The elongation phase of protein synthesis.
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Animals↗
Biomedical subjects
P B Moore
Publications and source records attributed to P B Moore.
Molecular mimicry in protein synthesis?
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Binding Sites↗
Ribosomes seen through a glass less darkly.
Electron microscopists have made important progress recently in their quest to determine the structure of the ribosome. New insights into the mechanism of protein synthesis are beginning to emerge, and substantial progress is likely in the immediate future.
Escherichia coli↗
The sarcin/ricin loop, a modular RNA.
The conformation of a 29 base oligonucleotide called E73 has been determined in solution by NMR. E73 includes a 23 nucleotide sequence that is identical with that of a the alpha-sarcin and ricin-sensitive loop (SRL) from rat 28 S rRNA, and like the SRL in intact ribosomes, E73 is a substrate for both toxins. The SRL includes a long, conserved sequence found in the RNA of all large ribosomal subunits, which plays a critical role in the factor-dependent steps of protein synthesis. The spectroscopic observations and analysis that led to the determination of the conformation of E73 are presented. The SRL in E73 has a highly structured conformation, which is stabilized by several non-Watson-Crick base-pairs, and many properties of the SRL in the ribosome can be understood assuming that the conformation of E73 and that of the SRL in the ribosome are the same. The role of the SRL in protein synthesis is discussed in light of the conformation of E73, as is the modular relationship that exists between the conformation of the SRL and other smaller RNAs.
Base Sequence↗
The crystal structure of elongation factor G complexed with GDP, at 2.7 A resolution.
Elongation factor G (EF-G) catalyzes the translocation step of protein synthesis in bacteria, and like the other bacterial elongation factor, EF-Tu--whose structure is already known--it is a member of the GTPase superfamily. We have determined the crystal structure of EF-G--GDP from Thermus thermophilus. It is an elongated molecule whose large, N-terminal domain resembles the G domain of EF-Tu, except for a 90 residue insert, which covers a surface that is involved in nucleotide exchange in EF-Tu and other G proteins. The tertiary structures of the second domains of EF-G and EF-Tu are nearly identical, but the relative placement of the first two domains in EF-G--GDP resembles that seen in EF-Tu--GTP, not EF-Tu--GDP. The remaining three domains of EF-G look like RNA binding domains, and have no counterparts in EF-Tu.
Amino Acid Sequence↗
Comparison of primary angioplasty versus thrombolytic therapy for acute myocardial infarction. Alabama Registry of Myocardial Ischemia Investigators.
To determine the relative merits of primary percutaneous transluminal coronary angioplasty (PTCA) and intravenous thrombolytic therapy for acute myocardial infarction, 12 tertiary care hospitals entered patients who had > or = 30 minutes of chest pain and were admitted to a cardiac intensive care unit within 12 hours of symptom onset into a prospective registry. Of 1,170 such patients, 118 (10%) underwent primary PTCA and 230 (19%) received intravenous thrombolytic therapy within 6 hours of registry hospital admission (144 at the registry hospital and 86 prior to arrival at the registry hospital). Baseline demographic characteristics of PTCA and thrombolytic subgroups were remarkably similar. The interval from initial evaluation at the registry hospital to treatment was shorter with intravenous thrombolytic therapy than with primary PTCA (64 vs 104 minutes, p < 0.001), as was the interval from pain onset to treatment (184 vs 252 minutes, p < 0.001). Among the 230 thrombolytic patients, coronary arteriography and PTCA were performed within the first 24 hours in 44% and 18%, respectively, and during the entire hospitalization in 90% and 49%, respectively. During hospitalization, blood was transfused in 16% of the 230 thrombolytic patients versus 5.9% of the 118 PTCA patients (p < 0.001). Otherwise, adverse events during the initial hospitalization were similar in PTCA and thrombolytic groups. Survival at 1-year follow-up was 88% in the PTCA group and 91% in the thrombolytic group (p = NS), and survival free of reinfarction was 85% and 88%, respectively (p = NS).(ABSTRACT TRUNCATED AT 250 WORDS)
Adult↗
Structural characterization of a ribonuclease III processing signal.
The structure of a ribonuclease III processing signal from bacteriophage T7 was examined by NMR spectroscopy, optical melting, and chemical and enzymatic modification. A 41 nucleotide variant of the T7 R1.1 processing signal has two Watson-Crick base-paired helices separated by an internal loop, consistent with its predicted secondary structure. The internal loop is neither rigidly structured nor completely exposed to solvent, and seems to be helical. The secondary structure of R1.1 RNA is largely insensitive to the monovalent cation concentration, which suggests that the monovalent cation sensitivity of secondary site cleavage by RNase III is not due to a low salt-induced RNA conformational change. However, spectroscopic data show that Mg2+ affects the conformation of the internal loop, suggesting a divalent cation binding site(s) within this region. The Mg(2+)-dependence of RNase III processing of some substrates may reflect not only a requirement for a divalent cation as a catalytic cofactor, but also a requirement for a local RNA conformation which is divalent cation-stabilized.
