabolismo
4.
Curr Oncol ; 28(5): 3573-3584, 2021 09 16.
Artigo em Inglês | MEDLINE | ID: mdl-34590601

RESUMO

BACKGROUND: cervical cancer is one of the most common malignancies in women worldwide and its management remains challenging and complex. As Cytochrome4Z1 (CYP4Z1) is overexpressed in many tumours, its expression in cervical cancer is unknown. Therefore, the present study aimed to evaluate CYP4Z1 expression in cervical cancers. METHODS: CYP4Z1 expression was immunohistochemically assessed in 100 cases of cervical cancers along with ten normal cervix tissues, and the enzyme's relationship to several clinicopathological features and survival was explored. RESULTS: CYP4Z1 was strongly expressed in 55% of cervical cancer patients. Normal cervix samples were negative for CYP4Z1 expression. Importantly, this expression was significantly found in patients with the late stage of the disease, lymph node metastasis, and high tumour invasion (p < 0.05). Interestingly, CYP4Z1 expression was significantly correlated with shorter survival times of cervical cancer patients. Univariate analysis showed that CYP4Z1 expression, tumour stage, lymph node metastasis, and tumour invasion were significantly correlated with patient survival (p < 0.05). The multivariate analysis revealed that only CYP4Z1 expression and tumour stage were significantly correlated with patient survival (p < 0.05). CONCLUSIONS: CYP4Z1 expression is associated with cervical cancer patients' survival and may serve as an independent predictor of poor prognosis in cervical cancer patients.


Assuntos
Neoplasias do Colo do Útero , Família 4 do Citocromo P450 , Citocromos , Feminino , Humanos , Metástase Linfática , Prognóstico , Neoplasias do Colo do Útero/genética
5.
PLoS One ; 16(8): e0244260, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34424897

RESUMO

Mitochondrial alternative oxidase (AOX) is predicted to be present in mitochondria of several invertebrate taxa including tardigrades. Independently of the reason concerning the enzyme occurrence in animal mitochondria, expression of AOX in human mitochondria is regarded as a potential therapeutic strategy. Till now, relevant data were obtained due to heterologous AOX expression in cells and animals without natively expressed AOX. Application of animals natively expressing AOX could importantly contribute to the research. Thus, we decided to investigate AOX activity in intact specimens of the tardigrade Hypsibius exemplaris. We observed that H. exemplaris specimens' tolerance to the blockage of the mitochondrial respiratory chain (MRC) cytochrome pathway was diminished in the presence of AOX inhibitor and the inhibitor-sensitive respiration enabled the tardigrade respiration under condition of the blockage. Importantly, these observations correlated with relevant changes of the mitochondrial inner membrane potential (Δψ) detected in intact animals. Moreover, detection of AOX at protein level required the MRC cytochrome pathway blockage. Overall, we demonstrated that AOX activity in tardigrades can be monitored by the animals' behavior observation as well as by measurement of intact specimens' whole-body respiration and Δψ. Furthermore, it is also possible to check the impact of the MRC cytochrome pathway blockage on AOX level as well as AOX inhibition in the absence of the blockage on animal functioning. Thus, H. exemplaris could be consider as a whole-animal model suitable to study AOX.


Assuntos
Mitocôndrias/metabolismo , Mitocôndrias/fisiologia , Proteínas Mitocondriais/metabolismo , Oxirredutases/metabolismo , Proteínas de Plantas/metabolismo , Tardígrados/metabolismo , Tardígrados/fisiologia , Animais , Comportamento Animal/fisiologia , Respiração Celular/fisiologia , Citocromos/metabolismo , Potencial da Membrana Mitocondrial/fisiologia , Membranas Mitocondriais/metabolismo , Membranas Mitocondriais/fisiologia , Oxirredução , Transdução de Sinais/fisiologia
6.
Sheng Li Xue Bao ; 73(4): 577-583, 2021 Aug 25.
Artigo em Chinês | MEDLINE | ID: mdl-34405214

