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Pesquisa : D12.776.835.725.934.562 [Categoria DeCS]
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[PMID]:28342293
[Au] Autor:Carlson MA; Haddad BG; Weis AJ; Blackwood CS; Shelton CD; Wuerth ME; Walter JD; Spiegel PC
[Ad] Endereço:Department of Chemistry, Western Washington University, Bellingham, WA, USA.
[Ti] Título:Ribosomal protein L7/L12 is required for GTPase translation factors EF-G, RF3, and IF2 to bind in their GTP state to 70S ribosomes.
[So] Source:FEBS J;284(11):1631-1643, 2017 Jun.
[Is] ISSN:1742-4658
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Ribosomal protein L7/L12 is associated with translation initiation, elongation, and termination by the 70S ribosome. The guanosine 5' triphosphate hydrolase (GTPase) activity of elongation factor G (EF-G) requires the presence of L7/L12, which is critical for ribosomal translocation. Here, we have developed new methods for the complete depletion of L7/L12 from Escherichia coli 70S ribosomes to analyze the effect of L7/L12 on the activities of the GTPase factors EF-G, RF3, IF2, and LepA. Upon removal of L7/L12 from ribosomes, the GTPase activities of EF-G, RF3, and IF2 decreased to basal levels, while the activity of LepA decreased marginally. Upon reconstitution of ribosomes with recombinant L12, the GTPase activities of all GTPases returned to full activity. Moreover, ribosome binding assays indicated that EF-G, RF3, and IF2 require L7/L12 for stable binding in the GTP state, and LepA retained > 50% binding. Lastly, an EF-G∆G' truncation mutant possessed ribosome-dependent GTPase activity, which was insensitive to L7/L12. Our results indicate that L7/L12 is required for stable binding of ribosome-dependent GTPases that harbor direct interactions to the L7/L12 C-terminal domains, either through a G' domain (EF-G, RF3) or a unique N-terminal domain (IF2). Furthermore, we hypothesize this interaction is concomitant with counterclockwise ribosomal intersubunit rotation, which is required for translocation, initiation, and post-termination.
[Mh] Termos MeSH primário: Proteínas de Escherichia coli/metabolismo
Proteínas de Escherichia coli/fisiologia
Guanosina Trifosfato/metabolismo
Fator G para Elongação de Peptídeos/metabolismo
Fatores de Terminação de Peptídeos/metabolismo
Fator de Iniciação 2 em Procariotos/metabolismo
Proteínas Ribossômicas/fisiologia
Ribossomos/metabolismo
[Mh] Termos MeSH secundário: Ativação Enzimática
Proteínas de Escherichia coli/genética
Hidrólise
Mutagênese Sítio-Dirigida
Fatores de Iniciação de Peptídeos/metabolismo
Proteínas Recombinantes/metabolismo
Proteínas Ribossômicas/deficiência
Proteínas Ribossômicas/genética
[Pt] Tipo de publicação:EDITORIAL
[Nm] Nome de substância:
0 (Escherichia coli Proteins); 0 (LepA protein, E coli); 0 (Peptide Elongation Factor G); 0 (Peptide Initiation Factors); 0 (Peptide Termination Factors); 0 (Prokaryotic Initiation Factor-2); 0 (Recombinant Proteins); 0 (Ribosomal Proteins); 0 (prfC protein, E coli); 0 (rplL protein, E coli); 86-01-1 (Guanosine Triphosphate)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170918
[Lr] Data última revisão:
170918
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170326
[St] Status:MEDLINE
[do] DOI:10.1111/febs.14067


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[PMID]:27809767
[Au] Autor:Miftahussurur M; Shrestha PK; Subsomwong P; Sharma RP; Yamaoka Y
[Ad] Endereço:Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita, 879-5593, Japan.
[Ti] Título:Emerging Helicobacter pylori levofloxacin resistance and novel genetic mutation in Nepal.
[So] Source:BMC Microbiol;16(1):256, 2016 Nov 04.
