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1.
Angew Chem Int Ed Engl ; 63(16): e202401379, 2024 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-38407997

RESUMO

Ferritins are multimeric cage-forming proteins that play a crucial role in cellular iron homeostasis. All H-chain-type ferritins harbour a diiron site, the ferroxidase centre, at the centre of a 4 α-helical bundle, but bacterioferritins are unique in also binding 12 hemes per 24 meric assembly. The ferroxidase centre is known to be required for the rapid oxidation of Fe2+ during deposition of an immobilised ferric mineral core within the protein's hollow interior. In contrast, the heme of bacterioferritin is required for the efficient reduction of the mineral core during iron release, but has little effect on the rate of either oxidation or mineralisation of iron. Thus, the current view is that these two cofactors function in iron uptake and release, respectively, with no functional overlap. However, rapid electron transfer between the heme and ferroxidase centre of bacterioferritin from Escherichia coli was recently demonstrated, suggesting that the two cofactors may be functionally connected. Here we report absorbance and (magnetic) circular dichroism spectroscopies, together with in vitro assays of iron-release kinetics, which demonstrate that the ferroxidase centre plays an important role in the reductive mobilisation of the bacterioferritin mineral core, which is dependent on the heme-ferroxidase centre electron transfer pathway.


Assuntos
Ceruloplasmina , Ferro , Ferro/química , Ceruloplasmina/química , Escherichia coli/metabolismo , Ferritinas/química , Proteínas de Bactérias/metabolismo , Grupo dos Citocromos b/química , Minerais , Oxirredução , Heme/metabolismo
2.
FEBS Lett ; 597(4): 547-556, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36460943

RESUMO

Cytochrome bd-I from Escherichia coli is a terminal oxidase in the respiratory chain that plays an important role under stress conditions. Cytochrome bd-I was thought to consist of the major subunits CydA and CydB plus the small CydX subunit. Recent high-resolution structures of cytochrome bd-I demonstrated the presence of an additional subunit, CydH/CydY (called CydH here), the function of which is unclear. In this report, we show that in the absence of CydH, cytochrome bd-I is catalytically active, can sustain bacterial growth and displays haem spectra and susceptibility for haem-binding inhibitors comparable to the wild-type enzyme. Removal of CydH did not elicit catalase activity of cytochrome bd-I in our experimental system. Taken together, in the absence of the CydH subunit cytochrome bd-I retained key enzymatic properties.


Assuntos
Proteínas de Escherichia coli , Escherichia coli , Grupo dos Citocromos b/genética , Grupo dos Citocromos b/química , Citocromos/genética , Citocromos/química , Complexo de Proteínas da Cadeia de Transporte de Elétrons/genética , Complexo de Proteínas da Cadeia de Transporte de Elétrons/química , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Heme
3.
Biochemistry ; 61(19): 2063-2072, 2022 10 04.
Artigo em Inglês | MEDLINE | ID: mdl-36106943

RESUMO

Metals can play key roles in stabilizing protein structures, but ensuring their proper incorporation is a challenge when a metalloprotein is overexpressed in a non-native cellular environment. Here, we have used computational protein design tools to redesign cytochrome b562 (cyt b562), which relies on the binding of its heme cofactor to achieve its proper fold, into a stable, heme-free protein. The resulting protein, ApoCyt, features only four mutations and no metal-ligand or covalent bonds, yet displays improved stability over cyt b562. Mutagenesis studies and X-ray crystal structures reveal that the increase in stability is due to the computationally prescribed mutations, which stabilize the protein fold through a combination of hydrophobic packing interactions, hydrogen bonds, and cation-π interactions. Upon installation of the relevant mutations, ApoCyt is capable of assembling into previously reported, cytochrome-based trimeric and tetrameric assemblies, demonstrating that ApoCyt retains the structure and assembly properties of cyt b562. The successful design of ApoCyt therefore enables further functional diversification of cytochrome-based assemblies and demonstrates that structural metal cofactors can be replaced by a small number of well-designed, non-covalent interactions.