RESUMO

The objective of this study was to explore the roles of arachidonic acid cytochrome P450ω hydroxylase CYP4A14 in skeletal muscle regeneration after injury. Wild-type (WT) control mice and Cyp4a14 knockout (A14-/-) mice were used to establish the muscle injury and regeneration model by intramuscular injection with cardiotoxin (CTX) on the tibial anterior (TA) muscle. The TA muscles were harvested at the time points of 0, 3, 5 and 15 days after injury. The changes in skeletal muscle regeneration and fibrosis were assessed by wheat germ agglutinin (WGA) staining and Sirius Red staining. Immunohistochemical staining was used to observe the expression of proliferation-related protein Ki-67 and macrophage marker protein Mac-2. The mRNA levels of regeneration and inflammation associated genes were analyzed by real-time PCR. The results showed that the cross-section area (CSA) of regenerated myofibers in A14-/- mice was significantly smaller (P < 0.05), while the percentage of fibrosis area was significantly higher than those in WT mice at 15 days after injury (P < 0.05). In A14-/- muscles, both the ratio of Ki-67 positive proliferating cells and the mRNA levels of differentiation associated genes Myod1 and Myog were significantly lower than those in WT muscles (P < 0.05). At 3 days after injury, the mRNA expression of inflammatory cells marker genes CD45 and CD11b and Mac-2 positive macrophages in A14-/- muscles were significantly lower than those in WT skeletal muscle (P < 0.05). Macrophages derived pro-regeneration cytokines IL-1ß, IGF-1 and SDF-1 were also significantly decreased in A14-/- muscles (P < 0.05). These results suggest that arachidonic acid cytochrome P450ω hydroxylase CYP4A14 plays a critical role in skeletal muscle regeneration after injury.


Assuntos
Oxigenases de Função Mista , Regeneração , Animais , Ácido Araquidônico , Citocromos , Técnicas de Inativação de Genes , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Músculo Esquelético
7.
Inorg Chem ; 60(17): 12870-12882, 2021 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-34370470

RESUMO

Diheme cytochromes, the simplest members in the multiheme family, play substantial biochemical roles in enzymatic catalysis as well as in electron transfer. A series of diiron(III) porphyrin dimers have been synthesized as active site analogues of diheme cytochromes. The complexes contain six-coordinated iron(III) having thiophenol and imidazole at the fifth and sixth coordination sites, respectively. The iron centers in the complexes have been found to be in a low-spin state, as confirmed through solid-state Mössbauer and electron paramagnetic resonance (EPR) spectroscopic investigations. Mössbauer quadrupole splitting of complexes having mixed ligands is substantially larger than that observed when both axial ligands are the same. Rhombic types of EPR spectra with narrow separation between gx, gy, and gz clearly distinguish heme thiolate coordination compared to bis(imidazole)-ligated low-spin heme centers. The redox potential in diheme cytochromes has been found to be tuned by interheme interactions along with the nature of axial ligands. The effect of mixed-axial ligation within the diiron(III) porphyrin dimers is demonstrated by a positive shift in the Fe(III)/Fe(II) redox couple upon thiophenolate coordination compared to their bis(imidazole) analogues. The pKa of the imidazole also decides the extent of the shift for the Fe(III)/Fe(II) couple, while the potential of the mixed-ligated diiron(III) porphyrin dimer is more positive compared to their monomeric analogue. A variation of around 1.1 V for the Fe(III)/Fe(II) redox potential in the diiron(III) porphyrin dimer can be achieved with the combined effect of axial ligation and a metal spin state, while such a large variation in the redox potential, compared to their monomeric analogues, is attributed to the heme-heme interactions observed in dihemes. Moreover, theoretical calculations also support the experimental shifts in the redox potential values.


Assuntos
Imidazóis/química , Metaloporfirinas/química , Fenóis/química , Compostos de Sulfidrila/química , Citocromos/química , Teoria da Densidade Funcional , Espectroscopia de Ressonância de Spin Eletrônica , Heme/química , Ferro/química , Ligantes , Metaloporfirinas/síntese química , Modelos Químicos , Oxirredução , Espectroscopia de Prótons por Ressonância Magnética , Espectroscopia de Mossbauer
8.
Photosynth Res ; 149(3): 265-273, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34228227

RESUMO

Martin Kamen was a giant of twentieth century science. Trained as a physical chemist, he was the co-discoverer of radioactive Carbon 14, which has transformed many areas of science as a tracer and as a way to date artifacts. He later switched to the study of metabolism and biochemistry and made important contributions to the understanding of nitrogen fixation and photosynthesis. Finally, he studied cytochromes, primarily from anoxygenic photosynthetic bacteria.