[Is] ISSN:1471-2180
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The prevalence of Helicobacter pylori antibiotic susceptibility in the Nepalese strains is untracked. We determined the antibiotic susceptibility for H. pylori and analyzed the presence of genetic mutations associated with antibiotic resistance in Nepalese strains. RESULTS: This study included 146 consecutive patients who underwent gastroduodenal endoscopy in Kathmandu, Nepal. Among 42 isolated H. pylori, there was no resistance to amoxicillin and tetracycline. In contrast, similar with typical South Asian patterns; metronidazole resistance rate in Nepalese strains were extremely high (88.1 %, 37/42). Clarithromycin resistance rate in Nepalese strains were modestly high (21.4 %, 9/42). Most of metronidazole resistant strains had highly distributed rdxA and frxA mutations, but were relative coincidence without a synergistic effect to increase the minimum inhibitory concentration (MIC). Among strains with the high MIC, 63.6 % (7/11) were associated with frameshift mutation at position 18 of frxA with or without rdxA involvement. However, based on next generation sequencing data we found that one strain with the highest MIC value had a novel mutation in the form of amino acid substituted at Ala-212, Gln-382, Ile-485 of dppA and Leu-145, Thr-168, Glu-117, Val-121, Arg-221 in dapF aside from missense mutations in full-length rdxA. Mutations at Asn-87 and/or Asp-91 of the gyrA were predominantly in levofloxacin-resistant strains. The gyrB mutation had steady relationship with the gyrA 87-91 mutations. Although three (44.4 %) and two (22.2 %) of clarithromycin resistant strains had point mutation on A2143G and A2146G, we confirmed the involvement of rpl22 and infB in high MIC strains without an 23SrRNA mutation. CONCLUSIONS: The rates of resistance to clarithromycin, metronidazole and levofloxacin were high in Nepalese strains, indicating that these antibiotics-based triple therapies are not useful as first-line treatment in Nepal. Bismuth or non-bismuth-based quadruple regimens, furazolidone-based triple therapy or rifabutin-based triple therapy may become alternative strategy in Nepal.
[Mh] Termos MeSH primário: Farmacorresistência Bacteriana/efeitos dos fármacos
Farmacorresistência Bacteriana/genética
Infecções por Helicobacter/epidemiologia
Helicobacter pylori/efeitos dos fármacos
Helicobacter pylori/genética
Helicobacter pylori/patogenicidade
Levofloxacino/farmacologia
Mutação
[Mh] Termos MeSH secundário: Adolescente
Adulto
Idoso
Amoxicilina/farmacologia
Antibacterianos/farmacologia
Proteínas de Bactérias/genética
Sequência de Bases
Claritromicina/farmacologia
DNA Girase/genética
DNA Bacteriano/genética
Endoscopia
Feminino
Genes Bacterianos
Infecções por Helicobacter/tratamento farmacológico
Infecções por Helicobacter/microbiologia
Helicobacter pylori/isolamento & purificação
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Seres Humanos
Masculino
Metronidazol/farmacologia
Testes de Sensibilidade Microbiana
Meia-Idade
Nepal/epidemiologia
Nitrorredutases/genética
Mutação Puntual
Prevalência
Fator de Iniciação 2 em Procariotos/genética
RNA Ribossômico 23S/genética
Tetraciclina/farmacologia
Adulto Jovem
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anti-Bacterial Agents); 0 (Bacterial Proteins); 0 (DNA, Bacterial); 0 (Prokaryotic Initiation Factor-2); 0 (RNA, Ribosomal, 23S); 140QMO216E (Metronidazole); 6GNT3Y5LMF (Levofloxacin); 804826J2HU (Amoxicillin); EC 1.7.- (Nitroreductases); EC 1.7.- (RdxA protein, Helicobacter pylori); EC 5.99.1.3 (DNA Gyrase); F8VB5M810T (Tetracycline); H1250JIK0A (Clarithromycin)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170831
[Lr] Data última revisão:
170831
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161105
[St] Status:MEDLINE


  3 / 195 MEDLINE  
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[PMID]:27364543
[Au] Autor:Dongre R; Folkers GE; Gualerzi CO; Boelens R; Wienk H
[Ad] Endereço:Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands.
