Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 43
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
Proc Natl Acad Sci U S A ; 116(44): 22275-22281, 2019 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-31611393

RESUMO

Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a major target for clinically useful antibiotics. We report here the cryo-electron microscopy structures of the ribosome of a pathogenic aminoglycoside (AG)-resistant Pseudomonas aeruginosa strain, as well as of a nonresistance strain isolated from a cystic fibrosis patient. The structural studies disclosed defective ribosome complex formation due to a conformational change of rRNA helix H69, an essential intersubunit bridge, and a secondary binding site of the AGs. In addition, a stable conformation of nucleotides A1486 and A1487, pointing into helix h44, is created compared to a non-AG-bound ribosome. We suggest that altering the conformations of ribosomal protein uL6 and rRNA helix H69, which interact with initiation-factor IF2, interferes with proper protein synthesis initiation.

2.
Sci Rep ; 9(1): 11460, 2019 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-31391518

RESUMO

The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit tunnel. Additional effective resistance mechanisms include deletion or insertion mutations in ribosomal protein uL22, which lead to alterations of the exit tunnel shape, located 16 Å away from the drug's binding site. We determined the cryo-EM structures of the Staphylococcus aureus 70S ribosome, and its ery bound complex with a two amino acid deletion mutation in its ß hairpin loop, which grants the bacteria resistance to ery. The structures reveal that, although the binding of ery is stable, the movement of the flexible shorter uL22 loop towards the tunnel wall creates a wider path for nascent proteins, thus enabling bypass of the barrier formed by the drug. Moreover, upon drug binding, the tunnel widens further.

3.
FEBS J ; 286(18): 3558-3565, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31230411

RESUMO

Protein synthesis is one of the most energy demanding cellular processes. The ability to regulate protein synthesis is essential for cells under normal as well as stress conditions, such as nutrient deficiencies. One mechanism for protein synthesis suppression is the dimerization of ribosomes into hibernation complexes. In most cells, this process is promoted by the hibernating promoting factor (HPF) and in a small group of Gram-negative bacteria (γ-proteobacteria), the dimer formation is induced by a shorter version of HPF (HPFshort ) and by an additional protein, the ribosome modulation factor. In most bacteria, the product of this process is the 100S ribosome complex. Recent advances in cryogenic electron microscopy methods resulted in an abundance of detailed structures of near atomic resolutions 100S complexes that allow for a better understanding of the dimerization process and the way it inhibits protein synthesis. As ribosomal dimerization is vital for cell survival, this process is an attractive target for the development of novel antimicrobial substances that might inhibit or stabilize the complex formation. As different dimerization processes exist among bacteria, including pathogens, this process may provide the basis for species-specific design of antimicrobial agents. Here, we review in detail the various dimerization mechanisms and discuss how they affect the overall dimer structures of the bacterial ribosomes.

4.
Nat Commun ; 8(1): 1589, 2017 11 17.
Artigo em Inglês | MEDLINE | ID: mdl-29150609

RESUMO

Leishmania is a single-celled eukaryotic parasite afflicting millions of humans worldwide, with current therapies limited to a poor selection of drugs that mostly target elements in the parasite's cell envelope. Here we determined the atomic resolution electron cryo-microscopy (cryo-EM) structure of the Leishmania ribosome in complex with paromomycin (PAR), a highly potent compound recently approved for treatment of the fatal visceral leishmaniasis (VL). The structure reveals the mechanism by which the drug induces its deleterious effects on the parasite. We further show that PAR interferes with several aspects of cytosolic translation, thus highlighting the cytosolic rather than the mitochondrial ribosome as the primary drug target. The results also highlight unique as well as conserved elements in the PAR-binding pocket that can serve as hotspots for the development of novel therapeutics.


Assuntos
Leishmania/metabolismo , Paromomicina/metabolismo , Ribossomos/metabolismo , Sequência de Aminoácidos , Sequência de Bases , Sítios de Ligação/genética , Microscopia Crioeletrônica , Citosol/efeitos dos fármacos , Citosol/metabolismo , Humanos , Leishmania/genética , Leishmania/ultraestrutura , Modelos Moleculares , Paromomicina/química , Paromomicina/farmacologia , Biossíntese de Proteínas/efeitos dos fármacos , RNA Ribossômico/química , RNA Ribossômico/metabolismo , Proteínas Ribossômicas/química , Proteínas Ribossômicas/metabolismo , Ribossomos/química , Ribossomos/ultraestrutura , Homologia de Sequência de Aminoácidos
5.
Nucleic Acids Res ; 45(17): 10284-10292, 2017 Sep 29.
Artigo em Inglês | MEDLINE | ID: mdl-28973455