Assuntos
Bactérias/metabolismo , Carbono/química , Citocromos/química , Citocromos/metabolismo , Fotossíntese/fisiologia , História do Século XX , História do Século XXI , Humanos , Masculino , Estados Unidos
9.
Photosynth Res ; 148(3): 137-152, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-34236566

RESUMO

The heliobacteria, a family of anoxygenic phototrophs, possess the simplest known photosynthetic apparatus. Although they are photoheterotrophs in the light, the heliobacteria can also grow chemotrophically via pyruvate metabolism in the dark. In the heliobacteria, the cytochrome bc complex is responsible for oxidizing menaquinol and reducing cytochrome c553 in the electron flow cycle used for phototrophy. However, there is no known electron acceptor for the mobile cytochrome c553 other than the photochemical reaction center. We have, therefore, hypothesized that the cytochrome bc complex is necessary for phototrophy, but unnecessary for chemotrophic growth in the dark. We used a two-step method for CRISPR-based genome editing in Heliobacterium modesticaldum to delete the genes encoding the four major subunits of the cytochrome bc complex. Genotypic analysis verified the deletion of the petCBDA gene cluster encoding the catalytic components of the complex. Spectroscopic studies revealed that re-reduction of cytochrome c553 after flash-induced photo-oxidation was over 100 times slower in the ∆petCBDA mutant compared to the wild-type. Steady-state levels of oxidized P800 (the primary donor of the photochemical reaction center) were much higher in the ∆petCBDA mutant at every light level, consistent with a limitation in electron flow to the reaction center. The ∆petCBDA mutant was unable to grow phototrophically on acetate plus CO2 but could grow chemotrophically on pyruvate as a carbon source similar to the wild-type strain in the dark. The mutants could be complemented by reintroduction of the petCBDA gene cluster on a plasmid expressed from the clostridial eno promoter.


Assuntos
Sobrevivência Celular/fisiologia , Clostridiales/genética , Clostridiales/metabolismo , Citocromos/genética , Citocromos/metabolismo , Deleção de Genes , Fotossíntese/fisiologia , Adaptação Ocular/genética , Adaptação Ocular/fisiologia , Adaptação à Escuridão/genética , Adaptação à Escuridão/fisiologia , Mutação , Fotossíntese/genética
10.
Environ Sci Technol ; 55(14): 10142-10151, 2021 07 20.
Artigo em Inglês | MEDLINE | ID: mdl-34196176

RESUMO

Direct interspecies electron transfer (DIET) between microbial species prevails in some key microbial consortia. However, the electron transfer mechanism(s) in these consortia is controversial due to lack of efficient characterization methods. Here, we provide an in situ anaerobic spectroelectrochemical coculture cell (in situ ASCC) to induce the formation of DIET coculture biofilm on the interdigitated microelectrode arrays and characterize the electron transfer directly. Two typical Geobacter DIET cocultures, Geobacter metallireducens and wild-type Geobacter sulfurreducens (G.m&G.s) and G. metallireducens and a G. sulfurreducens strain deficient in citrate synthase (G.m&G.s-ΔgltA), were selected. In situ Raman and electrochemical Fourier transform infrared (FTIR) spectroscopy indicated that cytochromes are abundant in the electric syntrophic coculture. Cyclic voltammetry and potential step experiment revealed a diffusion-controlled electron transfer process and the electrochemical gating measurements further demonstrated a cytochrome-mediated electron transfer in the DIET coculture. Furthermore, the G.m&G.s-ΔgltA coculture displayed a higher redox conductivity than the G.m&G.s coculture, consistent with the existence of an intimate and efficient electrical connection between these two species. Our findings provide the first report of a redox-gradient-driven electron transport facilitated by c-type cytochromes in DIET coculture, supporting the model that DIET is mediated by cytochromes and suggest a platform to explore the other DIET consortia.