[Ti] Título:A model for the interaction of the G3-subdomain of Geobacillus stearothermophilus IF2 with the 30S ribosomal subunit.
[So] Source:Protein Sci;25(9):1722-33, 2016 Sep.
[Is] ISSN:1469-896X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Bacterial translation initiation factor IF2 complexed with GTP binds to the 30S ribosomal subunit, promotes ribosomal binding of fMet-tRNA, and favors the joining of the small and large ribosomal subunits yielding a 70S initiation complex ready to enter the translation elongation phase. Within the IF2 molecule subdomain G3, which is believed to play an important role in the IF2-30S interaction, is positioned between the GTP-binding G2 and the fMet-tRNA binding C-terminal subdomains. In this study the solution structure of subdomain G3 of Geobacillus stearothermophilus IF2 has been elucidated. G3 forms a core structure consisting of two ß-sheets with each four anti-parallel strands, followed by a C-terminal α-helix. In line with its role as linker between G3 and subdomain C1, this helix has no well-defined orientation but is endowed with a dynamic nature. The structure of the G3 core is that of a typical OB-fold module, similar to that of the corresponding subdomain of Thermus thermophilus IF2, and to that of other known RNA-binding modules such as IF2-C2, IF1 and subdomains II of elongation factors EF-Tu and EF-G. Structural comparisons have resulted in a model that describes the interaction between IF2-G3 and the 30S ribosomal subunit.
[Mh] Termos MeSH primário: Proteínas de Bactérias/química
Geobacillus stearothermophilus/química
Modelos Moleculares
Fator de Iniciação 2 em Procariotos/química
Subunidades Ribossômicas Menores de Bactérias/química
[Mh] Termos MeSH secundário: Proteínas de Bactérias/metabolismo
Geobacillus stearothermophilus/metabolismo
Fator de Iniciação 2 em Procariotos/metabolismo
Domínios Proteicos
Subunidades Ribossômicas Menores de Bactérias/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Prokaryotic Initiation Factor-2)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170902
[Lr] Data última revisão:
170902
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160702
[St] Status:MEDLINE
[do] DOI:10.1002/pro.2977


  4 / 195 MEDLINE  
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[PMID]:26973877
[Au] Autor:Sprink T; Ramrath DJ; Yamamoto H; Yamamoto K; Loerke J; Ismer J; Hildebrand PW; Scheerer P; Bürger J; Mielke T; Spahn CM
[Ad] Endereço:Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
[Ti] Título:Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association.
[So] Source:Sci Adv;2(3):e1501502, 2016 Mar.
[Is] ISSN:2375-2548
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trGTPase). Although the structural basis for trGTPase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with the ribosome, remains elusive. We determine the structure of IF2 complexed with a nonhydrolyzable guanosine triphosphate analog and initiator fMet-tRNAi (Met) in the context of the Escherichia coli ribosome to 3.7-Å resolution using cryo-electron microscopy. The structural analysis reveals previously unseen intrinsic conformational modes of the 70S initiation complex, establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome and providing the structural foundation for a mechanistic understanding of the final steps of translation initiation.
[Mh] Termos MeSH primário: Fator de Iniciação 2 em Procariotos/química
Ribossomos/química
[Mh] Termos MeSH secundário: Microscopia Crioeletrônica
Modelos Moleculares
Conformação Proteica
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Prokaryotic Initiation Factor-2)
[Em] Mês de entrada:1604
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160315
[St] Status:MEDLINE
[do] DOI:10.1126/sciadv.1501502


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[PMID]:26800121
[Au] Autor:Liu B; Luo J; Li W; Long XF; Zhang YQ; Zeng ZG; Tian YQ
[Ad] Endereço:Key laboratory of Leather Chemistry and engineering, College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu, Sichuan, P. R. China.
[Ti] Título:Erwinia teleogrylli sp. nov., a Bacterial Isolate Associated with a Chinese Cricket.
[So] Source:PLoS One;11(1):e0146596, 2016.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A bacterial isolate (SCU-B244T) was obtained in China from crickets (Teleogryllus occipitalis) living in cropland deserted for approximately 10 years. The isolated bacteria were Gram-negative, facultatively anaerobic, oxidase-negative rods. A preliminary analysis of the 16S rRNA gene sequence indicated that the strain belongs to either the genus Erwinia or Pantoea. Analysis of multilocus sequence typing based on concatenated partial atpD, gyrB and infB gene sequences and physiological and biochemical characteristics indicated that the strain belonged to the genus Erwinia, as member of a new species as it was distinct from other known Erwinia species. Further analysis of the 16S rRNA gene showed SCU-B244T to have 94.71% identity to the closest species of that genus, Erwinia oleae (DSM 23398T), which is below the threshold of 97% used to discriminate bacterial species. DNA-DNA hybridization results (5.78±2.52%) between SCU-B244T and Erwinia oleae (DSM 23398T) confirmed that SCU-B244T and Erwinia oleae (DSM 23398T) represent different species combined with average nucleotide identity values which range from 72.42% to 74.41. The DNA G+C content of SCU-B244T was 55.32 mol%, which also differs from that of Erwinia oleae (54.7 to 54.9 mol%). The polyphasic taxonomic approach used here confirmed that the strain belongs to the Erwinia group and represents a novel species. The name Erwinia teleogrylli sp. nov. is proposed for this novel taxon, for which the type strain is SCU-B244T (= CGMCC 1.12772T = DSM 28222T = KCTC 42022T).
[Mh] Termos MeSH primário: Clorpirifos/farmacologia
Resistência a Medicamentos/genética
Erwinia/isolamento & purificação
Erwinia/metabolismo
Gryllidae/efeitos dos fármacos
Gryllidae/microbiologia
Inseticidas/farmacologia
[Mh] Termos MeSH secundário: Animais
Técnicas de Tipagem Bacteriana
Composição de Bases/genética
China
Clorpirifos/metabolismo
DNA Girase/genética
DNA Bacteriano/genética
DNA Ribossômico/genética
Erwinia/classificação
Erwinia/genética
Inseticidas/metabolismo
Tipagem de Sequências Multilocus
Fator de Iniciação 2 em Procariotos/genética
RNA Ribossômico 16S/genética
Análise de Sequência de DNA
Fatores de Transcrição/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Bacterial); 0 (DNA, Ribosomal); 0 (Insecticides); 0 (Prokaryotic Initiation Factor-2); 0 (RNA, Ribosomal, 16S); 0 (Transcription Factors); EC 5.99.1.3 (DNA Gyrase); JCS58I644W (Chlorpyrifos)
[Em] Mês de entrada:1607
[Cu] Atualização por classe:160131
[Lr] Data última revisão:
160131
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160123
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0146596


  6 / 195 MEDLINE  
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[PMID]:26700147
[Au] Autor:Nikonov O; Kravchenko O; Arkhipova V; Stolboushkina E; Nikonov S; Garber M
[Ad] Endereço:Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation. Electronic address: alik@vega.protres.ru.
[Ti] Título:Water clusters in the nucleotide-binding pocket of the protein aIF2γ from the archaeon Sulfolobus solfataricus: Proton transmission.
[So] Source:Biochimie;121:197-203, 2016 Feb.
[Is] ISSN:1638-6183
[Cp] País de publicação:France
[La] Idioma:eng
[Ab] Resumo:In Archaea and Eukaryotes, the binding of Met-tRNAi(Met) to the P-site of the ribosome is mediated by translation initiation factor 2 (a/eIF2) which consists of three subunits: α, ß and γ. Here, we present the high-resolution structure of intact aIF2γ from Sulfolobus solfataricus (SsoIF2γ) in complex with GTP analog, GDPCP. The comparison of the nucleotide-binding pockets in this structure and in the structure of the ribosome-bound form of EF-Tu reveals their close conformation similarity. The nucleotide-binding pocket conformation observed in this structure could be consider as corresponding to intermediate conformation of EF-Tu nucleotide-binding pocket in its transition from the GTP-bound form to the GDP-bound one. Three clusters of well defined water molecules are associated with amino acid residues of the SsoIF2γ nucleotide-binding pocket and stabilize its conformation. We suppose that two water bridges between the oxygen atoms of the GTP γ-phosphate and negatively charged residues of the pocket can serve as ways to transmit protons arising from the catalytic reaction.
[Mh] Termos MeSH primário: Fator de Iniciação 2 em Procariotos/metabolismo
Sulfolobus solfataricus/metabolismo
[Mh] Termos MeSH secundário: Catálise
Guanosina Difosfato/metabolismo
Guanosina Trifosfato/metabolismo
Fator Tu de Elongação de Peptídeos/química
Fator Tu de Elongação de Peptídeos/metabolismo
Fator de Iniciação 2 em Procariotos/química
Ligação Proteica
Ribossomos/metabolismo
Solventes/química
Água/metabolismo
Difração de Raios X
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Prokaryotic Initiation Factor-2); 0 (Solvents); 059QF0KO0R (Water); 146-91-8 (Guanosine Diphosphate); 86-01-1 (Guanosine Triphosphate); EC 3.6.1.- (Peptide Elongation Factor Tu)
[Em] Mês de entrada:1610
[Cu] Atualização por classe:161230
[Lr] Data última revisão:
161230
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151225
[St] Status:MEDLINE


  7 / 195 MEDLINE  
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[PMID]:26597455
[Au] Autor:Kämpfer P; McInroy JA; Doijad S; Chakraborty T; Glaeser SP
[Ad] Endereço:Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany. Electronic address: peter.kaempfer@umwelt.uni-giessen.de.
[Ti] Título:Kosakonia pseudosacchari sp. nov., an endophyte of Zea mays.
[So] Source:Syst Appl Microbiol;39(1):1-7, 2016 Feb.
[Is] ISSN:1618-0984
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:A beige pigmented bacterial strain (JM-387(T)), isolated from field-grown corn root tissue, Tallassee, Alabama, was studied for its taxonomic allocation. A comparison of the 16S rRNA gene sequence with those of the type strains of most closely related species of the family Enterobacteriaceae showed highest sequence similarities to the type strain of Kosakonia sacchari (99.5%), "Enterobacter oryzendophyticus" (98.8%), and Kosakonia radicincitans (98.6%). Construction of phylogenetic trees based on the 16S rRNA gene and partial sequences of four protein-coding genes, rpoB, gyrB, infB, and atpD (multilocus sequence analysis, MLSA) showed a distinct clustering of strain JM-387(T) with Kosakonia sacchari. DNA-DNA hybridizations between JM-387(T) and the type strains of most similar Kosakonia/"Enterobacter" species including K. sacchari LMG 26783(T), "E. oryzendophyticus" LMG 26432(T), K. radicincitans D5/23(T), K. oryzae LMG 24251(T), E. cancerogenus LMG 2693(T), and E. cloacae subsp. dissolvens CCUG 25230(T) were in the range of 14.4-60.2%. The average nucleotide identity (ANI) of the genome sequence of the new strain to K. sacchari SP1(T) was 94.47%. Strain JM-387(T) had a typical enterobacterial fatty acid pattern consisting of the major fatty acids C16:0, C16:1 ω7c/C16:1 ω6c/C15:0 2OH, C18:1 ω7c/C18:1 ω6c with C14:0 3-OH as hydroxylated fatty acid. Genotypic data and the differentiating biochemical and chemotaxonomic properties showed that strain JM-387(T) represents a novel species of the genus Kosakonia, for which the name Kosakonia pseudosacchari sp. nov. (type strain JM-387(T)=CIP 110597(T)=DSM 27151(T)) is proposed.