Assuntos
Hemeproteínas , Metaloproteínas , Grupo dos Citocromos b/química , Citocromos b , Heme/química , Ligantes
4.
Nanoscale ; 14(34): 12322-12331, 2022 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-35969005

RESUMO

The thermal and chemical stability of 24mer ferritins has led to attempts to exploit their naturally occurring nanoscale (8 nm) internal cavities for biotechnological applications. An area of increasing interest is the encapsulation of molecules either for medical or biocatalysis applications. Encapsulation requires ferritin dissociation, typically induced using high temperature or acidic conditions (pH ≥ 2), which generally precludes the inclusion of fragile cargo such as proteins or peptide fragments. Here we demonstrate that minimizing salt concentration combined with adjusting the pH to ≤8.5 (i.e. low proton/metal ion concentration) reversibly shifts the naturally occurring equilibrium between dimeric and 24meric assemblies of Escherichia coli bacterioferritin (Bfr) in favour of the disassembled form. Interconversion between the different oligomeric forms of Bfr is sufficiently slow under these conditions to allow the use of size exclusion chromatography to obtain wild type protein in the purely dimeric and 24meric forms. This control over association state was exploited to bind heme at natural sites that are not accessible in the assembled protein. The potential for biotechnological applications was demonstrated by the encapsulation of a small, acidic [3Fe-4S] cluster-containing ferredoxin within the Bfr internal cavity. The capture of ∼4-6 negatively charged ferredoxin molecules per cage indicates that charge complementarity with the inner protein surface is not an essential determinant of successful encapsulation.


Assuntos
Grupo dos Citocromos b , Ferredoxinas , Proteínas de Bactérias/química , Grupo dos Citocromos b/química , Grupo dos Citocromos b/metabolismo , Escherichia coli/metabolismo , Ferredoxinas/metabolismo , Ferritinas/química
5.
Biochemistry ; 61(22): 2506-2521, 2022 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-21028883

RESUMO

The functioning of cytochrome c oxidases involves orchestration of long-range electron transfer (ET) events among the four redox active metal centers. We report the temperature dependence of electron transfer from the CuAr site to the low-spin heme-(a)bo site, i.e., CuAr + heme-a(b)o → CuAo + heme-a(b)r in three structurally characterized enzymes: A-type aa3 from Paracoccus denitrificans (PDB code 3HB3) and bovine heart tissue (PDB code 2ZXW), and the B-type ba3 from T. thermophilus (PDB codes 1EHK and 1XME). k,T data sets were obtained with the use of pulse radiolysis as described previously. Semiclassical Marcus theory revealed that λ varies from 0.74 to 1.1 eV, Hab, varies from ∼2 × 10-5 eV (0.16 cm-1) to ∼24 × 10-5 eV (1.9 cm-1), and ßD varies from 9.3 to 13.9. These parameters are consistent with diabatic electron tunneling. The II-Asp111Asn CuA mutation in cytochrome ba3 had no effect on the rate of this reaction whereas the II-Met160Leu CuA-mutation was slower by an amount corresponding to a decreased driving force of ∼0.06 eV. The structures support the presence of a common, electron-conducting "wire" between CuA and heme-a(b). The transfer of an electron from the low-spin heme to the high-spin heme, i.e., heme-a(b)r + heme-a3o → heme-a(b)o + heme-a3r, was not observed with the A-type enzymes in our experiments but was observed with the Thermus ba3; its Marcus parameters are λ = 1.5 eV, Hab = 26.6 × 10-5 eV (2.14 cm-1), and ßD = 9.35, consistent also with diabatic electron tunneling between the two hemes. The II-Glu15Ala mutation of the K-channel structure, ∼ 24 Å between its CA and Fe-a3, was found to completely block heme-br to heme-a3o electron transfer. A structural mechanism is suggested to explain these observations.