Base Sequence↗
An evaluation of the predictive validity and inter-rater reliability of clinical diagnostic criteria for senile dementia of Lewy body type.
Several recent autopsy studies suggest that senile dementia of Lewy body type (SDLT) may be the second most common neuropathologic cause of dementia in the elderly, accounting for 7 to 30% of all cases. Operational criteria for the antemortem clinical diagnosis of SDLT have already been proposed by our group. The performance of these is now examined by randomizing the case notes from a new series of SDLT, Alzheimer, and multi-infarct dementia patients for psychiatric assessment by four raters of varying clinical experience and blind to pathologic diagnosis. Using the SDLT criteria, the two most experienced raters agreed in 94% of cases (kappa = 0.87), with the least experienced rater agreeing in 78% (kappa = 0.50). Diagnostic specificity for SDLT was uniformly high (90.0 to 97.0%), with a mean sensitivity of detection of 74%, and was greater by the experienced (90.0%) than the least experienced (55%) clinician. The antemortem identification of SDLT patients can therefore be achieved with a high degree of diagnostic specificity using such operationalized criteria, although there remains a minority of patients who present with either "typical" Alzheimer-type symptoms or with paranoid or delusional symptoms in the absence of substantial cognitive impairment. Sensitivity to neuroleptics may be a useful diagnostic pointer in these patients.
Aged↗
The conformation of the sarcin/ricin loop from 28S ribosomal RNA.
The sarcin/ricin loop is a highly conserved sequence found in the RNA of all large ribosomal subunits. The cytotoxins alpha-sarcin and ricin both inactivate ribosomes by cleaving a single bond in that loop. Once it has been attacked, ribosomes no longer interact with elongation factors properly, and translation stops. We have determined the conformation of the sarcin/ricin loop by multinuclear NMR spectroscopy using E73, a 29-nucleotide RNA that has the sarcin/ricin loop sequence and that is sensitive to both toxins in vitro. The sarcin/ricin loop has a compact structure that contains several purine.purine base pairs, a GAGA tetraloop, and a bulged guanosine adjacent to a reverse Hoogsteen A.U pair. It is stabilized by an unusual set of cross-strand base-stacking interactions and imino proton to phosphate oxygen hydrogen bonds. In addition to having interesting structural features, this model explains many of the biochemical observations made about the loop's structure and its reactivity with cytotoxins, and it sheds light on the loop's interactions with elongation factors.
Animals↗
Assignment of NH resonances in nucleic acids using natural abundance 15N-1H correlation spectroscopy with spin-echo and gradient pulses.
It is well known that 2D 15N-1H correlation spectra can resolve overlapped imino proton resonances in the downfield NMR spectra of nucleic acids according to their 15N chemical shifts, and that these resonances can be assigned by base type on that basis, independent of conformation. This information can be extremely important in determining the solution structure of a nucleic acid by NMR, but previously could only be obtained using 15N-labeled, or very concentrated samples. Here we report the design of a gradient-enhanced, jump-return spin echo version of an 15N-1H HMQC experiment (GE-JRSE HMQC) that is sensitive enough to work on unlabeled nucleic acid samples at normal NMR concentrations. This experiment has led to the assignment of imino proton resonances with non-Watson Crick chemical shifts in the spectrum of a 29 residue oligoribonucleotide that models the sarcin/ricin loop from 28S rRNA.
Animals↗
Effect of silicon on gastrointestinal absorption of aluminium.
The reported geographical association between Alzheimer's disease and levels of aluminium (Al) in water supplies may reflect the inverse relation between Al and silicon (Si) concentrations in water, and the potential for Si to reduce the bioavailability of the metal. We tested this hypothesis using isotopic 26Al tracer administered orally to five healthy volunteers in the presence and absence of Si. Dissolved Si, at a concentration found in some water supplies (100 mumol/L), reduced the peak plasma 26Al concentration to 15% of the value obtained in the absence of Si. The results indicate that dissolved Si is an important factor in limiting the absorption of dietary Al.
Administration, Oral↗
Differential regulation of IGF-1 and IGF-binding protein-1 by dietary composition in humans.
Although it is known that circulating levels of the insulin-like growth factors (IGFs) and the IGF-binding proteins (IGFBPs) fluctuate in response to changes in nutritional status, there is little information regarding either relative contributions from different dietary components or regulation by insulin in nondiabetic subjects. To define dietary contributions to IGF regulation, the authors examined the effects of fasting and hypocaloric diets of differing nutritional composition on serum IGF-1 and a IGFBP-1 in 16 healthy, obese adult women. Subjects received an isocaloric diet for 6 days, followed by 14 days of calorie restriction (fasting or a hypocaloric diet enriched in either protein, fat, or carbohydrate), and by 4 days refeeding. All diets produced 6-8% weight loss over 14 days with little difference between groups. The "protein-sparing" diet sustained nitrogen balance (+1.2 g/d, versus -4.5 g/d for the other three groups; p < 0.05). Serum IGF-1 levels decreased during calorie restriction with fasting or with diets high in fat or carbohydrates (CHO; combined mean 40 +/- 7%) but showed little change with the high protein regimen (3 +/- 16%; p < 0.05 compared to the other diets). In contrast, IGFBP-1 increased during calorie restriction in all four groups but significantly less with the high CHO diet (43 +/- 17% above baseline) than with the other diets (168 +/- 31%; p < 0.05). Levels of IGF-1 were correlated with nitrogen balance (r = 0.51; p < 0.05) but levels of IGFBP-1 were not. Although IGFBP-1 levels inversely correlated with measures of insulin secretion, IGF-1 levels did not.(ABSTRACT TRUNCATED AT 250 WORDS)
Adult↗
Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures.
A model for the solution structure of an RNA tetraplex, (rUGGGGU)4, has been obtained by two-dimensional NMR spectroscopy and molecular dynamics. The molecule is parallel stranded and Hoogsteen base-paired in 50 mM KCl, and it is so stable that three of its six imino protons have exchange half-lives measured in days at 40 degrees C. The tetraplex is stabilized by base stacking and by the hydrogen bonds in four G quartets and at least one U quartet. This is the first indication of the existence of U-quartet structures of which we are aware.
Hydrogen Bonding↗
RNA catalysis. The universe expands.
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Animals↗
NMR analysis of helix I from the 5S RNA of Escherichia coli.
The structure of helix I of the 5S rRNA from Escherichia coli has been determined using a nucleolytic digest fragment of the intact molecule. The fragment analyzed, which corresponds to bases (-1)-11 and 108-120 of intact 5S rRNA, contains a G-U pair and has unpaired bases at its termini. Its proton resonances were assigned by two-dimensional NMR methods, and both NOE distance and coupling constant information have been used to calculate structural models for it using the full relaxation matrix algorithm of the molecular dynamics program XPLOR. Helix I has A-type helical geometry, as expected. Its most striking departure from regular helical geometry occurs at its G-U, which stacks on the base pair to the 5' side of its G but not on the base pair to its 3' side. This stacking pattern maximizes interstrand guanine-guanine interactions and explains why the G-U in question fails to give imino proton NOE's to the base pair to 5' side of its G. These results are consistent with the crystal structures that have been obtained for wobble base pairs in tRNAPhe [Mizuno, H., & Sundaralingam, M. (1978) Nucleic Acids Res. 5, 4451-4461] and A-form DNA [Rabbinovich, D., Haran, T., Eisenstein, M., & Shakked, Z. (1988) J. Mol. Biol. 200, 151-161]. The conformations of the terminal residues of helix I, which corresponds to bases (-1)-11 and 108-120 of native 5S RNA, are less well-determined, and their sugar puckers are intermediate between C2' and C3'-endo, on average.
Base Composition↗
Mentally handicapped epileptic patients: psychiatric illness and personality disorder.
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Carbamazepine↗
An NMR characterization of the regA protein-binding site of bacteriophage T4 gene 44 mRNA.
The conformations of two RNA dodecamers that differ markedly in affinity for the regA protein from bacteriophage T4 have been examined by NMR to see if the ability of that protein to discriminate between mRNAs is based on pre-existing differences in their three-dimensional structures. One of the RNAs examined has the same sequence as the site where regA protein binds when it inhibits the expression of gene 44's mRNA. The second RNA differs from the first in having a U instead of a G at position -9; it binds regA protein 100 times less tightly. The NMR data indicate that both RNAs have similar single-stranded conformations and that they each resemble an isolated strand of a double helix. They also show that most, if not all of the ribose rings in both molecules have appreciable 2'-endo puckering. It is unlikely that regA protein distinguishes between these two molecules on the basis of differences in their global conformations in solution.
ADP Ribose Transferases↗
Tetramerization of an RNA oligonucleotide containing a GGGG sequence.
Poly rG can form four-stranded helices. The Hoogsteen-paired quartets of G residues on which such structures depend are so stable that they will form in 5'-GMP solutions, provided that Na+ or K+ are present (see for example, refs 2-4). Telomeric DNA sequences, which are G-rich, adopt four-stranded antiparallel G-quartet conformations in vitro, and parallel tetramerization of G-rich sequences may be involved in meiosis. Here we show that RNAs containing short runs of Gs can also tetramerize. A 19-base oligonucleotide derived from the 5S RNA of Escherichia coli (strand III), 5'GCCGAUGGUAGUGUGGGGU3', forms a K(+)-stabilized tetrameric aggregate that depends on the G residues at its 3' end. This complex is so stable that it would be surprising if similar structures do not occur in nature.
Base Sequence↗