[Mh] Termos MeSH primário: Enterobacteriaceae/classificação
Enterobacteriaceae/isolamento & purificação
Raízes de Plantas/microbiologia
Zea mays/microbiologia
[Mh] Termos MeSH secundário: Alabama
Sequência de Bases
DNA Girase/genética
DNA Bacteriano/genética
RNA Polimerases Dirigidas por DNA/genética
Endófitos
Enterobacteriaceae/genética
Tipagem de Sequências Multilocus
Filogenia
Fator de Iniciação 2 em Procariotos/genética
RNA Ribossômico 16S/genética
Análise de Sequência de DNA
Fatores de Transcrição/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Bacterial); 0 (Prokaryotic Initiation Factor-2); 0 (RNA, Ribosomal, 16S); 0 (Transcription Factors); EC 2.7.7.6 (DNA-Directed RNA Polymerases); EC 5.99.1.3 (DNA Gyrase)
[Em] Mês de entrada:1612
[Cu] Atualização por classe:161230
[Lr] Data última revisão:
161230
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151125
[St] Status:MEDLINE


  8 / 195 MEDLINE  
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[PMID]:26668356
[Au] Autor:Ling C; Ermolenko DN
[Ad] Endereço:Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642.
[Ti] Título:Initiation factor 2 stabilizes the ribosome in a semirotated conformation.
[So] Source:Proc Natl Acad Sci U S A;112(52):15874-9, 2015 Dec 29.
[Is] ISSN:1091-6490
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Intersubunit rotation and movement of the L1 stalk, a mobile domain of the large ribosomal subunit, have been shown to accompany the elongation cycle of translation. The initiation phase of protein synthesis is crucial for translational control of gene expression; however, in contrast to elongation, little is known about the conformational rearrangements of the ribosome during initiation. Bacterial initiation factors (IFs) 1, 2, and 3 mediate the binding of initiator tRNA and mRNA to the small ribosomal subunit to form the initiation complex, which subsequently associates with the large subunit by a poorly understood mechanism. Here, we use single-molecule FRET to monitor intersubunit rotation and the inward/outward movement of the L1 stalk of the large ribosomal subunit during the subunit-joining step of translation initiation. We show that, on subunit association, the ribosome adopts a distinct conformation in which the ribosomal subunits are in a semirotated orientation and the L1 stalk is positioned in a half-closed state. The formation of the semirotated intermediate requires the presence of an aminoacylated initiator, fMet-tRNA(fMet), and IF2 in the GTP-bound state. GTP hydrolysis by IF2 induces opening of the L1 stalk and the transition to the nonrotated conformation of the ribosome. Our results suggest that positioning subunits in a semirotated orientation facilitates subunit association and support a model in which L1 stalk movement is coupled to intersubunit rotation and/or IF2 binding.
[Mh] Termos MeSH primário: Proteínas de Escherichia coli/metabolismo
Fator de Iniciação 2 em Procariotos/metabolismo
Biossíntese de Proteínas
Ribossomos/metabolismo
[Mh] Termos MeSH secundário: Escherichia coli/genética
Escherichia coli/metabolismo
Transferência Ressonante de Energia de Fluorescência
Guanosina Trifosfato/metabolismo
Microscopia de Fluorescência
Modelos Moleculares
Conformação Molecular
Fator de Iniciação 1 em Procariotos/metabolismo
Fator de Iniciação 3 em Procariotos/metabolismo
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
RNA de Transferência de Metionina/genética
RNA de Transferência de Metionina/metabolismo
Subunidades Ribossômicas/química
Subunidades Ribossômicas/metabolismo
Ribossomos/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (Escherichia coli Proteins); 0 (Prokaryotic Initiation Factor-1); 0 (Prokaryotic Initiation Factor-2); 0 (Prokaryotic Initiation Factor-3); 0 (RNA, Messenger); 0 (RNA, Transfer, Met); 86-01-1 (Guanosine Triphosphate)
[Em] Mês de entrada:1608
[Cu] Atualização por classe:161019
[Lr] Data última revisão:
161019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151216
[St] Status:MEDLINE
[do] DOI:10.1073/pnas.1520337112


  9 / 195 MEDLINE  
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[PMID]:26249348
[Au] Autor:Urzhumtsev A; Afonine PV; Van Benschoten AH; Fraser JS; Adams PD
[Ad] Endereço:Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-INSERM-UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France.