Assuntos
Geobacter , Técnicas de Cocultura , Citocromos/metabolismo , Transporte de Elétrons , Geobacter/metabolismo , Oxirredução
11.
Sci Rep ; 11(1): 15140, 2021 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-34302023

RESUMO

Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica-dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, Geobacter OTU650, which was phylogenetically close to Ca. G. eutrophica, was outcompeted in the control but remained abundant and active under electrochemical stimulation, indicating Ca. G. eutrophica's EET ability. The high-quality draft genome further showed high phylogenomic similarity with Ca. G. eutrophica, and the genes encoding outer membrane cytochromes and enzymes for hydrogen metabolism were actively expressed. A Bayesian network was trained with the genes encoding enzymes for alcohol metabolism, hydrogen metabolism, EET, and methanogenesis from dominant fermentative bacteria, Geobacter, and Methanobacterium. Methane production could not be accurately predicted when the genes for IHT were in silico knocked out, inferring its more important role in methanogenesis. The genomics-enabled machine learning modeling approach can provide predictive insights into the importance of IHT and DIET.


Assuntos
Transporte de Elétrons/fisiologia , Geobacter/metabolismo , Hidrogênio/metabolismo , Teorema de Bayes , Citocromos/metabolismo , Elétrons , Aprendizado de Máquina , Redes e Vias Metabólicas/fisiologia , Metano/metabolismo , Methanobacterium/metabolismo
12.
Biochem J ; 478(14): 2871-2887, 2021 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-34190983

RESUMO

The redox potential values of cytochromes can be modulated by the protonation/deprotonation of neighbor groups (redox-Bohr effect), a mechanism that permits the proteins to couple electron/proton transfer. In the respiratory chains, this effect is particularly relevant if observed in the physiological pH range, as it may contribute to the electrochemical gradient for ATP synthesis. A constitutively produced family of five triheme cytochromes (PpcA-E) from the bacterium Geobacter sulfurreducens plays a crucial role in extracellular electron transfer, a hallmark that permits this bacterium to be explored for several biotechnological applications. Two members of this family (PpcA and PpcD) couple electron/proton transfer in the physiological pH range, a feature not shared with PpcB and PpcE. That ability is crucial for G. sulfurreducens' growth in Fe(III)-reducing habitats since extra contributors to the electrochemical gradient are needed. It was postulated that the redox-Bohr effect is determined by the nature of residue 6, a leucine in PpcA/PpcD and a phenylalanine in PpcB/PpcE. To confirm this hypothesis, Phe6 was replaced by leucine in PpcB and PpcE. The functional properties of these mutants were investigated by NMR and UV-visible spectroscopy to assess their capability to couple electron/proton transfer in the physiological pH range. The results obtained showed that the mutants have an increased redox-Bohr effect and are now capable of coupling electron/proton transfer. This confirms the determinant role of the nature of residue 6 in the modulation of the redox-Bohr effect in this family of cytochromes, opening routes to engineer Geobacter cells with improved biomass production.


Assuntos
Proteínas de Bactérias/metabolismo , Citocromos/metabolismo , Geobacter/metabolismo , Heme/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Citocromos/química , Citocromos/genética , Transporte de Elétrons/genética , Elétrons , Geobacter/genética , Heme/química , Concentração de Íons de Hidrogênio , Modelos Moleculares , Estrutura Molecular , Mutação , Oxirredução , Conformação Proteica , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Prótons , Espectrofotometria/métodos , Termodinâmica
13.
Antimicrob Agents Chemother ; 65(9): e0066221, 2021 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-34152821