Assuntos
Complexo IV da Cadeia de Transporte de Elétrons , Thermus thermophilus , Bovinos , Animais , Complexo IV da Cadeia de Transporte de Elétrons/química , Grupo dos Citocromos b/química , Elétrons , Radiólise de Impulso , Temperatura , Oxirredução , Heme/química
6.
Inorg Chem ; 60(22): 16937-16952, 2021 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-34695354

RESUMO

The uptake and utilization of iron remains critical for the survival/virulence of the host/pathogens in spite of the limitations (low bioavailability/high toxicity) associated with this nutrient. Both the host and pathogens manage to overcome these problems by utilizing the iron repository protein nanocages, ferritins, which not only sequester and detoxify the free Fe(II) ions but also decrease the iron solubility gap by synthesizing/encapsulating the Fe(III)-oxyhydroxide biomineral in its central hollow nanocavity. Bacterial pathogens including Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, encode a distinct subclass of ferritins called bacterioferritin (BfrA), which binds heme, the versatile redox cofactor, via coaxial, conserved methionine (M52) residues at its subunit-dimer interfaces. However, the exact role of heme in Mtb BfrA remains yet to be established. Therefore, its coaxial ligands were altered via site-directed mutagenesis, which resulted in both heme-bound (M52C; ∼1 heme per cage) and heme-free (M52H and M52L) variants, indicating the importance of M52 residues as preferential heme binding axial ligands in Mtb BfrA. All these variants formed intact nanocages of similar size and iron-loading ability as that of wild-type (WT) Mtb BfrA. However, the as-isolated heme-bound variants (WT and M52C) exhibited enhanced protein stability and reductive iron mobilization as compared to their heme-free analogues (M52H and M52L). Further, increasing the heme content in BfrA variants by reconstitution not only enhanced the cage stability but also facilitated the iron mobilization, suggesting the role of heme. In contrary, heme altered the ferroxidase activity to a lesser extent despite facilitating the accumulation of the reactive intermediates formed during the course of the reaction. The current study suggests that heme in Mtb BfrA enhances the overall stability of the protein and possibly acts as an intrinsic electron relay station to influence the iron mineral dissolution and thus may be associated with Mtb's pathogenicity.


Assuntos
Proteínas de Bactérias/metabolismo , Grupo dos Citocromos b/metabolismo , Ferritinas/metabolismo , Heme/metabolismo , Mycobacterium tuberculosis/química , Proteínas de Bactérias/química , Grupo dos Citocromos b/química , Ferritinas/química , Heme/química , Ligantes , Estrutura Molecular , Mycobacterium tuberculosis/metabolismo
7.
Science ; 373(6560): 1225-1229, 2021 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-34516790

RESUMO

Understanding the mechanistic coupling of molecular oxygen reduction and proton pumping for adenosine triphosphate synthesis during cellular respiration is the primary goal of research on heme-copper oxidases­the terminal complex in the membrane-bound electron transport chain. Cleavage of the oxygen-oxygen bond by the heme-copper oxidases forms the key intermediate PM, which initiates proton pumping. This intermediate is now experimentally defined by variable-temperature, variable-field magnetic circular dichroism spectroscopy on a previously unobserved excited state feature associated with its heme iron(IV)-oxo center. These data provide evidence that the iron(IV)-oxo in PM is magnetically coupled to both a copper(II) and a cross-linked tyrosyl radical in the active site. These results provide new insight into the oxygen-oxygen bond cleavage and proton-pumping mechanisms of heme-copper oxidases.


Assuntos
Cobre/química , Grupo dos Citocromos b/química , Complexo IV da Cadeia de Transporte de Elétrons/química , Proteínas de Escherichia coli/química , Hemeproteínas/química , Oxirredutases/química , Bombas de Próton/química , Domínio Catalítico
8.
Nat Commun ; 12(1): 5236, 2021 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-34475399

RESUMO

New drugs are urgently needed to combat the global TB epidemic. Targeting simultaneously multiple respiratory enzyme complexes of Mycobacterium tuberculosis is regarded as one of the most effective treatment options to shorten drug administration regimes, and reduce the opportunity for the emergence of drug resistance. During infection and proliferation, the cytochrome bd oxidase plays a crucial role for mycobacterial pathophysiology by maintaining aerobic respiration at limited oxygen concentrations. Here, we present the cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 Å. In conjunction with atomistic molecular dynamics (MD) simulation studies we discovered a previously unknown MK-9-binding site, as well as a unique disulfide bond within the Q-loop domain that defines an inactive conformation of the canonical quinol oxidation site in Actinobacteria. Our detailed insights into the long-sought atomic framework of the cytochrome bd oxidase from M. tuberculosis will form the basis for the design of highly specific drugs to act on this enzyme.