[Ti] Título:From deep TLS validation to ensembles of atomic models built from elemental motions.
[So] Source:Acta Crystallogr D Biol Crystallogr;71(Pt 8):1668-83, 2015 Aug.
[Is] ISSN:1399-0047
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The translation-libration-screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.
[Mh] Termos MeSH primário: Proteínas/química
[Mh] Termos MeSH secundário: Algoritmos
Animais
Calmodulina/química
Seres Humanos
Modelos Moleculares
Movimento (Física)
Fator de Iniciação 2 em Procariotos/química
Conformação Proteica
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Calmodulin); 0 (Prokaryotic Initiation Factor-2); 0 (Proteins)
[Em] Mês de entrada:1605
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150808
[St] Status:MEDLINE
[do] DOI:10.1107/S1399004715011426


  10 / 195 MEDLINE  
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[PMID]:25596426
[Au] Autor:Wang J; Caban K; Gonzalez RL
[Ad] Endereço:Department of Chemistry, Columbia University, 3000 Broadway, MC3126, New York, NY 10027, USA.
[Ti] Título:Ribosomal initiation complex-driven changes in the stability and dynamics of initiation factor 2 regulate the fidelity of translation initiation.
[So] Source:J Mol Biol;427(9):1819-34, 2015 May 08.
[Is] ISSN:1089-8638
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Joining of the large, 50S, ribosomal subunit to the small, 30S, ribosomal subunit initiation complex (IC) during bacterial translation initiation is catalyzed by the initiation factor (IF) IF2. Because the rate of subunit joining is coupled to the IF, transfer RNA (tRNA), and mRNA codon compositions of the 30S IC, the subunit joining reaction functions as a kinetic checkpoint that regulates the fidelity of translation initiation. Recent structural studies suggest that the conformational dynamics of the IF2·tRNA sub-complex forming on the intersubunit surface of the 30S IC may play a significant role in the mechanisms that couple the rate of subunit joining to the IF, tRNA, and codon compositions of the 30S IC. To test this hypothesis, we have developed a single-molecule fluorescence resonance energy transfer signal between IF2 and tRNA that has enabled us to monitor the conformational dynamics of the IF2·tRNA sub-complex across a series of 30S ICs. Our results demonstrate that 30S ICs undergoing rapid subunit joining display a high affinity for IF2 and an IF2·tRNA sub-complex that primarily samples a single conformation. In contrast, 30S ICs that undergo slower subunit joining exhibit a decreased affinity for IF2 and/or a change in the conformational dynamics of the IF2·tRNA sub-complex. These results strongly suggest that 30S IC-driven changes in the stability of IF2 and the conformational dynamics of the IF2·tRNA sub-complex regulate the efficiency and fidelity of subunit joining during translation initiation.
[Mh] Termos MeSH primário: Fator de Iniciação 2 em Procariotos/metabolismo
Biossíntese de Proteínas
Subunidades Ribossômicas Menores de Bactérias/metabolismo
Ribossomos/metabolismo
[Mh] Termos MeSH secundário: Escherichia coli/metabolismo
Transferência Ressonante de Energia de Fluorescência
Guanosina Trifosfato/metabolismo
Modelos Moleculares
Conformação Molecular
Fator de Iniciação 2 em Procariotos/química
Fator de Iniciação 2 em Procariotos/genética
RNA Mensageiro/genética
RNA de Transferência de Metionina/metabolismo
Subunidades Ribossômicas Menores de Bactérias/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Prokaryotic Initiation Factor-2); 0 (RNA, Messenger); 0 (RNA, Transfer, Met); 86-01-1 (Guanosine Triphosphate)
[Em] Mês de entrada:1506
[Cu] Atualização por classe:161019
[Lr] Data última revisão:
161019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150118
[St] Status:MEDLINE



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