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1.
bioRxiv ; 2024 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-38915634

RESUMO

Single-stranded DNA bacteriophages of the Microviridae family are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut microbiome, where their diversity has been linked to various chronic health disorders. Despite the clear importance of microviruses, little is known about the molecular mechanism of host infection. Here, we have characterized an exceptionally large microvirus, Ebor, and provide crucial insights into long-standing mechanistic questions. Cryogenic electron microscopy of Ebor revealed a capsid with trimeric protrusions that recognise lipopolysaccharides on the host surface. Cryogenic electron tomography of the host cell colonized with virus particles demonstrated that the virus initially attaches to the cell via five such protrusions, located at the corners of a single pentamer. This interaction triggers a stargate mechanism of capsid opening along the 5-fold symmetry axis, enabling delivery of the virus genome. Despite variations in specific virus-host interactions among different Microviridae family viruses, structural data indicate that the stargate mechanism of infection is universally employed by all members of the family. Startlingly, our data reveal a mechanistic link for the opening of relatively small capsids made out of a single jelly-roll fold with the structurally unrelated giant viruses.

2.
Int J Biol Macromol ; 252: 126345, 2023 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-37619685

RESUMO

Low-density lipoprotein (LDL) plays a crucial role in cholesterol metabolism. Responsible for cholesterol transport from the liver to the organs, LDL accumulation in the arteries is a primary cause of cardiovascular diseases, such as atherosclerosis. This work focuses on the fundamental question of the LDL molecular structure, as well as the topology and molecular motions of apolipoprotein B-100 (apo B-100), which is addressed by single-particle cryo-electron microscopy (cryo-EM) and high-speed atomic force microscopy (HS-AFM). Our results suggest a revised model of the LDL core organization with respect to the cholesterol ester (CE) arrangement. In addition, a high-density region close to the flattened poles could be identified, likely enriched in free cholesterol. The most remarkable new details are two protrusions on the LDL surface, attributed to the protein apo B-100. HS-AFM adds the dimension of time and reveals for the first time a highly dynamic direct description of LDL, where we could follow large domain fluctuations of the protrusions in real time. To tackle the inherent flexibility and heterogeneity of LDL, the cryo-EM maps are further assessed by 3D variability analysis. Our study gives a detailed explanation how to approach the intrinsic flexibility of a complex system comprising lipids and protein.


Assuntos
Colesterol , Lipoproteínas LDL , Lipoproteínas LDL/metabolismo , Microscopia Crioeletrônica , Apolipoproteína B-100 , Microscopia de Força Atômica/métodos
3.
Structure ; 31(4): 455-463.e4, 2023 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-36841236

RESUMO

Conjugative DNA transfer is a major factor in the dissemination of antibiotic resistance and virulence genes. In the Gram-positive pathogen Clostridium perfringens, the majority of conjugative plasmids share the conserved tcp locus that governs the assembly of the transfer system. Here, we describe multiple structures of the coupling protein TcpA, an essential ATPase that is suggested to provide the mechanical force to propel the DNA through the transfer apparatus. The structures of TcpA in the presence and absence of nucleotides revealed conformational rearrangements and highlight a crucial role for the unstructured C terminus. Our findings reveal that TcpA shares most structural similarity with the FtsK DNA translocase, a central component of the bacterial cell division machinery. Our structural data suggest that conjugation in C. perfringens may have evolved from the bacterial chromosome segregation system and, accordingly, suggest the possibility that double-stranded DNA is transferred through the Tcp conjugation apparatus.


Assuntos
Clostridium perfringens , DNA , Clostridium perfringens/genética , Clostridium perfringens/metabolismo , Plasmídeos/genética , DNA/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo
4.
Nat Rev Phys ; 5(2): 74-75, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36275781

RESUMO

Africa is the only habitable continent that is not yet host to a light source - an important tool across disciplines. Scientists from the Executive Committee of the African Light Source Foundation discuss work towards building an advanced light source in Africa, and what remains to be done.