RESUMO

An effective strategy to control blood-borne diseases and prevent outbreak recrudescence involves targeting conserved metabolic processes that are essential for pathogen viability. One such target for Plasmodium and Babesia, the infectious agents of malaria and babesiosis, respectively, is the mitochondrial cytochrome bc1 protein complex, which can be inhibited by endochin-like quinolones (ELQ) and atovaquone. We used the tick-transmitted and culturable blood-borne pathogen Babesia duncani to evaluate the structure-activity relationship, safety, efficacy, and mode of action of ELQs. We identified a potent and highly selective ELQ prodrug (ELQ-502), which, alone or in combination with atovaquone, eliminates B. microti and B. duncani infections in vitro and in mouse models of parasitemia and lethal infection. The strong efficacy at low dose, excellent safety, bioavailability, and long half-life of this experimental therapy make it an ideal clinical candidate for the treatment of human infections caused by Babesia and its closely related apicomplexan parasites.


Assuntos
Babesia , Babesiose , Animais , Atovaquona/farmacologia , Babesiose/tratamento farmacológico , Babesiose/prevenção & controle , Citocromos , Camundongos , Parasitemia/tratamento farmacológico
14.
Antimicrob Agents Chemother ; 65(9): e0095621, 2021 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-34152815

RESUMO

Mycobacterium tuberculosis, the causative agent of human tuberculosis, harbors a branched electron transport chain, preventing the bactericidal action of cytochrome bc1 inhibitors (e.g., TB47). Here, we investigated, using luminescent mycobacterial strains, the in vitro combination activity of cytochrome bc1 inhibitors and nitric oxide (NO) donors including pretomanid (PMD) and explored the mechanisms of combination activity. The TB47 and PMD combination quickly abolished the light emission of luminescent bacilli, as was the case for the combination of TB47 and aurachin D, a putative cytochrome bd inhibitor. The TB47 and PMD combination inhibited M. tuberculosis oxygen consumption, decreased ATP levels, and had a delayed bactericidal effect. The NO scavenger carboxy-PTIO prevented the bactericidal activity of the drug combination, suggesting the requirement for NO. In addition, cytochrome bc1 inhibitors were largely bactericidal when administered with DETA NONOate, another NO donor. Proteomic analysis revealed that the cotreated bacilli had a compromised expression of the dormancy regulon proteins, PE/PPE proteins, and proteins required for the biosynthesis of several cofactors, including mycofactocin. Some of these proteomic changes, e.g., the impaired dormancy regulon induction, were attributed to PMD. In conclusion, combination of cytochrome bc1 inhibitors with PMD inhibited M. tuberculosis respiration and killed the bacilli. The activity of cytochrome bc1 inhibitors can be greatly enhanced by NO donors. Monitoring of luminescence may be further exploited to screen cytochrome bd inhibitors.


Assuntos
Mycobacterium tuberculosis , Citocromos , Transporte de Elétrons , Complexo III da Cadeia de Transporte de Elétrons , Humanos , Óxido Nítrico , Nitroimidazóis , Proteômica
15.
Biomed Res Int ; 2021: 5574789, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34046497

RESUMO

Cytochrome (CYP) enzymes catalyze the metabolic reactions of endogenous and exogenous compounds. The superfamily of enzymes is found across many organisms, regardless of type, except for plants. Information was gathered about CYP2D enzymes through protein sequences of humans and other organisms. The secondary structure was predicted using the SOPMA. The structural and functional study of human CYP2D was conducted using ProtParam, SOPMA, Predotar 1.03, SignalP, TMHMM 2.0, and ExPASy. Most animals shared five central motifs according to motif analysis results. The tertiary structure of human CYP2D, as well as other animal species, was predicted by Phyre2. Human CYP2D proteins are heavily conserved across organisms, according to the findings. This indicates that they are descended from a single ancestor. They calculate the ratio of alpha-helices to extended strands to beta sheets to random coils. Most of the enzymes are alpha-helix, but small amounts of the random coil were also found. The data were obtained to provide us with a better understanding of mammalian proteins' functions and evolutionary relationships.