RESUMO

Antimicrobial resistance within a wide range of pathogenic bacteria is an increasingly serious threat to global public health. Among these pathogenic bacteria are the highly resistant, versatile and possibly aggressive bacteria, Staphylococcus aureus. Lincosamide antibiotics were proved to be effective against this pathogen. This small, albeit important group of antibiotics is mostly active against Gram-positive bacteria, but also used against selected Gram-negative anaerobes and protozoa. S. aureus resistance to lincosamides can be acquired by modifications and/or mutations in the rRNA and rProteins. Here, we present the crystal structures of the large ribosomal subunit of S. aureus in complex with the lincosamides lincomycin and RB02, a novel semisynthetic derivative and discuss the biochemical aspects of the in vitro potency of various lincosamides. These results allow better understanding of the drugs selectivity as well as the importance of the various chemical moieties of the drug for binding and inhibition.


Assuntos
Lincosamidas/farmacologia , Subunidades Ribossômicas Maiores de Bactérias/efeitos dos fármacos , Staphylococcus aureus/efeitos dos fármacos , Benzamidas/química , Benzamidas/farmacologia , Sítios de Ligação , Clindamicina/química , Clindamicina/farmacologia , Cristalização , Cristalografia por Raios X , Resistência Microbiana a Medicamentos , Galactosídeos/química , Galactosídeos/farmacologia , Ligações de Hidrogênio , Lincomicina/química , Lincomicina/farmacologia , Lincosamidas/química , Estrutura Molecular , Subunidades Ribossômicas Maiores de Bactérias/ultraestrutura , Staphylococcus aureus/ultraestrutura , Eletricidade Estática , Relação Estrutura-Atividade
6.
Nat Commun ; 8(1): 723, 2017 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-28959035

RESUMO

Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors.


Assuntos
Ribossomos/química , Ribossomos/metabolismo , Staphylococcus aureus/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Microscopia Crioeletrônica , Dimerização , Ligação Proteica , Proteínas Ribossômicas/química , Proteínas Ribossômicas/genética , Proteínas Ribossômicas/metabolismo , Ribossomos/genética , Staphylococcus aureus/química , Staphylococcus aureus/genética , Staphylococcus aureus/ultraestrutura
7.
Structure ; 25(8): 1233-1241.e3, 2017 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-28689968

RESUMO

Erythromycin is a clinically useful antibiotic that binds to an rRNA pocket in the ribosomal exit tunnel. Commonly, resistance to erythromycin is acquired by alterations of rRNA nucleotides that interact with the drug. Mutations in the ß hairpin of ribosomal protein uL22, which is rather distal to the erythromycin binding site, also generate resistance to the antibiotic. We have determined the crystal structure of the large ribosomal subunit from Deinococcus radiodurans with a three amino acid insertion within the ß hairpin of uL22 that renders resistance to erythromycin. The structure reveals a shift of the ß hairpin of the mutated uL22 toward the interior of the exit tunnel, triggering a cascade of structural alterations of rRNA nucleotides that propagate to the erythromycin binding pocket. Our findings support recent studies showing that the interactions between uL22 and specific sequences within nascent chains trigger conformational rearrangements in the exit tunnel.


Assuntos
Proteínas de Bactérias/química , Proteínas Ribossômicas/química , Antibacterianos/química , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Deinococcus/química , Eritromicina/química , Eritromicina/farmacologia , Mutação , Ligação Proteica , RNA Ribossômico/química , RNA Ribossômico/metabolismo , Proteínas Ribossômicas/genética , Proteínas Ribossômicas/metabolismo
8.
Annu Rev Biochem ; 86: 567-583, 2017 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-28654325

RESUMO

Multidrug resistance is a global threat as the clinically available potent antibiotic drugs are becoming exceedingly scarce. For example, increasing drug resistance among gram-positive bacteria is responsible for approximately one-third of nosocomial infections. As ribosomes are a major target for these drugs, they may serve as suitable objects for novel development of next-generation antibiotics. Three-dimensional structures of ribosomal particles from Staphylococcus aureus obtained by X-ray crystallography have shed light on fine details of drug binding sites and have revealed unique structural motifs specific for this pathogenic strain, which may be used for the design of novel degradable pathogen-specific, and hence, environmentally friendly drugs.