5.
Biol Open ; 11(8)2022 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-35972051

RESUMO

Structural biology is an essential tool for understanding the molecular basis of diseases, which can guide the rational design of new drugs, vaccines, and the optimisation of existing medicines. However, most African countries do not conduct structural biology research due to limited resources, lack of trained persons, and an exodus of skilled scientists. The most urgent requirement is to build on the emerging centres in Africa - some well-established, others growing. This can be achieved through workshops that improve networking, grow skills, and develop mechanisms for access to light source beamlines for defining X-ray structures across the continent. These would encourage the growth of structural biology, which is central to understanding biological functions and developing new antimicrobials and other drugs. In this light, a hands-on training workshop in structural biology series 4 was organised by BioStruct-Africa and the Malaria Research and Training Center (MRTC) in Bamako, Mali, to help bridge this gap. The workshop was hosted by MRTC from the 25th to 28th of April 2022. Through a series of lectures and practicals, the workshop enlightened the participants on how structural biology can be utilised to find solutions to the prevalent diseases in Africa. The short training gave them an overview of target selection, protein production and purification, structural determination techniques, and analysis in combination with high-throughput, structure-guided, fragment-based drug design.


Assuntos
Biologia , Desenvolvimento Sustentável , África , Humanos
6.
Soft Matter ; 18(35): 6529-6537, 2022 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-35894255

RESUMO

In this work, the inclusion complexes of alkyl ethoxy carboxylates with α-cyclodextrin (αCD) and ß-cyclodextrin (ßCD) were investigated. The thermodynamics of the complexation process was probed by isothermal titration calorimetry (ITC) and volumetry as a function of the degree of ionization of the surfactant. The complexation process was shown to be an enthalpically driven pH-independent process. For both types of cyclodextrins, the complexes were found to spontaneously self-assemble into highly-ordered supramolecular aggregates probed by small-angle neutron scattering and electron and optical microscopy. Herein, we report the formation of thin platelets for nonionized surfactant systems and equally spaced multilayered hollow cylinders for ionized systems in a hierarchical self-assembly process. In addition, the analysis allowed unveiling the effect of the number of ethylene oxides in the surfactants and the CD cavity size on the morphology of the aggregates. Finally, this study also highlights the importance of examining the tuning parameters' influence on the short and long-range interactions involved in the control of the assembly process.

7.
mBio ; 13(4): e0135622, 2022 08 30.
Artigo em Inglês | MEDLINE | ID: mdl-35726914

RESUMO

Plasmids that encode the same replication machinery are generally unable to coexist in the same bacterial cell. However, Clostridium perfringens strains often carry multiple conjugative toxin or antibiotic resistance plasmids that are closely related and encode similar Rep proteins. In many bacteria, plasmid partitioning upon cell division involves a ParMRC system; in C. perfringens plasmids, there are approximately 10 different ParMRC families, with significant differences in amino acid sequences between each ParM family (15% to 54% identity). Since plasmids carrying genes belonging to the same ParMRC family are not observed in the same strain, these families appear to represent the basis for plasmid compatibility in C. perfringens. To understand this process, we examined the key recognition steps between ParR DNA-binding proteins and their parC binding sites. The ParR proteins bound to sequences within a parC site from the same ParMRC family but could not interact with a parC site from a different ParMRC family. These data provide evidence that compatibility of the conjugative toxin plasmids of C. perfringens is mediated by their parMRC-like partitioning systems. This process provides a selective advantage by enabling the host bacterium to maintain separate plasmids that encode toxins that are specific for different host targets. IMPORTANCE Toxins produced by the Gram-positive pathogen Clostridium perfringens are primarily encoded by genes found on different conjugative plasmids. These plasmids encode highly similar replication proteins and therefore should be incompatible, but they are often found to coexist within the same isolate. In this study, we showed that a series of phylogenetically related ParMRC plasmid partitioning systems, structures that are normally responsible for ensuring that plasmids segregate correctly at cell division, dictate which toxin plasmid combinations can coexist within the same bacterial cell. We dissected the recognition steps between the DNA-binding ParMRC component, ParR, and the plasmid-derived centromere, parC. Our data suggested a mechanism by which plasmids encoding ParMRC systems from the same family are incompatible, whereas plasmids encoding ParMRC systems from distinct families are compatible. This work provides insight into how these cells can maintain multiple highly similar toxin plasmids, which is a critical first step in understanding how to limit the disease-causing potential of C. perfringens.