Assuntos
Citocromos/química , Citocromos/classificação , Filogenia , Proteínas/química , Sequência de Aminoácidos , Animais , Biologia Computacional/métodos , Simulação por Computador , Sistema Enzimático do Citocromo P-450/química , Sistema Enzimático do Citocromo P-450/classificação , Sistema Enzimático do Citocromo P-450/genética , Sistema Enzimático do Citocromo P-450/metabolismo , Citocromos/genética , Citocromos/metabolismo , Humanos , Ligantes , Camundongos , Modelos Moleculares , Conformação Proteica em alfa-Hélice , Domínios e Motivos de Interação entre Proteínas , Estrutura Secundária de Proteína , Proteínas/classificação , Proteínas/genética , Alinhamento de Sequência , Software
16.
J Biol Chem ; 296: 100711, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33915126

RESUMO

Geobacter bacteria are able to transfer electrons to the exterior of the cell and reduce extracellular electron acceptors including toxic/radioactive metals and electrode surfaces, with potential applications in bioremediation or electricity harvesting. The triheme c-type cytochrome PpcA from Geobacter metallireducens plays a crucial role in bridging the electron transfer from the inner to the outer membrane, ensuring an effective extracellular electron transfer. This cytochrome shares 80% identity with PpcA from Geobacter sulfurreducens, but their redox properties are markedly different, thus determining the distinctive working redox potential ranges in the two bacteria. PpcA from G. metallireducens possesses two extra aromatic amino acids (Phe-6 and Trp-45) in its hydrophobic heme core, whereas PpcA from G. sulfurreducens has a leucine and a methionine in the equivalent positions. Given the different nature of these residues in the two cytochromes, we have hypothesized that the extra aromatic amino acids could be partially responsible for the observed functional differences. In this work, we have replaced Phe-6 and Trp-45 residues by their nonaromatic counterparts in PpcA from G. sulfurreducens. Using redox titrations followed by UV-visible and NMR spectroscopy we observed that residue Trp-45 shifted the redox potential range 33% toward that of PpcA from G. sulfurreducens, whereas Phe-6 produced a negligible effect. For the first time, it is shown that the inclusion of an aromatic residue at the heme core can modulate the working redox range in abundant periplasmic proteins, paving the way to engineer bacterial strains for optimal microbial bioelectrochemical applications.


Assuntos
Citocromos/química , Citocromos/metabolismo , Geobacter/citologia , Geobacter/enzimologia , Heme , Periplasma/enzimologia , Interações Hidrofóbicas e Hidrofílicas , Cinética , Modelos Moleculares , Oxirredução , Domínios Proteicos
17.
J Chem Inf Model ; 61(4): 1840-1849, 2021 04 26.
Artigo em Inglês | MEDLINE | ID: mdl-33793213

RESUMO

Cytochrome bc1 is a fundamental enzyme for cellular respiration and photosynthesis. This dimeric protein complex catalyzes a proton-coupled electron transfer (PCET) from the reduced coenzyme-Q substrate (Q) to a bimetallic iron-sulfur cluster in the Qo active site. Herein, we combine molecular dynamics simulations of the complete cytochrome bc1 protein with electronic-structure calculations of truncated models and a semiclassical tunneling theory to investigate the electron-proton adiabaticity of the initial reaction catalyzed in the Qo site. After sampling possible orientations between the Q substrate and a histidine side chain that functions as hydrogen acceptor, we find that a truncated model composed by ubiquinol-methyl and imidazole-iron(III)-sulfide captures the expected changes in oxidation and spin states of the electron donor and acceptor. Diabatic electronic surfaces obtained for this model with multiconfigurational wave function calculations demonstrate that this reaction is electronic nonadiabatic, and proton tunneling is faster than mixing of electronic configurations. These results indicate the formalism that should be used to calculate vibronic couplings and kinetic parameters for the initial reaction in the Qo site of cytochrome bc1. This framework for molecular simulation may also be applied to investigate other PCET reactions in the Q-cycle or in various metalloproteins that catalyze proton translocation coupled to redox processes.