Assuntos
Antibacterianos/síntese química , Proteínas de Bactérias/química , Desenho de Drogas , Ribossomos/efeitos dos fármacos , Staphylococcus aureus/efeitos dos fármacos , Antibacterianos/metabolismo , Antibacterianos/farmacologia , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/microbiologia , Cristalografia por Raios X , Deinococcus/efeitos dos fármacos , Deinococcus/genética , Deinococcus/metabolismo , Farmacorresistência Bacteriana Múltipla , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Humanos , Modelos Moleculares , Ribossomos/metabolismo , Ribossomos/ultraestrutura , Infecções Estafilocócicas/tratamento farmacológico , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/genética , Staphylococcus aureus/metabolismo , Thermus thermophilus/efeitos dos fármacos , Thermus thermophilus/genética , Thermus thermophilus/metabolismo
9.
mBio ; 8(3)2017 05 09.
Artigo em Inglês | MEDLINE | ID: mdl-28487427

RESUMO

An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of Staphylococcus aureus This high-resolution structural information demonstrated that a single amino acid deletion in ribosomal protein uL3 confers linezolid resistance despite being located 24 Å away from the linezolid binding pocket in the peptidyl-transferase center. The mutation induces a cascade of allosteric structural rearrangements of the rRNA that ultimately results in the alteration of the antibiotic binding site.IMPORTANCE The growing burden on human health caused by various antibiotic resistance mutations now includes prevalent Staphylococcus aureus resistance to last-line antimicrobial drugs such as linezolid and daptomycin. Structure-informed drug modification represents a frontier with respect to designing advanced clinical therapies, but success in this strategy requires rapid, facile means to shed light on the structural basis for drug resistance (D. Brown, Nat Rev Drug Discov 14:821-832, 2015, https://doi.org/10.1038/nrd4675). Here, detailed structural information demonstrates that a common mechanism is at play in linezolid resistance and provides a step toward the redesign of oxazolidinone antibiotics, a strategy that could thwart known mechanisms of linezolid resistance.


Assuntos
Antibacterianos/metabolismo , Linezolida/metabolismo , Ribossomos/química , Staphylococcus aureus/metabolismo , Antibacterianos/farmacologia , Sítios de Ligação , Microscopia Crioeletrônica , Cristalografia por Raios X , Farmacorresistência Bacteriana , Linezolida/farmacologia , Testes de Sensibilidade Microbiana , Mutação , Peptidil Transferases/metabolismo , Proteínas Ribossômicas/genética , Proteínas Ribossômicas/metabolismo , Ribossomos/genética , Ribossomos/metabolismo , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/genética , Staphylococcus aureus/ultraestrutura
10.
Sci Rep ; 6: 39004, 2016 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-27958389

RESUMO

The increasing appearance of pathogenic bacteria with antibiotic resistance is a global threat. Consequently, clinically available potent antibiotics that are active against multidrug resistant pathogens are becoming exceedingly scarce. Ribosomes are a main target for antibiotics, and hence are an objective for novel drug development. Lefamulin, a semi-synthetic pleuromutilin compound highly active against multi-resistant pathogens, is a promising antibiotic currently in phase III trials for the treatment of community-acquired bacterial pneumonia in adults. The crystal structure of the Staphylococcus aureus large ribosomal subunit in complex with lefamulin reveals its protein synthesis inhibition mechanism and the rationale for its potency. In addition, analysis of the bacterial and eukaryotes ribosome structures around the pleuromutilin binding pocket has elucidated the key for the drug's selectivity.


Assuntos
Antibacterianos , Subunidades Ribossômicas Maiores de Bactérias , Staphylococcus aureus , Antibacterianos/química , Antibacterianos/farmacologia , Proteínas de Bactérias/biossíntese , Ensaios Clínicos Fase III como Assunto , Diterpenos/química , Diterpenos/farmacologia , Humanos , Compostos Policíclicos , Biossíntese de Proteínas/efeitos dos fármacos , Subunidades Ribossômicas Maiores de Bactérias/química , Subunidades Ribossômicas Maiores de Bactérias/metabolismo , Infecções Estafilocócicas/tratamento farmacológico , Infecções Estafilocócicas/metabolismo , Infecções Estafilocócicas/patologia , Staphylococcus aureus/química , Staphylococcus aureus/crescimento & desenvolvimento
11.
Proc Natl Acad Sci U S A ; 113(44): E6796-E6805, 2016 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-27791159