Assuntos
Bactérias , Clostridium perfringens , Bactérias/genética , Clostridium perfringens/genética , Resistência Microbiana a Medicamentos , Humanos , Plasmídeos/genética
8.
FEBS J ; 289(10): 2959-2970, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-34921499

RESUMO

The ATP-binding cassette transporter MsbA is a lipid flippase, translocating lipid A, glycolipids, and lipopolysaccharides from the inner to the outer leaflet of the inner membrane of Gram-negative bacteria. It has been used as a model system for time-resolved structural studies as several MsbA structures in different states and reconstitution systems (detergent/nanodiscs/peptidiscs) are available. However, due to the limited resolution of the available structures, detailed structural information on the bound nucleotides has remained elusive. Here, we have reconstituted MsbA in saposin A-lipoprotein nanoparticles (Salipro) and determined the structure of ADP-vanadate-bound MsbA by single-particle cryo-electron microscopy to 3.5 Å resolution. This procedure has resulted in significantly improved resolution and enabled us to model all side chains and visualise detailed ADP-vanadate interactions in the nucleotide-binding domains. The approach may be applicable to other dynamic membrane proteins.


Assuntos
Nanopartículas , Saposinas , Difosfato de Adenosina , Proteínas de Bactérias/metabolismo , Microscopia Crioeletrônica/métodos , Lipossomos , Nanopartículas/química , Saposinas/química , Vanadatos/química
9.
Nucleic Acids Res ; 49(9): 5177-5188, 2021 05 21.
Artigo em Inglês | MEDLINE | ID: mdl-33939800

RESUMO

In Staphylococcus aureus, most multiresistance plasmids lack conjugation or mobilization genes for horizontal transfer. However, most are mobilizable due to carriage of origin-of-transfer (oriT) sequences mimicking those of conjugative plasmids related to pWBG749. pWBG749-family plasmids have diverged to carry five distinct oriT subtypes and non-conjugative plasmids have been identified that contain mimics of each. The relaxasome accessory factor SmpO, encoded by each conjugative plasmid, determines specificity for its cognate oriT. Here we characterized the binding of SmpO proteins to each oriT. SmpO proteins predominantly formed tetramers in solution and bound 5'-GNNNNC-3' sites within each oriT. Four of the five SmpO proteins specifically bound their cognate oriT. An F7K substitution in pWBG749 SmpO switched oriT-binding specificity in vitro. In vivo, the F7K substitution reduced but did not abolish self-transfer of pWBG749. Notably, the substitution broadened the oriT subtypes that were mobilized. Thus, this substitution represents a potential evolutionary intermediate with promiscuous DNA-binding specificity that could facilitate a switch between oriT specificities. Phylogenetic analysis suggests pWBG749-family plasmids have switched oriT specificity more than once during evolution. We hypothesize the convergent evolution of oriT specificity in distinct branches of the pWBG749-family phylogeny reflects indirect selection pressure to mobilize plasmids carrying non-cognate oriT-mimics.


Assuntos
Plasmídeos/genética , Staphylococcus aureus/genética , Substituição de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Conjugação Genética , Pegada de DNA , Evolução Molecular , Filogenia , Plasmídeos/classificação
10.
J Synchrotron Radiat ; 26(Pt 5): 1843-1850, 2019 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-31490179