Assuntos
Grupo dos Citocromos b/química , Grupo dos Citocromos d/química , Complexo de Proteínas da Cadeia de Transporte de Elétrons/química , Mycobacterium tuberculosis/enzimologia , Proteínas de Bactérias/química , Sítios de Ligação , Microscopia Crioeletrônica , Simulação de Dinâmica Molecular , Oxirredutases/química , Conformação Proteica , Subunidades Proteicas , Vitamina K 2/análogos & derivados , Vitamina K 2/química
9.
Acta Crystallogr D Struct Biol ; 77(Pt 8): 1077-1083, 2021 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-34342280

RESUMO

The use of cryo-EM continues to expand worldwide and calls for good-quality standard proteins with simple protocols for their production. Here, a straightforward expression and purification protocol is presented that provides an apoferritin, bacterioferritin B (BfrB), from Mycobacterium tuberculosis with high yield and purity. A 2.12 Šresolution cryo-EM structure of BfrB is reported, showing the typical cage-like oligomer constituting of 24 monomers related by 432 symmetry. However, it also contains a unique C-terminal extension (164-181), which loops into the cage region of the shell and provides extra stability to the protein. Part of this region was ambiguous in previous crystal structures but could be built within the cryo-EM map. These findings and this protocol could serve the growing cryo-EM community in characterizing and pushing the limits of their electron microscopes and workflows.


Assuntos
Ferritinas/química , Mycobacterium tuberculosis/metabolismo , Apoferritinas/química , Apoferritinas/ultraestrutura , Proteínas de Bactérias/química , Proteínas de Bactérias/ultraestrutura , Microscopia Crioeletrônica , Grupo dos Citocromos b/química , Grupo dos Citocromos b/ultraestrutura , Ferritinas/ultraestrutura , Conformação Proteica
10.
Proc Natl Acad Sci U S A ; 118(34)2021 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-34417297

RESUMO

Two independent structures of the proton-pumping, respiratory cytochrome bo3 ubiquinol oxidase (cyt bo3 ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme b, heme o3 , and CuB), the redox-active cross-linked histidine-tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome c oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75I and R71I In both structures, residue H98I occupies two conformations. In conformation 1, H98I forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98I has flipped to form a hydrogen bond with E14I at the N-terminal end of TM0. We propose that H98I dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98I.


Assuntos
Grupo dos Citocromos b/química , Grupo dos Citocromos b/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Heme/metabolismo , Fosfolipídeos/metabolismo , Bombas de Próton , Ubiquinona/metabolismo , Sítios de Ligação , Microscopia Crioeletrônica , Heme/química , Oxirredução , Conformação Proteica
11.
Nat Commun ; 12(1): 4621, 2021 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-34330928

RESUMO

Cytochromes bd are ubiquitous amongst prokaryotes including many human-pathogenic bacteria. Such complexes are targets for the development of antimicrobial drugs. However, an understanding of the relationship between the structure and functional mechanisms of these oxidases is incomplete. Here, we have determined the 2.8 Å structure of Mycobacterium smegmatis cytochrome bd by single-particle cryo-electron microscopy. This bd oxidase consists of two subunits CydA and CydB, that adopt a pseudo two-fold symmetrical arrangement. The structural topology of its Q-loop domain, whose function is to bind the substrate, quinol, is significantly different compared to the C-terminal region reported for cytochromes bd from Geobacillus thermodenitrificans (G. th) and Escherichia coli (E. coli). In addition, we have identified two potential oxygen access channels in the structure and shown that similar tunnels also exist in G. th and E. coli cytochromes bd. This study provides insights to develop a framework for the rational design of antituberculosis compounds that block the oxygen access channels of this oxidase.


Assuntos
Proteínas de Bactérias/ultraestrutura , Microscopia Crioeletrônica/métodos , Grupo dos Citocromos b/ultraestrutura , Complexo de Proteínas da Cadeia de Transporte de Elétrons/ultraestrutura , Mycobacterium smegmatis/enzimologia , Oxirredutases/ultraestrutura , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Grupo dos Citocromos b/química , Grupo dos Citocromos b/metabolismo , Transporte de Elétrons , Complexo de Proteínas da Cadeia de Transporte de Elétrons/química , Complexo de Proteínas da Cadeia de Transporte de Elétrons/metabolismo , Heme/química , Heme/metabolismo , Modelos Moleculares , Mycobacterium smegmatis/genética , Oxirredutases/química , Oxirredutases/metabolismo , Oxigênio/metabolismo , Conformação Proteica , Subunidades Proteicas/química , Subunidades Proteicas/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/ultraestrutura , Especificidade por Substrato
12.
Angew Chem Int Ed Engl ; 60(15): 8361-8369, 2021 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-33482043

