Biomedical subjects

P B Moore

Publications and source records attributed to P B Moore.

At least 55 records · Page 3Linked to original sources

PubMed1998

Gastrointestinal absorption of aluminium and citrate in man.

Aluminium (Al) is an abundant terrestrial element, but toxic to tissues, including brain. The body is largely protected because systemic Al absorption is very low and in normal individuals almost all absorbed Al is excreted from the body. However gastrointestinal (Gl) absorption is enhanced by organic acids, including citrate. Aluminium and citrate Gl absorption was measured in three healthy males, aged 40-46. After overnight fast, subjects drank a 100 ml fruit drink containing 280 mg Al and 3.2 g citrate (104 and 167 mM, respectively). Al was measured in timed blood and urine samples by GFAAS and serum citrate by enzymatic assay. Blood Al peaked by an increase of 13 +/- 2.1 micrograms/l after 87 +/- 19 min then fell slowly over 24 h. Plasma citrate peaked after 32 min, returning to baseline by 90 min. Al was excreted at a constant rate for the first 24 h, 0.4% of the dose being excreted in urine by this time. It is unlikely that Al is absorbed as Al citrate because the blood citrate peak preceded the Al peak by 45-60 min.

Administration, Oral↗

PubMed1998

Sensory and hedonic judgments of common foods by lean consumers and consumers with obesity.

OBJECTIVE: To establish differences between lean subjects and subjects with obesity in subjective reports of predominant taste and texture attributes of common foods, and the relationships of these qualities and foods with overall liking. RESEARCH METHODS AND PROCEDURES: Twenty lean (body mass index: 20 to 25 kg/m2) nondieting healthy adults and 23 (body mass index: > or = 30 kg/m2) nondieting healthy adults with obesity assigned ratings for pleasantness and predominant sensory attributes to 50 common foods in 14 food groups using a questionnaire. They completed the Dutch Eating Behavior Questionnaire. Body composition was assessed by bioelectrical impedance. RESULTS: There were no significant group differences between pleasantness scores overall; however, lean subjects assigned higher scores to fruits and vegetables, to foods self-classified as sweet and as salty/savory, and to foods grouped in the highest and lowest quintiles of percentage food energy from fat. There were no group differences in free-choice texture descriptors applied to foods, but correspondence analysis revealed that subjects with obesity associated coarse, slippery, tough, and fatty textures with "dislike extremely," whereas lean subjects associated grainy, moist, doughy, and fibrous texture with "like extremely." Analyses reduced texture terms to 39 key descriptors for use in subsequent work. Groups did not significantly differ in reported external or restrained eating behaviors, but subjects with obesity scored significantly higher for reported emotional eating. DISCUSSION: Differences in preferences for listed common foods exist between weight status groups according to taste, food group, and texture. Consumers can make textural descriptions of foods that could be used to assess sensory and hedonic qualities of actual food choices.

Adolescent↗

PubMed1998

Molecular dynamics simulation of a synthetic ion channel.

A molecular dynamics simulation has been performed on a synthetic membrane-spanning ion channel, consisting of four alpha-helical peptides, each of which is composed of the amino acids leucine (L) and serine (S), with the sequence Ac-(LSLLLSL)3-CONH2. This four-helix bundle has been shown experimentally to act as a proton-conducting channel in a membrane environment. In the present simulation, the channel was initially assembled as a parallel bundle in the octane portion of a phase-separated water/octane system, which provided a membrane-mimetic environment. An explicit reversible multiple-time-step integrator was used to generate a dynamical trajectory, a few nanoseconds in duration for this composite system on a parallel computer, under ambient conditions. After more than 1 ns, the four helices were found to adopt an associated dimer state with twofold symmetry, which evolved into a coiled-coil tetrameric structure with a left-handed twist. In the coiled-coil state, the polar serine side chains interact to form a layered structure with the core of the bundle filled with H2O. The dipoles of these H2O molecules tended to align opposite the net dipole of the peptide bundle. The calculated dipole relaxation function of the pore H2O molecules exhibits two reorientation times. One is approximately 3.2 ps, and the other is approximately 100 times longer. The diffusion coefficient of the pore H2O is about one-third of the bulk H2O value. The total dipole moment and the inertia tensor of the peptide bundle have been calculated and reveal slow (300 ps) collective oscillatory motions. Our results, which are based on a simple united atom force-field model, suggest that the function of this synthetic ion channel is likely inextricably coupled to its dynamical behavior.

Amino Acid Sequence↗

PubMed1998

Mood disturbances in motor neurone disease.