RESUMO

Being able to visualize biology at the molecular level is essential for our understanding of the world. A structural biology approach reveals the molecular basis of disease processes and can guide the design of new drugs as well as aid in the optimization of existing medicines. However, due to the lack of a synchrotron light source, adequate infrastructure, skilled persons and incentives for scientists in addition to limited financial support, the majority of countries across the African continent do not conduct structural biology research. Nevertheless, with technological advances such as robotic protein crystallization and remote data collection capabilities offered by many synchrotron light sources, X-ray crystallography is now potentially accessible to Africa-based scientists. This leap in technology led to the establishment in 2017 of BioStruct-Africa, a non-profit organization (Swedish corporate ID: 802509-6689) whose core aim is capacity building for African students and researchers in the field of structural biology with a focus on prevalent diseases in the African continent. The team is mainly composed of, but not limited to, a group of structural biologists from the African diaspora. The members of BioStruct-Africa have taken up the mantle to serve as a catalyst in order to facilitate the information and technology transfer to those with the greatest desire and need within Africa. BioStruct-Africa achieves this by organizing workshops onsite at our partner universities and institutions based in Africa, followed by post-hoc online mentoring of participants to ensure sustainable capacity building. The workshops provide a theoretical background on protein crystallography, hands-on practical experience in protein crystallization, crystal harvesting and cryo-cooling, live remote data collection on a synchrotron beamline, but most importantly the links to drive further collaboration through research. Capacity building for Africa-based researchers in structural biology is crucial to win the fight against the neglected tropical diseases, e.g. ascariasis, hookworm, trichuriasis, lymphatic filariasis, active trachoma, loiasis, yellow fever, leprosy, rabies, sleeping sickness, onchocerciasis, schistosomiasis, etc., that constitute significant health, social and economic burdens to the continent. BioStruct-Africa aims to build local and national expertise that will have direct benefits for healthcare within the continent.


Assuntos
Tutoria , Biologia Molecular , Transferência de Tecnologia , África , Fortalecimento Institucional , Humanos , Poder Psicológico
11.
Glob Health Action ; 12(sup1): 1815272, 2019 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-32909519

RESUMO

BACKGROUND: The majority of existing studies aimed at investigating the incidence and prevalence of multidrug-resistance by bacteria have been performed in healthcare settings. Relatively few studies have been conducted in community settings, but these have consistently shown a high prevalence of multidrug-resistant bacteria in low- and middle-income countries (LMICs). OBJECTIVES: To provide an appraisal of the evidence on the high prevalence of multidrug-, extensive drug-, and pandrug-resistance in commensal Escherichia coli isolates from human sources in community settings in LMICs. METHODS: Using the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines, PubMed, EMBASE, MEDLINE, Web of Science, CINAHL, and Cochrane Library databases were systematically searched with the search string: 'Enterobacteriaceae', OR 'E. coli', OR 'Escherichia coli', AND 'antibiotic resistance', OR 'antimicrobial resistance', OR 'drug-resistance', AND 'prevalence', OR 'incidence', OR 'morbidity', OR 'odds ratio', OR 'risk ratio', OR 'confidence interval', OR 'p-value', OR 'rate'. Data were extracted and proportional meta-analysis was performed using the Freeman-Tukey transformation random effect model. RESULTS: The prevalence of multidrug-, extensive drug- and pandrug-resistance were extracted from articles that met our inclusion criteria and pooled together after a systematic screening of 9,369 items. The prevalence of multidrug-resistance was 28% of 14,336 total cases of isolates tested, 95% CI: 23-32. Extensive drug-resistance was 24% of 8,686 total cases of isolates tested, 95% CI: 14-36. Lastly, pandrug-resistance was 5% of 5,670 total cases of isolates tested, 95% CI: 3-8. CONCLUSION: This paper provides an appraisal of the evidence on the high prevalence of multidrug-, extensive drug- and pandrug-resistance by commensal E. coli in community settings in LMICs. Our results call for greater effort to be placed at the community level in the design of new and improved public health policies to counter the global threat of antibiotic-resistant infections and bacteria.


Assuntos
Farmacorresistência Bacteriana Múltipla , Escherichia coli/isolamento & purificação , Países em Desenvolvimento , Escherichia coli/efeitos dos fármacos , Humanos , Incidência , Prevalência
12.
Nat Commun ; 9(1): 3732, 2018 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-30213934

RESUMO

Conjugation is fundamental for the acquisition of new genetic traits and the development of antibiotic resistance in pathogenic organisms. Here, we show that a hypothetical Clostridium perfringens protein, TcpK, which is encoded by the tetracycline resistance plasmid pCW3, is essential for efficient conjugative DNA transfer. Our studies reveal that TcpK is a member of the winged helix-turn-helix (wHTH) transcription factor superfamily and that it forms a dimer in solution. Furthermore, TcpK specifically binds to a nine-nucleotide sequence that is present as tandem repeats within the pCW3 origin of transfer (oriT). The X-ray crystal structure of the TcpK-TcpK box complex reveals a binding mode centered on and around the ß-wing, which is different from what has been previously shown for other wHTH proteins. Structure-guided mutagenesis experiments validate the specific interaction between TcpK and the DNA molecule. Additional studies highlight that the TcpK dimer is important for specific DNA binding.