Assuntos
Elétrons , Prótons , Respiração Celular , Citocromos , Transporte de Elétrons , Compostos Férricos , Oxirredução
18.
Biochemistry (Mosc) ; 86(1): 8-21, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33705278

RESUMO

Bacillus subtilis serves as a model Gram-positive bacterium and an experimental system for research on respiratory enzymes. This review presents the heme proteins currently known for the well-characterized laboratory strain B. subtilis 168. It focuses on advances in research made during the last three decades concerning the function and composition of the cytochrome bc complex, terminal oxidases, and succinate:menaquinone oxidoreductase. The aerobic respiratory system of strain 168 seems representative for the species B. subtilis, as determined by the cytochrome composition of the undomesticated strain B. subtilis NCIB 3610 and a set of constructed cytochrome-deficient mutants of this strain. Unexplained and unsettled aspects of the molecular biology of respiratory cytochromes in B. subtilis are highlighted in the review.


Assuntos
Bacillus subtilis/metabolismo , Citocromos/metabolismo , Proteínas de Bactérias , Citocromos/genética , Transporte de Elétrons
19.
Biosens Bioelectron ; 180: 113117, 2021 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-33677358

RESUMO

Direct electron transfer based enzymatic biosensors are highly efficient systems where electrons are transferred directly from the enzyme's electroactive site to the electrode. One way of achieving it is by 'wiring' the enzyme to the electrode surface. The wiring of enzymes to electrode surfaces can be reached in many different ways but controlling its orientation towards the electrode surface is still a challenge. In this study we have designed a Flavin-adenine dinucleotide dependent glucose dehydrogenase that is fused to a minimal cytochrome with a site-specifically incorporated unnatural amino acid to control its orientation towards the electrode. Several site-specifically wired mutant enzymes were compared to each other and to a non-specifically wired enzyme using atomic force microscopy and electrochemical techniques. The surface and activity analyses suggest that the site-specific wiring through different sites maintains the correct folding of the enzyme and have a positive effect on the apparent electrochemical electron transfer rate constant kETapp. Electrochemical analysis revealed an efficient electron transfer rate with more than 15 times higher imax and 10-fold higher sensitivity of the site-specifically wired enzyme variants compared to the non-specifically wired ones. This approach can be utilized to control the orientation of other redox enzymes on electrodes to allow a significant improvement of their electron transfer communication with electrodes.


Assuntos
Técnicas Biossensoriais , Glucose 1-Desidrogenase , Citocromos , Eletrodos , Transporte de Elétrons , Enzimas Imobilizadas , Flavina-Adenina Dinucleotídeo/metabolismo , Glucose , Glucose 1-Desidrogenase/genética , Glucose 1-Desidrogenase/metabolismo
20.
Appl Environ Microbiol ; 87(10)2021 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-33741623

RESUMO

Extracellular electron transfer (EET) is an important biological process in microbial physiology as found in dissimilatory metal oxidation/reduction and interspecies electron transfer in syntrophy in natural environments. EET also plays a critical role in microorganisms relevant to environmental biotechnology in metal-contaminated areas, metal corrosion, bioelectrochemical systems, and anaerobic digesters. Geobacter species exist in a diversity of natural and artificial environments. One of the outstanding features of Geobacter species is the capability of direct EET with solid electron donors and acceptors, including metals, electrodes, and other cells. Therefore, Geobacter species are pivotal in environmental biogeochemical cycles and biotechnology applications. Geobacter sulfurreducens, a representative Geobacter species, has been studied for direct EET as a model microorganism. G. sulfurreducens employs electrically conductive pili (e-pili) and c-type cytochromes for the direct EET. The biological function and electronics applications of the e-pili have been reviewed recently, and this review focuses on the cytochromes. Geobacter species have an unusually large number of cytochromes encoded in their genomes. Unlike most other microorganisms, Geobacter species localize multiple cytochromes in each subcellular fraction, outer membrane, periplasm, and inner membrane, as well as in the extracellular space, and differentially utilize these cytochromes for EET with various electron donors and acceptors. Some of the cytochromes are functionally redundant. Thus, the EET in Geobacter is complicated. Geobacter coordinates the cytochromes with other cellular components in the elaborate EET system to flourish in the environment.


Assuntos
Citocromos/metabolismo , Geobacter/metabolismo , Membrana Externa Bacteriana/metabolismo , Transporte de Elétrons , Membranas Intracelulares/metabolismo , Periplasma/metabolismo
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