This study explores the severity of depression and anxiety experienced by patients suffering from motor neurone disease and seeks to link this to illness progression, recent life events and personality factors. The 18 patients who participated in the study were assessed for the presence of psychiatric symptoms using the Beck Depressive Inventory and the Hospital Anxiety and Depression Scale. The severity of the illness and the life events during the course of the illness were measured using the Norris scale and the Holmes and Rahe Social Readjustment Rating Scale. A personality assessment was made using the Eysenck Personality Questionnaire (EPQ). Only four out of these 18 patients (23%) in the study suffered depression and of these three (17%) were mild and one (6%) was of moderate severity. A further six patients (33%) were rated as borderline depression. Only two patients suffered from an anxiety state and both had concurrent mild depression. No correlations of depression were found with the life events or illness progression. Only the L sub-scale of the EPQ (15.6+/-4.9) exceeds values expected for the general population. Despite the severity and frequency of life events during the course of the illness, most patients do not develop a depressive illness. The reason for this unexpected result is unclear. Depression is believed to result from underactivity of the serotonergic neurotransmitter system. However, in MND this system is relatively unaffected in contrast to dementia and other neurodegenerative disorders. The patients' high L scores suggest that many may cope with their illness by widespread use of denial as a psychological defence.

Adult↗

PubMed1998

Structure and stability of variants of the sarcin-ricin loop of 28S rRNA: NMR studies of the prokaryotic SRL and a functional mutant.

NMR has been used to examine the conformational properties of two variants of the sarcin-ricin loop (SRL) from eukaryotic 28S rRNA, which is essential for elongation factor interactions with the ribosome: (1) its bacterial homologue, which lacks two of the bases that flank the conserved 12-nt sequence in the middle of the SRL, but which is functionally equivalent, and (2) a functionally active variant of the eukaryotic SRL in which the bulged G within the conserved sequence is replaced by an A. The data indicate that, although the bacterial SRL is less stable than the eukaryotic SRL, its conformation is closely similar. Furthermore, even though replacement of the bulged G in the SRL with an A seriously destabilizes the center of the loop, its effect on the overall conformation of the SRL appears to be modest. In the course of this work, it was serendipitously discovered that at neutral pH, the C8 proton of the bulged G, in both PRO-SRL and E73, exchanges about 10 times faster than it does in GMP.

Adenosine↗

PubMed1998

Molecular dynamics simulation of a hydrated diphytanol phosphatidylcholine lipid bilayer containing an alpha-helical bundle of four transmembrane domains of the influenza A virus M2 protein.

An alpha-helical bundle composed of four transmembrane portions of the M2 protein from the Influenza A virus has been studied in a hydrated diphytanol phosphatidylcholine bilayer using molecular dynamics (MD) calculations. Experimentally, the sequence utilized is known to aggregate as a four-helix bundle and act as a pH-gated proton-selective ion channel, which is blocked by the drug amantadine hydrochloride. In the presented simulation, the ion channel was initially set up as a parallel four-helix bundle. The all-atom simulation consisted of almost 16,000 atoms, described classically, using a forcefield from the CHARMM22 database. Bilayers with and without the bundle were shown to be stable throughout the nanosecond timescale of the MD simulation. Structural and dynamical properties of the bilayer both with and without the transmembrane protein are reported.

Computer Simulation↗

PubMed1998

The three-dimensional structure of the ribosome and its components.

Exciting progress has been made in the last decade by those who use physical methods to study the structure of the ribosome and its components. The structures of 10 ribosomal proteins and three isolated ribosomal protein domains are known, and the conformations of a significant number of rRNA sequences have been determined. Electron microscopists have made major advances in the analysis of images of ribosomes, and microscopically derived ribosome models at resolutions approaching 10A are likely quite soon. Furthermore, ribosome crystallographers are on the verge of phasing the diffraction patterns they have had for several years, and near-atomic resolution models for entire ribosomal subunits could emerge from this source at any time. The literature relevant to these developments is reviewed below.

Animals↗

PubMed1998

Solution structure of a substrate for the archaeal pre-tRNA splicing endonucleases: the bulge-helix-bulge motif.

The structure of the bulge-helix-bulge motif that constitutes the intron/exon splice site in H. volcanii pre-tRNATrp has been determined by NMR spectroscopy. The conformations of the two 3 nt bulges, where the pre-tRNA is cleaved, are stabilized by stacking interactions between bulge nucleotides and bases in the adjacent Watson-Crick helices and by a network of backbone hydrogen bonds. Both bulges are presented on the same minor groove face of the central 4 bp helix, and the overall structure has approximate two-fold symmetry, which makes it well-suited for attack by archaeal splicing endonucleases, which are symmetric dimers.

Archaeal Proteins↗

PubMed1997

The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins.