Assuntos
Proteínas de Bactérias/química , Cristalografia por Raios X , DNA Bacteriano/química , Resistência Microbiana a Medicamentos/genética , Plasmídeos/química , Proteínas de Bactérias/genética , Clostridium perfringens , Conjugação Genética , DNA Bacteriano/genética , Bases de Dados de Proteínas , Escherichia coli , Teste de Complementação Genética , Mutagênese , Nucleotídeos/química , Plasmídeos/genética , Ligação Proteica , Conformação Proteica , Multimerização Proteica , Proteínas Recombinantes/química , Ressonância de Plasmônio de Superfície , Tetraciclina/farmacologia , Resistência a Tetraciclina/genética
13.
Nat Commun ; 9(1): 2223, 2018 06 08.
Artigo em Inglês | MEDLINE | ID: mdl-29884801

RESUMO

Macrophage migration inhibitory factor (MIF) exerts multiple effects on immune cells, as well as having functions outside the immune system. MIF can promote inflammation through the induction of other cytokines, including TNF, IL-6, and IL-1 family cytokines. Here, we show that inhibition of MIF regulates the release of IL-1α, IL-1ß, and IL-18, not by affecting transcription or translation of these cytokines, but via activation of the NLRP3 inflammasome. MIF is required for the interaction between NLRP3 and the intermediate filament protein vimentin, which is critical for NLRP3 activation. Further, we demonstrate that MIF interacts with NLRP3, indicating a role for MIF in inflammasome activation independent of its role as a cytokine. These data advance our understanding of how MIF regulates inflammation and identify it as a factor critical for NLRP3 inflammasome activation.


Assuntos
Inflamassomos/metabolismo , Fatores Inibidores da Migração de Macrófagos/metabolismo , Macrófagos/metabolismo , Proteína 3 que Contém Domínio de Pirina da Família NLR/metabolismo , Animais , Células Cultivadas , Citocinas/metabolismo , Feminino , Humanos , Proteínas de Filamentos Intermediários/metabolismo , Fatores Inibidores da Migração de Macrófagos/genética , Masculino , Camundongos Endogâmicos C57BL , Camundongos Knockout , Ligação Proteica , Células THP-1
14.
Ann Cardiol Angeiol (Paris) ; 67(1): 25-31, 2018 Feb.
Artigo em Francês | MEDLINE | ID: mdl-28800856

RESUMO

INTRODUCTION: Ischemic Mitral Regurgitation (IMR) is a serious complication of coronary artery disease and is associated with a poor prognosis. The optimal surgical treatment of IMR involves controversies in its indications and modalities. OBJECTIVES: To determine whether mitral annuloplasty associated with surgical revascularization improved short and mid terms outcomes compared with revascularization alone in patients with IMR. METHODS: Between January 2007 and January 2011, 81 patients operated on Department of Cardiovascular Surgery "B" were included in this study divided into 3 groups. Group 1: 28 patients with IMR had mitral valve surgery associated with surgical revascularization. Group 2: 26 patients with IMR had surgical revascularization without mitral valve surgery. Group 3: 27 patients without IMR had isolated revascularization. Clinical end-points were operative mortality, late mortality, postoperative functional status (NYHA), and the Effective Regurgitant Orifice (ERO) at last follow-up. The mean follow-up was 5 years for groups 1 and 2 and 4 years for group 3. RESULTS: There was no difference between the 3 groups regarding age, sex, cardiovascular risk factors, and extension of coronary artery disease. The Left Ventricle End Diastolic Diameter (LVEDD) and the Left Ventricle Ejection Fraction (LVEF) were slightly different. Late and operative mortality were higher in group 2 compared to groups 1 and 3. Postoperative functional status (NYHA) improved both in groups 1 and 2. In group 1, there was a decrease in ERO. CONCLUSION: Mitral annuloplasty combined to revascularization improves symptoms, postoperative ERO and short- and mid-term survival compared with revascularization alone.