RESUMO

Both O2 and H2 O2 can oxidize iron at the ferroxidase center (FC) of Escherichia coli bacterioferritin (EcBfr) but mechanistic details of the two reactions need clarification. UV/Vis, EPR, and Mössbauer spectroscopies have been used to follow the reactions when apo-EcBfr, pre-loaded anaerobically with Fe2+ , was exposed to O2 or H2 O2 . We show that O2 binds di-Fe2+ FC reversibly, two Fe2+ ions are oxidized in concert and a H2 O2 molecule is formed and released to the solution. This peroxide molecule further oxidizes another di-Fe2+ FC, at a rate circa 1000 faster than O2 , ensuring an overall 1:4 stoichiometry of iron oxidation by O2 . Initially formed Fe3+ can further react with H2 O2 (producing protein bound radicals) but relaxes within seconds to an H2 O2 -unreactive di-Fe3+ form. The data obtained suggest that the primary role of EcBfr in vivo may be to detoxify H2 O2 rather than sequester iron.


Assuntos
Proteínas de Bactérias/metabolismo , Ceruloplasmina/metabolismo , Grupo dos Citocromos b/metabolismo , Escherichia coli/química , Ferritinas/metabolismo , Peróxido de Hidrogênio/metabolismo , Ferro/metabolismo , Oxigênio/metabolismo , Proteínas de Bactérias/química , Ceruloplasmina/química , Grupo dos Citocromos b/química , Escherichia coli/metabolismo , Ferritinas/química , Peróxido de Hidrogênio/química , Ferro/química , Modelos Moleculares , Oxirredução , Oxigênio/química
13.
Angew Chem Int Ed Engl ; 60(15): 8376-8379, 2021 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-33460502

RESUMO

The iron redox cycle in ferritins is not completely understood. Bacterioferritins are distinct from other ferritins in that they contain haem groups. It is acknowledged that the two iron motifs in bacterioferritins, the di-nuclear ferroxidase centre and the haem B group, play key roles in two opposing processes, iron sequestration and iron mobilisation, respectively, and the two redox processes are independent. Herein, we show that in Escherichia coli bacterioferritin, there is an electron transfer pathway from the haem to the ferroxidase centre suggesting a new role(s) haem might play in bacterioferritins.


Assuntos
Proteínas de Bactérias/metabolismo , Ceruloplasmina/metabolismo , Grupo dos Citocromos b/metabolismo , Ferritinas/metabolismo , Heme/metabolismo , Proteínas de Bactérias/química , Ceruloplasmina/química , Grupo dos Citocromos b/química , Transporte de Elétrons , Escherichia coli/química , Escherichia coli/metabolismo , Ferritinas/química , Heme/química
14.
Antioxid Redox Signal ; 34(16): 1280-1318, 2021 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-32924537

RESUMO

Significance: Cytochrome bd is a ubiquinol:oxygen oxidoreductase of many prokaryotic respiratory chains with a unique structure and functional characteristics. Its primary role is to couple the reduction of molecular oxygen, even at submicromolar concentrations, to water with the generation of a proton motive force used for adenosine triphosphate production. Cytochrome bd is found in many bacterial pathogens and, surprisingly, in bacteria formally denoted as anaerobes. It endows bacteria with resistance to various stressors and is a potential drug target. Recent Advances: We summarize recent advances in the biochemistry, structure, and physiological functions of cytochrome bd in the light of exciting new three-dimensional structures of the oxidase. The newly discovered roles of cytochrome bd in contributing to bacterial protection against hydrogen peroxide, nitric oxide, peroxynitrite, and hydrogen sulfide are assessed. Critical Issues: Fundamental questions remain regarding the precise delineation of electron flow within this multihaem oxidase and how the extraordinarily high affinity for oxygen is accomplished, while endowing bacteria with resistance to other small ligands. Future Directions: It is clear that cytochrome bd is unique in its ability to confer resistance to toxic small molecules, a property that is significant for understanding the propensity of pathogens to possess this oxidase. Since cytochrome bd is a uniquely bacterial enzyme, future research should focus on harnessing fundamental knowledge of its structure and function to the development of novel and effective antibacterial agents.


Assuntos
Bactérias/crescimento & desenvolvimento , Grupo dos Citocromos b/química , Grupo dos Citocromos b/metabolismo , Grupo dos Citocromos d/química , Grupo dos Citocromos d/metabolismo , Bactérias/enzimologia , Bactérias/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Grupo dos Citocromos b/genética , Grupo dos Citocromos d/genética , Farmacorresistência Bacteriana , Regulação Bacteriana da Expressão Gênica , Modelos Moleculares , Família Multigênica , Conformação Proteica , Estresse Fisiológico
15.
J Am Chem Soc ; 142(49): 20640-20650, 2020 12 09.
Artigo em Inglês | MEDLINE | ID: mdl-33252237

RESUMO

Controlling the assembly and disassembly of nanoscale protein cages for the capture and internalization of protein or non-proteinaceous components is fundamentally important to a diverse range of bionanotechnological applications. Here, we study the reversible, pressure-induced dissociation of a natural protein nanocage, E. coli bacterioferritin (Bfr), using synchrotron radiation small-angle X-ray scattering (SAXS) and circular dichroism (CD). We demonstrate that hydrostatic pressures of 450 MPa are sufficient to completely dissociate the Bfr 24-mer into protein dimers, and the reversibility and kinetics of the reassembly process can be controlled by selecting appropriate buffer conditions. We also demonstrate that the heme B prosthetic group present at the subunit dimer interface influences the stability and pressure lability of the cage, despite its location being discrete from the interdimer interface that is key to cage assembly. This indicates a major cage-stabilizing role for heme within this family of ferritins.


Assuntos
Proteínas de Bactérias/metabolismo , Grupo dos Citocromos b/metabolismo , Escherichia coli/metabolismo , Ferritinas/metabolismo , Proteínas de Bactérias/química , Dicroísmo Circular , Grupo dos Citocromos b/química , Dimerização , Ferritinas/química , Pressão Hidrostática , Cinética , Espalhamento a Baixo Ângulo , Termodinâmica , Difração de Raios X
16.
J Inorg Biochem ; 211: 111209, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32818710

RESUMO

We have analyzed the early stages of unfolding of cytochromes c-b562 (PDB ID: 2BC5) and Rd apo b562 (PDB ID: 1YYJ). Our geometrical approach proceeds from an analysis of the crystal structure reported for each protein. We quantify, residue-by-residue and region-by-region, the spatial and angular changes in the structure as the protein denatures, and quantify differences that result from the seven residues that differ in the two proteins. Using two independent analyses, one based on spatial metrics and the second on angular metrics, we establish the order of unfolding of the five helices in cyt c-b562 and the four helices in the apo protein. For the two helices nearest the N-terminal end of both proteins, the ones in the apo protein unfold first. For the two helices nearest the C-terminal end, the interior helix of the apo protein unfolds first, whereas the terminal helix of the holo protein unfolds first. Excluded-volume effects (repulsive interactions) are minimized in turning regions; the overall range in Δ values is Δ = 36.3 Å3 for cyt c-b562 and Δ = 36.6 Å3 for the apo protein, whereas the span for all 20 amino acids is Δ = 167.7 Å3. As our work indicates that the interior helix of cytochrome c-b562 is the first to fold, we suggest that this helix protects the heme from misligation, consistent with ultrafast folding over a minimally frustrated funneled landscape.


Assuntos
Apoproteínas/química , Grupo dos Citocromos b/química , Citocromos c/química , Proteínas de Escherichia coli/química , Escherichia coli/enzimologia , Heme/química , Cristalografia por Raios X , Cinética , Modelos Moleculares , Dobramento de Proteína
17.
mBio ; 11(3)2020 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-32605991

RESUMO

The integral membrane protein heme A synthase (HAS) catalyzes the biosynthesis of heme A, which is a prerequisite for cellular respiration in a wide range of aerobic organisms. Previous studies have revealed that HAS can form homo-oligomeric complexes, and this oligomerization appears to be evolutionarily conserved among prokaryotes and eukaryotes and is shown to be essential for the biological function of eukaryotic HAS. Despite its importance, little is known about the detailed structural properties of HAS oligomers. Here, we aimed to address this critical issue by analyzing the oligomeric state of HAS from Aquifex aeolicus (AaHAS) using a combination of techniques, including size exclusion chromatography coupled with multiangle light scattering (SEC-MALS), cross-linking, laser-induced liquid bead ion desorption mass spectrometry (LILBID-MS), and single-particle electron cryomicroscopy (cryo-EM). Our results show that HAS forms a thermostable trimeric complex. A cryo-EM density map provides information on the oligomerization interface of the AaHAS trimer. These results provide structural insights into HAS multimerization and expand our knowledge of this important enzyme.IMPORTANCE Heme A is a vital redox cofactor unique for the terminal cytochrome c oxidase in mitochondria and many microorganisms. It plays a key role in oxygen reduction by serving as an electron carrier and as the oxygen-binding site. Heme A is synthesized from heme O by an integral membrane protein, heme A synthase (HAS). Defects in HAS impair cellular respiration and have been linked to various human diseases, e.g., fatal infantile hypertrophic cardiomyopathy and Leigh syndrome. HAS exists as a stable oligomeric complex, and studies have shown that oligomerization of eukaryotic HAS is necessary for its proper function. However, the molecular architecture of the HAS oligomeric complex has remained uncharacterized. The present study shows that HAS forms trimers and reveals how the oligomeric arrangement contributes to the complex stability and flexibility, enabling HAS to perform its catalytic function effectively. This work provides the basic understanding for future studies on heme A biosynthesis.


Assuntos
Proteínas de Bactérias/química , Grupo dos Citocromos b/química , Proteínas de Membrana/química , Aquifex/enzimologia , Proteínas de Bactérias/isolamento & purificação , Grupo dos Citocromos b/isolamento & purificação , Heme/análogos & derivados , Heme/biossíntese , Proteínas de Membrana/isolamento & purificação , Modelos Moleculares , Oxigênio/metabolismo , Multimerização Proteica
18.
Sci Rep ; 10(1): 11669, 2020 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-32669569

RESUMO

G-protein-coupled receptors (GPCRs)-the largest family of cell-surface membrane proteins-mediate the intracellular signal transduction of many external ligands. Thus, GPCRs have become important drug targets. X-ray crystal structures of GPCRs are very useful for structure-based drug design (SBDD). Herein, we produced a new antibody (SRP2070) targeting the thermostabilised apocytochrome b562 from Escherichia coli M7W/H102I/R106L (BRIL). We found that a fragment of this antibody (SRP2070Fab) facilitated the crystallisation of the BRIL-tagged, ligand bound GPCRs, 5HT1B and AT2R. Furthermore, the electron densities of the ligands were resolved, suggesting that SPR2070Fab is versatile and adaptable for GPCR SBDD. We anticipate that this new tool will significantly accelerate structure determination of other GPCRs and the design of small molecular drugs targeting them.


Assuntos
Anticorpos Monoclonais/química , Grupo dos Citocromos b/química , Proteínas de Escherichia coli/química , Fragmentos Fab das Imunoglobulinas/química , Receptor Tipo 2 de Angiotensina/química , Receptor 5-HT1B de Serotonina/química , Proteínas Recombinantes de Fusão/química , Sequência de Aminoácidos , Angiotensina II/química , Angiotensina II/metabolismo , Animais , Anticorpos Monoclonais/genética , Anticorpos Monoclonais/isolamento & purificação , Anticorpos Monoclonais/metabolismo , Baculoviridae/genética , Baculoviridae/metabolismo , Sítios de Ligação , Clonagem Molecular , Cristalografia por Raios X , Grupo dos Citocromos b/genética , Grupo dos Citocromos b/metabolismo , Ergotamina/química , Ergotamina/metabolismo , Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Humanos , Fragmentos Fab das Imunoglobulinas/genética , Fragmentos Fab das Imunoglobulinas/isolamento & purificação , Fragmentos Fab das Imunoglobulinas/metabolismo , Camundongos , Modelos Moleculares , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Receptor Tipo 2 de Angiotensina/genética , Receptor Tipo 2 de Angiotensina/metabolismo , Receptor 5-HT1B de Serotonina/genética , Receptor 5-HT1B de Serotonina/metabolismo , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Células Sf9 , Spodoptera
19.
Proc Natl Acad Sci U S A ; 117(26): 15006-15017, 2020 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-32554497