BACKGROUND: 5S ribosomal RNA is the smallest rRNA. Its Watson-Crick helices were identified more than 20 years ago, but the conformations of its loops have long defied analysis. One of the three arms of 5S rRNA, residues 69-106 in Escherichia coli, contains a 14-residue internal loop called loop E. The sequence of loop E is conserved within kingdoms, and is terminated by a pyrimidine-rich loop called loop D. Loop E is the binding site for the ribosomal protein L25 in the E. coli ribosome. RESULTS: The solution structure of a 42-nucleotide derivative of E. coli 5S rRNA that includes loops D and E has been determined by nuclear magnetic resonance spectroscopy. Formally, loop E is not a loop at all; it is a double helical structure that contains seven, consecutive non-Watson-Crick base pairs. The major groove of the molecule is narrowed in loop E, and an unusual array of hydrogen-bond donors and acceptors appear in its minor groove. Loop D, which on paper looks like a three-pyrimidine terminal loop closed by a GC, is better thought of as a five-base loop because its closing GC is not a normal Watson-Crick pair. The two pyrimidines on the 5'-side of the loop are stacked on each other, and tilt into the minor groove of the adjacent helix. The third pyrimidine is fully exposed to solvent. CONCLUSIONS: This structure rationalizes all the biochemical and chemical protection data available for the loop E-loop D arm of intact 5S rRNA. While the molecule is double helical over its entire length, the geometry of its internal loop is highly irregular, and its irregularities may explain why the loop E-loop D arm of 5S rRNA interacts specifically with ribosomal protein L25 in E. coli.

Algorithms↗

PubMed1997

Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.

Two new RNA structures portray how non-Watson-Crick base pairs and metal ions can produce a unique RNA shape suitable for recognition by proteins. The crystal structures of a 62 nt domain of E. coli 5S ribosomal RNA and a duplex dodecamer encompassing an internal loop E have been determined at 3.0 and 1.5 A, respectively. This loop E region is distorted by three "cross-strand purine stacks" and three novel, water-mediated noncanonical base pairs and stabilized by a four metal ion zipper. These features give its minor groove a unique hydrogen-bonding surface and make the adjacent major groove wide enough to permit recognition by the ribosomal protein L25, which is expected to bind to this surface.

Cross-Linking Reagents↗

PubMed1997

The structure of an essential splicing element: stem loop IIa from yeast U2 snRNA.

BACKGROUND: Eukaryotic genes are usually transcribed as precursor mRNAs which are then spliced, removing introns to produce functional mRNAs. Splicing is performed by the spliceosome and provides an important level of post-translational control of gene expression. Stem loop IIa from U2 small nuclear (sn)RNA is required for the efficient association of the U2 small nuclear ribonuclear protein (snRNP) with the nascent spliceosome in yeast. Genetic analysis suggests that stem loop IIa is involved in RNA-protein interactions early in splicing, and it may also interact with other RNA sequences in U2. The sequence of loop IIa is well conserved, consistent with the idea that this loop is important for function. RESULTS: We have solved the structure of U2A, a 20-base analogue of stem loop IIa from Saccharomyces cerevisiae, using NMR and restrained molecular dynamics. In the process, we have demonstrated the efficacy of a new structure calculation protocol, torsion angle molecular dynamics. The structure that has emerged, which is consistent with the in vivo chemical protection data available for stem loop IIa in the context of intact U2 snRNA, contains a sheared GA pair followed by a U-turn in the loop. The U-turn conformation, which resembles the U-turns in tRNA anticodon loops, makes this stretch of U2 snRNA an obvious target for interactions with proteins and/or other RNA sequences. CONCLUSIONS: The phenotypes of many stem loop IIa mutants can be rationalized assuming that the U-turn conformation in the loop must be preserved for efficient splicing. This observation, combined with the phylogenetic conservation of its sequence, suggests that the conformation of the loop of stem loop IIa is essential for its function in pre-mRNA splicing.

Base Sequence↗

PubMed1997

The conformational properties of elongation factor G and the mechanism of translocation.

The elongation phase of protein synthesis is promoted by two G proteins, elongation factor Tu (EF-Tu), which delivers aminoacyl tRNAs to the ribosome, and elongation factor G (EF-G), which catalyzes translocation. Crystallographic investigations have revealed that EF-G.GDP resembles the EF-Tu.GTP.(aminoacyl tRNA) complex, and it has been proposed that the translocase function of EF-G is derived from this similarity [Nissen, P., et al. (1995) Science 270, 1464]. However, its significance is uncertain because the affinity of EF-G.GDP for the ribosome is much lower than that of the ternary complex it resembles and because EF-Tu.GDP, the form of EF-Tu that has low ribosome affinity, has a conformation radically different from that of EF-Tu.GTP or EF-Tu in the ternary complex. The small-angle X-ray scattering study described here was undertaken to ascertain if the form of EF-G that has high ribosome affinity, EF-G.GTP, the structure of which is unknown, could be a mimic of EF-Tu.GDP. The data show that nucleotide-free EF-G, EF-G.GDP, EF-G. GTP, and EF-G.GMPPCP cannot be distinguished by solution scattering and that it is likely they all resemble crystalline EF-G.GDP. Since an EF-Tu-like change would easily have been detected, it follows that it does not occur in EF-G. These observations have significant implications for the mechanism of translocation.