Assuntos
Anuloplastia da Valva Mitral , Insuficiência da Valva Mitral/cirurgia , Isquemia Miocárdica/cirurgia , Revascularização Miocárdica , Adulto , Idoso , Feminino , Seguimentos , Humanos , Masculino , Pessoa de Meia-Idade , Anuloplastia da Valva Mitral/métodos , Insuficiência da Valva Mitral/complicações , Insuficiência da Valva Mitral/mortalidade , Isquemia Miocárdica/etiologia , Isquemia Miocárdica/mortalidade , Revascularização Miocárdica/métodos , Estudos Retrospectivos , Análise de Sobrevida , Resultado do Tratamento
15.
Med Mal Infect ; 47(6): 415-423, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28648613

RESUMO

INTRODUCTION: We performed a transversal study to map resistance of malaria vectors (Anopheles mosquitoes) to insecticides in Niger within the frame of the National Malaria Control Program funded by the World Health Organization (WHO). METHOD: Larvae of Anopheles gambiae s.l were collected from November to December 2013 in seven locations selected on the basis of different patterns of use of insecticides and environment. WHO susceptibility test tubes were used on females Anopheles to detect resistance to insecticides. Eight insecticides were tested. Percentages of knockdown during exposure time to pyrethroids and DDT and mortality after 24hours of observation for all tested insecticides were calculated. PCR and biochemical tests were carried out to identify the species and mechanisms of resistance (Kdr allele frequencies and activity of detoxification enzymes). RESULTS: In all sites, Anopheles gambiae s.l was susceptible to bendiocarb and malathion but resistant to the five pyrethroids and DDT (24-hour mortality rate was <90%). The Kdr mutation was present in the molecular form M of Anopheles gambiae with an average frequency of 58%. Biochemical tests showed the activity of various enzyme families (esterase, oxidase, and glutathione s-transferase). CONCLUSION: This study showed multiple resistance of Anopheles mosquitoes to insecticides in Niger. A rigorous management of this resistance is imperative to preserve the efficacy of pyrethroids as it is the only class of insecticides used for insecticide-treated nets.


Assuntos
Anopheles , Insetos Vetores , Resistência a Inseticidas , Inseticidas , Malária/transmissão , Piretrinas , Animais , Anopheles/enzimologia , Anopheles/genética , Estudos Transversais , Esterases/metabolismo , Feminino , Frequência do Gene , Técnicas de Silenciamento de Genes , Glutationa Transferase/metabolismo , Insetos Vetores/enzimologia , Insetos Vetores/genética , Mosquiteiros Tratados com Inseticida , Malária/epidemiologia , Malária/prevenção & controle , Níger/epidemiologia , Oxirredutases/metabolismo , Fatores de Tempo
16.
Mol Microbiol ; 99(5): 884-96, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26560080

RESUMO

Conjugative transfer of toxin and antibiotic resistance plasmids in Clostridium perfringens is mediated by the tcp conjugation locus. Surprisingly, neither a relaxase gene nor an origin of transfer (oriT) has been identified on these plasmids, which are typified by the 47 kb tetracycline resistance plasmid pCW3. The tcpM gene (previously called intP) encodes a potential tyrosine recombinase that was postulated to be an atypical relaxase. Mutagenesis and complementation studies showed that TcpM was required for wild-type transfer of pCW3 and that a tyrosine residue, Y259, was essential for TcpM activity, which was consistent with the need for a relaxase-mediated hydrophilic attack at the oriT site. Other catalytic residues conserved in tyrosine recombinases were not required for TcpM activity, suggesting that TcpM was not a site-specific recombinase. Mobilization studies led to the identification of the oriT site, which was located in the 391 bp intergenic region upstream of tcpM. The oriT site was localized to a 150 bp region, and gel mobility shift studies showed that TcpM could bind to this region. Based on these studies we postulate that conjugative transfer of pCW3 involves the atypical relaxase TcpM binding to and processing the oriT site to initiate plasmid transfer.