RESUMO

Two structurally unique ribosomal antibiotics belonging to the orthosomycin family, avilamycin and evernimicin, possess activity against Enterococci, Staphylococci, and Streptococci, and other Gram-positive bacteria. Here, we describe the high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them. Their extended binding sites span the A-tRNA entrance corridor, thus inhibiting protein biosynthesis by blocking the binding site of the A-tRNA elbow, a mechanism not shared with other known antibiotics. Along with using the ribosomal components that bind and discriminate the A-tRNA-namely, ribosomal RNA (rRNA) helices H89, H91, and ribosomal proteins (rProtein) uL16-these structures revealed novel interactions with domain 2 of the CTC protein, a feature typical to various Gram-positive bacteria. Furthermore, analysis of these structures explained how single nucleotide mutations and methylations in helices H89 and H91 confer resistance to orthosomycins and revealed the sequence variations in 23S rRNA nucleotides alongside the difference in the lengths of the eukaryotic and prokaryotic α1 helix of protein uL16 that play a key role in the selectivity of those drugs. The accurate interpretation of the crystal structures that could be performed beyond that recently reported in cryo-EM models provide structural insights that may be useful for the design of novel pathogen-specific antibiotics, and for improving the potency of orthosomycins. Because both drugs are extensively metabolized in vivo, their environmental toxicity is very low, thus placing them at the frontline of drugs with reduced ecological hazards.


Assuntos
Aminoglicosídeos/farmacologia , Proteínas de Bactérias/efeitos dos fármacos , Sítios de Ligação/efeitos dos fármacos , Oligossacarídeos/farmacologia , RNA de Transferência/efeitos dos fármacos , Proteínas Ribossômicas/efeitos dos fármacos , Aminoglicosídeos/química , Antibacterianos/farmacologia , Cristalografia por Raios X , Farmacorresistência Bacteriana/efeitos dos fármacos , Farmacorresistência Bacteriana/genética , Bactérias Gram-Positivas/efeitos dos fármacos , Testes de Sensibilidade Microbiana , Modelos Moleculares , Mutação , Conformação de Ácido Nucleico , Oligossacarídeos/química , Biossíntese de Proteínas/efeitos dos fármacos , RNA Ribossômico , RNA Ribossômico 23S/efeitos dos fármacos , RNA Ribossômico 23S/genética , RNA de Transferência/metabolismo , Proteínas Ribossômicas/metabolismo , Ribossomos/efeitos dos fármacos , Ribossomos/metabolismo , Alinhamento de Sequência , Especificidade da Espécie
12.
Sci Rep ; 6: 37138, 2016 11 16.
Artigo em Inglês | MEDLINE | ID: mdl-27849042

RESUMO

Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the 'lubricant' for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.


Assuntos
Haloarcula marismortui/química , Simulação de Dinâmica Molecular , RNA Arqueal/química , RNA Mensageiro/química , Subunidades Ribossômicas Maiores de Arqueas/química , Subunidades Ribossômicas Menores de Arqueas/química , Difração de Nêutrons
13.
Cell Rep ; 16(2): 288-294, 2016 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-27373148

RESUMO

Leishmania is a single-cell eukaryotic parasite of the Trypanosomatidae family, whose members cause an array of tropical diseases. The often fatal outcome of infections, lack of effective vaccines, limited selection of therapeutic drugs, and emerging resistant strains, underline the need to develop strategies to combat these pathogens. The Trypanosomatid ribosome has recently been highlighted as a promising therapeutic target due to structural features that are distinct from other eukaryotes. Here, we present the 2.8-Å resolution structure of the Leishmania donovani large ribosomal subunit (LSU) derived from a cryo-EM map, further enabling the structural observation of eukaryotic rRNA modifications that play a significant role in ribosome assembly and function. The structure illustrates the unique fragmented nature of leishmanial LSU rRNA and highlights the irregular distribution of rRNA modifications in Leishmania, a characteristic with implications for anti-parasitic drug development.