Biological Transport↗

PubMed1997

On the conformation of the anticodon loops of initiator and elongator methionine tRNAs.

The solution conformations of analogues of initiator and elongator tRNA anticodon stem-loops have been compared by NMR. The data indicate that both have conformations closely similar to those reported for crystalline elongator tRNAs. The two loops differ in their dynamics, however: that of the elongator analogue is more flexible than its initiator counterpart. The anticodon stem-loops of initiator tRNAs are more likely to be distinguished from those of elongator tRNAs during initiation on the basis of their distinctive stem sequences, than they are by differences in the conformations of their anticodon loops.

Anticodon↗

PubMed1997

Ribosomes: protein synthesis in slow motion.

Using image reconstruction methods, electron microscopists can now visualize ribosomes at resolutions so high that the changes in the positions of ribosome-bound tRNAs which occur during protein synthesis can be seen.

Bacteria↗

PubMed1997

Gastrointestinal absorption of aluminum is increased in Down's syndrome.

Individuals with Down's Syndrome (DS) develop the neuropathological features of senile dementia of the Alzheimer's type (SDAT) by early middle age. Because of recent evidence that gastrointestinal (GI) aluminum (Al) absorption is increased in patients with SDAT, and that Al may contribute to associated neuropathological changes, we have investigated the GI uptake of Al in patients with DS by two methods. The first measured the absorption of 27Al at concentrations associated with antacid use, in the presence of citrate, using atomic absorption spectrometry. There was no difference between basal blood concentrations of 27Al in 15 DS subjects (36-46 years) and 15 age-matched controls. The mean increase in 27Al blood concentrations 60 minutes after the dose of Al was four times greater in the DS group than in controls (p < 0.001). The second measured GI absorption of 26Al under normal dietary conditions using accelerator mass spectrometry. With 26Al the mean Al absorption in DS subjects (n = 5) exceeded that of controls (n = 4) by a factor of 6 (p < 0.02). Although the mechanisms of enhanced absorption are unknown, the data indicate that similar abnormalities in the GI handling of Al occur in both SDAT and DS suggesting that it may be advisable to minimize dietary exposure to Al in subjects at risk of developing Alzheimer-type pathology.

Adult↗

PubMed1997

The conformation of ribosomes and rRNA.

During the past 18 months, electron microscopists have published two reconstructions of the Escherichia coli ribosome, independently derived from images of unstained particles. The resolutions of their images are 20-25 A-much higher than any previously available. During the same time, NMR spectroscopists have provided an atomic-resolution model for the A-site region of 16S rRNA complexed with paromomycin that explains much of what is known about the interaction of aminoglycoside antibiotics with ribosomes.

Microscopy, Electron↗

PubMed1997

Measurement of diffusion constants for nucleic acids by NMR.

Pulsed field-gradient NMR experiments can be used to measure the diffusion constants of nucleic acids. The diffusion constants measured in this way for double-helical DNAs of defined length agree well both with theory and with measurements done using other techniques. When applied to RNAs, this experiment easily distinguishes duplex RNAs from RNA hairpins and thus it can solve one of the perennial problems faced by RNA spectroscopists, i.e. assessing whether their samples are monomeric or not.

DNA↗

PubMed1997

Use of chemically modified nucleotides to determine a 62-nucleotide RNA crystal structure: a survey of phosphorothioates, Br, Pt and Hg.

Two important challenges confronting RNA crystallographers are producing crystals and finding isomorphous heavy-atom derivatives. Non-isomorphism can be addressed by determining the phases using the multiwavelength anomalous dispersion (MAD) method. These phases can be greatly improved by combining phases from MAD experiments done on different heavy-atom derivatives. Heavy-atom derivatives can be created by chemically modifying the RNA through covalent attachment of bromine or mercury to C5 of pyrimidines or [Pt(NH3)3]2+ to N7 of guanine. While phosphorothioates can provide mercury binding sites, disorder can reduce their value for phase determination. The location of these chemical modifications is critical since crystallization of these derivatized RNAs is sensitive to heavy atom induced conformational alterations and crystal packing.

Base Sequence↗