Assuntos
Clostridium perfringens/enzimologia , Clostridium perfringens/genética , Conjugação Genética/fisiologia , DNA Nucleotidiltransferases/genética , DNA Nucleotidiltransferases/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , DNA Intergênico , Resistência Microbiana a Medicamentos , Plasmídeos
17.
J Med Chem ; 58(19): 7707-18, 2015 Oct 08.
Artigo em Inglês | MEDLINE | ID: mdl-26359549

RESUMO

The Grb7 adaptor protein is a therapeutic target for both TNBC and HER2+ breast cancer. A nonphosphorylated cyclic peptide 1 (known as G7-18NATE) inhibits Grb7 via targeting the Grb7-SH2 domain, but requires the presence of phosphate ions for both affinity and specificity. Here we report the discovery of malonate bound in the phosphotyrosine binding pocket of the apo-Grb7-SH2 structure. Based on this, we carried out the rational design and synthesis of two analogues of peptide 1 that incorporate carboxymethylphenylalanine (cmF) and carboxyphenylalanine (cF) as mimics of phosphotyrosine (pY). Binding studies using SPR confirmed that affinity for Grb7-SH2 domain is improved up to 9-fold over peptide 1 under physiological phosphate conditions (KD = 2.1-5.7 µM) and that binding is specific for Grb7-SH2 over closely related domains (low or no detectable binding to Grb2-SH2 and Grb10-SH2). X-ray crystallographic structural analysis of the analogue bearing a cmF moiety in complex with Grb7-SH2 has identified the precise contacts conferred by the pY mimic that underpin this improved molecular interaction. Together this study identifies and characterizes the tightest specific inhibitor of Grb7 to date, representing a significant development toward a new Grb7-targeted therapeutic.


Assuntos
Antineoplásicos/química , Antineoplásicos/farmacologia , Proteína Adaptadora GRB7/antagonistas & inibidores , Peptídeos Cíclicos/química , Fosfotirosina/química , Antineoplásicos/síntese química , Sítios de Ligação , Neoplasias da Mama/tratamento farmacológico , Cristalografia por Raios X , Feminino , Proteína Adaptadora GRB7/metabolismo , Humanos , Malonatos/química , Terapia de Alvo Molecular , Peptídeos Cíclicos/síntese química , Peptidomiméticos , Fosfatos/química , Fosfatos/metabolismo , Conformação Proteica , Domínios de Homologia de src
18.
PLoS One ; 10(4): e0123338, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25923520

RESUMO

Phanta is a reversibly photoswitching chromoprotein (ΦF, 0.003), useful for pcFRET, that was isolated from a mutagenesis screen of the bright green fluorescent eCGP123 (ΦF, 0.8). We have investigated the contribution of substitutions at positions His193, Thr69 and Gln62, individually and in combination, to the optical properties of Phanta. Single amino acid substitutions at position 193 resulted in proteins with very low ΦF, indicating the importance of this position in controlling the fluorescence efficiency of the variant proteins. The substitution Thr69Val in Phanta was important for supressing the formation of a protonated chromophore species observed in some His193 substituted variants, whereas the substitution Gln62Met did not significantly contribute to the useful optical properties of Phanta. X-ray crystal structures for Phanta (2.3 Å), eCGP123T69V (2.0 Å) and eCGP123H193Q (2.2 Å) in their non-photoswitched state were determined, revealing the presence of a cis-coplanar chromophore. We conclude that changes in the hydrogen-bonding network supporting the cis-chromophore, and its contacts with the surrounding protein matrix, are responsible for the low fluorescence emission of eCGP123 variants containing a His193 substitution.


Assuntos
Corantes Fluorescentes/química , Proteínas de Fluorescência Verde/química , Proteínas de Fluorescência Verde/genética , Substituição de Aminoácidos , Cristalografia por Raios X , Escherichia coli/genética , Fluorescência , Corantes Fluorescentes/metabolismo , Ligação de Hidrogênio , Modelos Moleculares , Processos Fotoquímicos , Conformação Proteica
19.
PLoS Biol ; 13(2): e1002049, 2015 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-25654333

RESUMO

Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically characterised. Here we present an 11 Å resolution cryo-electron microscopy (cryo-EM) structure of the two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures of both components (the lipid binding PlyA protein and the pore-forming MACPF component PlyB). These data reveal a 13-fold pore 80 Å in diameter and 100 Å in height, with each subunit comprised of a PlyB molecule atop a membrane bound dimer of PlyA. The resolution of the EM map, together with biophysical and computational experiments, allowed confident assignment of subdomains in a MACPF pore assembly. The major conformational changes in PlyB are a ∼70° opening of the bent and distorted central ß-sheet of the MACPF domain, accompanied by extrusion and refolding of two α-helical regions into transmembrane ß-hairpins (TMH1 and TMH2). We determined the structures of three different disulphide bond-trapped prepore intermediates. Analysis of these data by molecular modelling and flexible fitting allows us to generate a potential trajectory of ß-sheet unbending. The results suggest that MACPF conformational change is triggered through disruption of the interface between a conserved helix-turn-helix motif and the top of TMH2. Following their release we propose that the transmembrane regions assemble into ß-hairpins via top down zippering of backbone hydrogen bonds to form the membrane-inserted ß-barrel. The intermediate structures of the MACPF domain during refolding into the ß-barrel pore establish a structural paradigm for the transition from soluble monomer to pore, which may be conserved across the whole superfamily. The TMH2 region is critical for the release of both TMH clusters, suggesting why this region is targeted by endogenous inhibitors of MACPF function.


Assuntos
Membrana Celular/química , Complexo de Ataque à Membrana do Sistema Complemento/química , Proteínas Fúngicas/química , Proteínas Hemolisinas/química , Pleurotus/química , Proteínas Recombinantes de Fusão/química , Animais , Complexo de Ataque à Membrana do Sistema Complemento/metabolismo , Microscopia Crioeletrônica , Cristalografia por Raios X , Eritrócitos/química , Eritrócitos/citologia , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Expressão Gênica , Proteínas Hemolisinas/genética , Proteínas Hemolisinas/metabolismo , Modelos Moleculares , Ligação Proteica , Dobramento de Proteína , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Ovinos
20.
Proteins ; 83(7): 1225-37, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25287913

RESUMO

In this article, we describe the engineering and X-ray crystal structure of Thermal Green Protein (TGP), an extremely stable, highly soluble, non-aggregating green fluorescent protein. TGP is a soluble variant of the fluorescent protein eCGP123, which despite being highly stable, has proven to be aggregation-prone. The X-ray crystal structure of eCGP123, also determined within the context of this paper, was used to carry out rational surface engineering to improve its solubility, leading to TGP. The approach involved simultaneously eliminating crystal lattice contacts while increasing the overall negative charge of the protein. Despite intentional disruption of lattice contacts and introduction of high entropy glutamate side chains, TGP crystallized readily in a number of different conditions and the X-ray crystal structure of TGP was determined to 1.9 Å resolution. The structural reasons for the enhanced stability of TGP and eCGP123 are discussed. We demonstrate the utility of using TGP as a fusion partner in various assays and significantly, in amyloid assays in which the standard fluorescent protein, EGFP, is undesirable because of aberrant oligomerization.


Assuntos
Proteínas de Fluorescência Verde/química , Engenharia de Proteínas/métodos , Proteínas Recombinantes de Fusão/química , Sequência de Aminoácidos , Amiloide/química , Bioensaio , Clonagem Molecular , Cristalografia por Raios X , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Proteínas de Fluorescência Verde/genética , Proteínas de Fluorescência Verde/metabolismo , Células HEK293 , Temperatura Alta , Humanos , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Modelos Moleculares , Dados de Sequência Molecular , Estabilidade Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Alinhamento de Sequência , Eletricidade Estática
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