Assuntos
Leishmania donovani , Subunidades Ribossômicas Maiores/química , Microscopia Crioeletrônica , Modelos Moleculares , Conformação de Ácido Nucleico , Estrutura Quaternária de Proteína , Proteínas de Protozoários/química , RNA de Protozoário/química , RNA Ribossômico/química , Proteínas Ribossômicas/química , Subunidades Ribossômicas Maiores/ultraestrutura
14.
Antibiotics (Basel) ; 5(3)2016 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-27367739

RESUMO

Most ribosomal antibiotics obstruct distinct ribosomal functions. In selected cases, in addition to paralyzing vital ribosomal tasks, some ribosomal antibiotics are involved in cellular regulation. Owing to the global rapid increase in the appearance of multi-drug resistance in pathogenic bacterial strains, and to the extremely slow progress in developing new antibiotics worldwide, it seems that, in addition to the traditional attempts at improving current antibiotics and the intensive screening for additional natural compounds, this field should undergo substantial conceptual revision. Here, we highlight several contemporary issues, including challenging the common preference of broad-range antibiotics; the marginal attention to alterations in the microbiome population resulting from antibiotics usage, and the insufficient awareness of ecological and environmental aspects of antibiotics usage. We also highlight recent advances in the identification of species-specific structural motifs that may be exploited for the design and the creation of novel, environmental friendly, degradable, antibiotic types, with a better distinction between pathogens and useful bacterial species in the microbiome. Thus, these studies are leading towards the design of "pathogen-specific antibiotics," in contrast to the current preference of broad range antibiotics, partially because it requires significant efforts in speeding up the discovery of the unique species motifs as well as the clinical pathogen identification.

15.
Proc Natl Acad Sci U S A ; 112(43): E5805-14, 2015 Oct 27.
Artigo em Inglês | MEDLINE | ID: mdl-26464510

RESUMO

The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.


Assuntos
Ribossomos/metabolismo , Staphylococcus aureus/metabolismo , Conformação Proteica , RNA Ribossômico/metabolismo , Proteínas Ribossômicas/química , Proteínas Ribossômicas/metabolismo
16.
Chembiochem ; 16(10): 1415-9, 2015 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-25930950

RESUMO

We have developed a collagen-mRNA platform for controllable protein production that is intended to be less prone to the problems associated with commonly used mRNA therapy as well as with collagen skin-healing procedures. A collagen mimic was constructed according to a recombinant method and was used as scaffold for translating mRNA chains into proteins. Cysteines were genetically inserted into the collagen chain at positions allowing efficient ribosome translation activity while minimizing mRNA misfolding and degradation. Enhanced green fluorescence protein (eGFP) mRNA bound to collagen was successfully translated by cell-free Escherichia coli ribosomes. This system enabled an accurate control of specific protein synthesis by monitoring expression time and level. Luciferase-mRNA was also translated on collagen scaffold by eukaryotic cell extracts. Thus we have demonstrated the feasibility of controllable protein synthesis on collagen scaffolds by ribosomal machinery.


Assuntos
Sistema Livre de Células , Colágeno/genética , Biossíntese de Proteínas , RNA Mensageiro/genética , Sistema Livre de Células/metabolismo , Colágeno/química , Escherichia coli/genética , Proteínas de Fluorescência Verde/análise , Proteínas de Fluorescência Verde/genética , Luciferases/análise , Luciferases/genética , Substâncias Luminescentes/análise , Substâncias Luminescentes/metabolismo , Proteínas Ligantes de Maltose/química , Proteínas Ligantes de Maltose/genética , Multimerização Proteica , Estabilidade Proteica , RNA Mensageiro/química , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/genética
17.
Proc Natl Acad Sci U S A ; 110(37): 14900-5, 2013 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-23980159

RESUMO

Experimental evidence suggests the existence of an RNA molecular prebiotic entity, called by us the "protoribosome," which may have evolved in the RNA world before evolution of the genetic code and proteins. This vestige of the RNA world, which possesses all of the capabilities required for peptide bond formation, seems to be still functioning in the heart of all of the contemporary ribosome. Within the modern ribosome this remnant includes the peptidyl transferase center. Its highly conserved nucleotide sequence is suggestive of its robustness under diverse environmental conditions, and hence on its prebiotic origin. Its twofold pseudosymmetry suggests that this entity could have been a dimer of self-folding RNA units that formed a pocket within which two activated amino acids might be accommodated, similar to the binding mode of modern tRNA molecules that carry amino acids or peptidyl moieties. Using quantum mechanics and crystal coordinates, this work studies the question of whether the putative protoribosome has properties necessary to function as an evolutionary precursor to the modern ribosome. The quantum model used in the calculations is density functional theory--B3LYP/3-21G*, implemented using the kernel energy method to make the computations practical and efficient. It occurs that the necessary conditions that would characterize a practicable protoribosome--namely (i) energetic structural stability and (ii) energetically stable attachment to substrates--are both well satisfied.