RESUMO

Cytochrome bo3 ubiquinol oxidase is a transmembrane protein, which oxidizes ubiquinone and reduces oxygen, while pumping protons. Apart from its combination with F1Fo-ATPase to assemble a minimal ATP regeneration module, the utility of the proton pump can be extended to other applications in the context of synthetic cells such as transport, signaling, and control of enzymatic reactions. In parallel, polymers have been speculated to be phospholipid mimics with respect to their ability to self-assemble in compartments with increased stability. However, their usability as interfaces for complex membrane proteins has remained questionable. In the present work, we optimized a fusion/electroformation approach to reconstitute bo3 oxidase in giant unilamellar vesicles made of PDMS-g-PEO and/or phosphatidylcholine (PC). This enabled optical access, while microfluidic trapping allowed for online analysis of individual vesicles. The tight polymer membranes and the inward oriented enzyme caused 1 pH unit difference in 30 min, with an initial rate of 0.35 pH·min-1 To understand the interplay in these composite systems, we studied the relevant mechanical and rheological membrane properties. Remarkably, the proton permeability of polymer/lipid hybrids decreased after protein insertion, while the latter also led to a 20% increase of the polymer diffusion coefficient in polymersomes. In addition, PDMS-g-PEO increased the activity lifetime and the resistance to free radicals. These advantageous properties may open diverse applications, ranging from cell-free biotechnology to biomedicine. Furthermore, the presented study serves as a comprehensive road map for studying the interactions between membrane proteins and synthetic membranes, which will be fundamental for the successful engineering of such hybrid systems.


Assuntos
Membrana Celular/enzimologia , Grupo dos Citocromos b/química , Proteínas de Escherichia coli/química , Escherichia coli/enzimologia , Membrana Celular/química , Membrana Celular/genética , Grupo dos Citocromos b/genética , Grupo dos Citocromos b/metabolismo , Transporte de Elétrons , Escherichia coli/química , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Fosfatidilcolinas/metabolismo , Polímeros/química , Prótons
20.
Biochim Biophys Acta Bioenerg ; 1861(10): 148239, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-32531221

RESUMO

Cytochrome c Oxidase (CcO) is the terminal electron acceptor in aerobic respiratory chain, reducing O2 to water. The released free energy is stored by pumping protons through the protein, maintaining the transmembrane electrochemical gradient. Protons are held transiently in a proton loading site (PLS) that binds and releases protons driven by the electron transfer reaction cycle. Multi-Conformation Continuum Electrostatics (MCCE) was applied to crystal structures and Molecular Dynamics snapshots of the B-type Thermus thermophilus CcO. Six residues are identified as the PLS, binding and releasing protons as the charges on heme b and the binuclear center are changed: the heme a3 propionic acids, Asp287, Asp372, His376 and Glu126B. The unloaded state has one proton and the loaded state two protons on these six residues. Different input structures, modifying the PLS conformation, show different proton distributions and result in different proton pumping behaviors. One loaded and one unloaded protonation states have the loaded/unloaded states close in energy so the PLS binds and releases a proton through the reaction cycle. The alternative proton distributions have state energies too far apart to be shifted by the electron transfers so are locked in loaded or unloaded states. Here the protein can use active states to load and unload protons, but has nearby trapped states, which stabilize PLS protonation state, providing new ideas about the CcO proton pumping mechanism. The distance between the PLS residues Asp287 and His376 correlates with the energy difference between loaded and unloaded states.


Assuntos
Grupo dos Citocromos b/metabolismo , Complexo IV da Cadeia de Transporte de Elétrons/metabolismo , Prótons , Grupo dos Citocromos b/química , Complexo IV da Cadeia de Transporte de Elétrons/química , Simulação de Dinâmica Molecular , Conformação Proteica , Thermus thermophilus/enzimologia
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