Assuntos
Evolução Biológica , RNA/química , RNA/metabolismo , Ribossomos/química , Ribossomos/metabolismo , Modelos Moleculares , Peptidil Transferases/química , Peptidil Transferases/metabolismo , Teoria Quântica , Dobramento de RNA , Termodinâmica
18.
Philos Trans R Soc Lond B Biol Sci ; 366(1580): 2972-8, 2011 Oct 27.
Artigo em Inglês | MEDLINE | ID: mdl-21930590

RESUMO

Based on the presumed capability of a prebiotic pocket-like entity to accommodate substrates whose stereochemistry enables the creation of chemical bonds, it is suggested that a universal symmetrical region identified within all contemporary ribosomes originated from an entity that we term the 'proto-ribosome'. This 'proto-ribosome' could have evolved from an earlier machine that was capable of performing essential tasks in the RNA world, called here the 'pre-proto-ribosome', which was adapted for producing proteins.


Assuntos
Evolução Molecular , RNA Mensageiro/química , Ribossomos/química , Aminoácidos/química , Sítios de Ligação , Catálise , Biossíntese de Proteínas , Dobramento de RNA , Estabilidade de RNA , RNA Catalítico/química , RNA Ribossômico/química , RNA de Transferência/química , Ribossomos/genética , Estereoisomerismo
19.
Proc Natl Acad Sci U S A ; 108(7): 2717-22, 2011 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-21282615

RESUMO

The structures of the large ribosomal subunit of Deinococcus radiodurans (D50S) in complex with the antibiotic lankamycin (3.2 Å) and a double antibiotic complex of lankamycin and lankacidin C (3.45 Å) have been determined, in continuation of previous crystallographic studies on lankacidin-D50S complex. These two drugs have been previously reported to inhibit ribosomal function with mild synergistic effect. Lankamycin, a member of the macrolide family, binds in a similar manner to erythromycin. However, when in complex with lankacidin, lankamycin is located so that it can form interactions with lankacidin in the adjacent ribosomal binding site. When compared to the well-documented synergistic antibiotics, Streptogramins A and B, the pair of lankacidin and lankamycin bind in similar sites, the peptidyl transferase center and nascent peptide exit tunnel, respectively. Herein, we discuss the structural basis for antibiotic synergism and highlight the key factors involved in ribosomal inhibition.


Assuntos
Antibacterianos/química , Eritromicina/análogos & derivados , Macrolídeos/química , Modelos Moleculares , Subunidades Ribossômicas Maiores/química , Sítios de Ligação/genética , Cristalografia , Pegada de DNA , Sinergismo Farmacológico , Eritromicina/química , Concentração Inibidora 50 , Estrutura Molecular , RNA Ribossômico 23S/genética , Difração de Raios X
20.
Biochem Soc Trans ; 38(2): 422-7, 2010 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-20298195

RESUMO

Structural analysis, supported by biochemical, mutagenesis and computational evidence, indicates that the peptidyltransferase centre of the contemporary ribosome is a universal symmetrical pocket composed solely of rRNA. This pocket seems to be a relic of the proto-ribosome, an ancient ribozyme, which was a dimeric RNA assembly formed from self-folded RNA chains of identical, similar or different sequences. This could have occurred spontaneously by gene duplication or gene fusion. This pocket-like entity was capable of autonomously catalysing various reactions, including peptide bond formation and non-coded or semi-coded amino acid polymerization. Efforts toward the structural definition of the early entity capable of genetic decoding involve the crystallization of the small ribosomal subunit of a bacterial organism harbouring a single functional rRNA operon.


Assuntos
RNA Catalítico/genética , RNA Catalítico/fisiologia , Ribossomos/genética , Ribossomos/fisiologia , Evolução Molecular , Modelos Biológicos , Modelos Moleculares , Conformação de Ácido Nucleico , Ligação Proteica , Biossíntese de Proteínas/fisiologia , RNA Catalítico/química , RNA Catalítico/metabolismo , Subunidades Ribossômicas Maiores de Bactérias/química , Subunidades Ribossômicas Maiores de Bactérias/metabolismo , Subunidades Ribossômicas Menores de Bactérias/química , Subunidades Ribossômicas Menores de Bactérias/metabolismo , Subunidades Ribossômicas Menores de Bactérias/ultraestrutura , Ribossomos/metabolismo
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA