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W R Taylor

Publications and source records attributed to W R Taylor.

At least 163 records · Page 9Linked to original sources
PubMed1991

Rapid charge movements and photosensitivity of visual pigments in salamander rods and cones.

1. Photosensitivities of visual pigments were determined by measuring early receptor currents (ERCs) in voltage-clamped photoreceptors from larval salamanders. 2. As expected from previous work of others, the ERC elicited by a brief flash consisted of a rapid inward component followed by a larger and slower outward component. The magnitude of the outward component corresponded to the movement of about 0.18 electronic charge across the membrane per photoisomerization. 3. The time course of the ERC was independent of the flash intensity, the flash wavelength and the magnitude of the response. The outward component of the cone ERC declined about twice as rapidly as the outward component of the rod ERC.. 4. The amplitude of the ERC decreased as successive flashes bleached the cell's pigment. Using the proportional relation between the size of the ERC and the number of pigment molecules photoisomerized, photosensitivities of the native A2 pigments in rods, red-sensitive cones, blue-sensitive cones and UV-sensitive cones were determined. Calculated solution photosensitivities for rhodopsin, red-sensitive and blue-sensitive cone pigments were not significantly different and the average value for all three pigments at their respective absorption maxima was (7.3 +/- 1.6) x 10(-9) micron 2 molecule-1. A value of 44.0 x 10(-9) micron 2 molecule-1 was obtained in a single UV-sensitive cone. 5. Substitution of the native dehydroretinal chromophore in the red-sensitive cone pigment with 11-cis-retinal increased the solution photosensitivity to (9.6 +/- 0.62) x 10(-9) micron 2 molecule-1. 6. We conclude that cone pigments have large molecular absorption cross-sections and high quantum efficiencies of photoisomerization. These properties seem well suited for the receptive molecules of a highly sensitive, miniaturized transducer.

Animals↗
PubMed1991

Sequence and structural analysis of surface protein antigen I/II (SpaA) of Streptococcus sobrinus.

Streptococcal antigen I/II or the surface protein antigen A (SpaA) of Streptococcus sobrinus is an adhesin which mediates binding of the organism to tooth surfaces. The complete sequence of the gene which encodes SpaA has been determined. The gene consists of 4,584 bp and encodes a protein of 1,528 amino acid residues. The deduced amino acid sequence shows extensive homology with those of the cell surface adhesins from Streptococcus mutans serotypes c and f and from Streptococcus sanguis. Structural analysis of the N-terminal region (residues 50 to 550), which is rich in alanine and includes four tandem repeats of an 82-residue sequence, suggests that it adopts an alpha-helical coiled-coil conformation. Cell surface hydrophobicity may be associated with this region. The C-terminal region is more conserved and includes two tandem repeats of a 39-residue proline-rich sequence. A further proline-rich sequence in this region is predicted to span the cell wall. Although a hydrophobic sequence is present in the C-terminal region, it appears to be too short to span the cell membrane. Anchoring of SpaA in the cell membrane may therefore require some form of posttranslational modification or association with another membrane protein.

Adhesins, Bacterial↗
PubMed1990

A rapid method of protein structure alignment.

A reduction in the time required to compare two protein structures has been achieved for a previously developed structure alignment method, by reducing the number of residue pair comparisons which must be performed between the two structures. Subsets of residue pairs are selected by an iterative procedure. Initially, selection is based on similarities in solvent accessible surface areas or torsional angles or a combination of both properties, giving subsets containing approximately 2% of the total number of residue pairs. Using these subsets, a rough comparison of the two structures is generated by the structural alignment program. The information returned from this can be used to identify more accurately topologically equivalent residues in the two proteins, thus enabling a new and much smaller subset (less than 0.2% of the total number of residue pairs) to be selected. The process of iterative refinement of the residue pair subsets is repeated once more, when in 95% of the structure comparisons tested, the correct alignment of the proteins was obtained. Times required to compare the structures using the refined subsets are insignificant compared to the initial comparison, so that considerable increases in speed are possible. The method was tested on two groups of proteins, a set of remotely related alpha/beta nucleotide proteins and the variable and constant domains of the immunoglobulins. Increases in speed ranging from 50-fold to greater than 150-fold were obtained depending on the degree of similarity of the two structures. In some comparisons the alignment was improved due to the reduction in noise obtained by comparing mainly equivalent residues.

Computer Simulation↗
PubMed1990

Hierarchical method to align large numbers of biological sequences.

The method presented here is intended as a compromise between finding a good overall alignment and the time taken to do so. Many multiple alignment algorithms spend an excessively large amount of effort trying to find the best global alignment. This time is often ill spent because the results of the standard dynamic programming alignment algorithm are dominated by the choice of gap penalty and the form of the score matrix, both of which have a poor theoretical foundation. Nonetheless, it is important that savings in time do not compromise the quality of the alignment. By using the consensus sequence approach, this danger is largely avoided as the conserved features of the sequences are quickly identified and preserved through further cycles. In the alignment of existing alignments, which is one of the more novel aspects of the method, each alignment was treated as an averaged consensus sequence with gaps making no contribution. This gives rise to the advantageous property that gaps will have a greater propensity to be inserted where there are already gaps and is equivalent to a local change in the gap penalty. This type of behavior represents a transition away from the homogeneous scoring schemes used in aligning two sequences toward a scoring scheme that depends on position in the sequence. The alignment of consensus sequences thus forms a bridge between simple pair alignment and the alignment of discrete patterns in which sequence features and allowed gap locations are exaggerated. To complete this transition the program described above has been integrated into the earlier pattern matching (template) program. Such templates can reliably locate sequence similarities that are too weak or scattered to be found by the more standard alignment methods and should therefore produce a further condensation of the sequence data bank. Only by continually extending our knowledge of the relationships between sequences to increasingly distant similarities can we hope to avoid being overwhelmed by the increasing amount of data.

Algorithms↗
PubMed1990

Concomitant activation of two types of glutamate receptor mediates excitation of salamander retinal ganglion cells.

1. Cells in the ganglion cell layer of salamander retinal slices were voltage clamped using patch pipettes. Light elicited transient excitatory postsynaptic currents (EPSCs) in on-off ganglion cells and sustained EPSCs in on ganglion cells. Light-evoked inhibitory postsynaptic currents in these cells could be blocked by 100 microM-bicuculline methobromide and 500 nM-strychnine. 2. In the presence of external Cd2+, at a concentration that blocked light-evoked synaptic inputs, N-methyl-D-aspartate (NMDA) and the non-NMDA-receptor agonists, quisqualate and kainate, gated conductances in both on-off and on ganglion cells. The current-voltage (I-V) curve for the conductance elicited by NMDA had a negative slope between -40 and -70 mV and a reversal potential near 0 mV. The I-V curves for the non-NMDA-receptor-mediated conductances were nearly linear and also had reversal potentials near 0 mV. 3. I-V curves were measured at an early time point near the peak of transient EPSCs and at a later time point during the decay phase of the responses. The late I-V curve had a negative slope below -40 mV. The early I-V curve had a positive slope over the entire voltage range but the slope was greater at positive than at negative potentials. The evoked current reversed near 0 mV at both time points. 4. The region of negative slope of the late I-V curve was eliminated when Mg2+ was removed from the external saline. A slowly decaying component of transient EPSCs was eliminated in 20 microM-DL-2-amino-7-phosphonoheptanoate (AP7), an NMDA-receptor antagonist. 5. Application of 1 microM-6-cyano-7-nitroquinoxaline-2,3-dione (CNQX), a non-NMDA-receptor antagonist at this concentration, blocked a fast component of transient EPSCs. 6. Our results demonstrate that the synaptic inputs to on-off ganglion cells have two components: a slower NMDA-receptor-mediated component having a time-to-peak of 110 +/- 45 ms and an e-fold decay time of 209 +/- 35 ms at -31 mV (mean +/- S.D., n = 5), and a faster non-NMDA-receptor-mediated component having a time-to-peak of 28 +/- 10 ms and an e-fold decay time of 43 +/- 20 ms at -31 mV (n = 8). 7. A similar analysis of sustained EPSCs of on ganglion cells showed that these currents resulted from sustained activation of both NMDA and non-NMDA receptors.

Ambystoma↗
PubMed1989

Protein structure alignment.

A new method of comparing protein structures is described, based on distance plot analysis. It is relatively insensitive to insertions and deletions in sequence and is tolerant of the displacement of equivalent substructures between the two molecules being compared. When presented with the co-ordinate sets of two structures, the method will produce automatically an alignment of their sequences based on structural criteria. The method uses the dynamic programming optimization technique, which is widely used in the comparison of protein sequences and thus unifies the techniques of protein structure and sequence comparison. Typical structure comparison problems were examined and the results of the new method compared to the published results obtained using conventional methods. In most examples, the new method produced a result that was equivalent, and in some cases superior, to those reported in the literature.

Algorithms↗
PubMed1989

The predicted secondary structures of the nucleotide-binding sites of six cation-transporting ATPases lead to a probable tertiary fold.

Six cation-dependent transporting ATPases have homologous sequences in the region asigned by chemical labelling to nucleotide binding. Comparison of the most highly conserved segments with other nucleotide-binding domains showed that the sequences were consistent with a mononucleotide-binding fold and enabled a number of likely folding topologies to be limited to two or three alternatives. One of these possible folds was topologically equivalent to adenylate kinase; this was taken as a model in which the significance of conserved amino acids was investigated. In this model conserved amino acids were grouped around a postulated ATP-binding cleft, satisfactorily accounting for their degree of conservation.

Adenosine Triphosphatases↗
PubMed1989

Predicted structure of a major Schistosoma mansoni eggshell protein.

The complete sequence for a major Schistosome mansoni eggshell protein gene has been determined from a genomic DNA fragment. The use of an open reading frame encoding a glycine-rich polypeptide was confirmed by in vitro translation of schistosome mRNA in the presence of [3H]glycine and comparison with the amino acid composition of purified, schistosome eggshells. Apart from the extraordinary abundance of glycine and tyrosine which are evenly distributed throughout the polypeptide chain, the most striking features of the deduced amino acid sequence are the presence of five well-conserved tandem repeats of 16-18 residues in the N-terminal region and the asymmetrical distribution of charged residues. Acidic residues (Asp) are confined to the N-terminal region, while basic residues (Lys, His), with the exception of a single histidine, are found in the C-terminal region. A model structure composed of short anti-parallel beta-strands is proposed, in which glycines and residues with small side chains lie within the strands and tyrosines and cysteines are arranged at the bends, where they would be available for cross-linking. Four such strands form one of the tandem repeats which are predicted in turn to form a stack of five closely packed beta-sheets, each of three strands and linked by the more variable fourth strand. The C-terminal region may form a similar but less compact structure. The ordered structure demonstrated by birefringence studies of the schistosome eggshell [Kusel, J. (1970) Parasitology 60, 79-88] could be formed by packing of the polypeptides such that the N-terminal domain contributes counter ions or cross-links to the C-terminal domain of adjacent molecules.

Amino Acid Sequence↗
PubMed1989

Identification of residues necessary for clonally specific recognition of a cytotoxic T cell determinant.

The residues in an influenza nucleoprotein (NP) cytotoxic T cell determinant necessary for cytotoxic T cell (CTL) recognition, were identified by assaying the ability of hybrid peptides to sensitize a target cell to lysis. The hybrid peptides were formed by substituting amino acids from one determinant (influenza NP 147-158) for the corresponding residues of a second peptide (HLA CW3 171-182) capable of binding to a common class I protein (H-2Kd). Six amino acids resulted in partial recognition; however, the presence of a seventh improved the potency of the peptide. Five of the six amino acids were shown to be required for recognition. The spacing of the six amino acids was consistent with the peptide adopting a helical conformation when bound. The importance of each amino acid in CTL recognition and binding to the restriction element was investigated further by assaying the ability of peptides containing point substitutions either to sensitize target cells or to compete with the natural NP sequence for recognition by CTL. The T cell response was much more sensitive to substitution than the ability of the peptide to bind the restriction element. Collectively the separate strategies identified an approximate conformation and orientation of the peptide when part of the complex and permitted a potential location in the MHC binding site to be identified. The model provides a rationalization for analogues which have previously been shown to exhibit greater affinity for the class I molecule and suggests that the binding site in major histocompatibility complex (MHC) class I molecules might have greater steric constraints that the corresponding area of class II proteins.

Amino Acid Sequence↗
PubMed1989

Structural analysis of a peptide--HLA class II complex: identification of critical interactions for its formation and recognition by T cell receptor.

An assay for the binding of peptides to major histocompatibility complex (MHC) class II proteins on the surface of cells has been used to determine the relative importance of the amino acids composing an influenza haemagglutinin T cell determinant in binding. The important contact residues were identified by the effect substitution of each residue with biotinylated lysine had on the ability of the peptide to bind. The spacing of the critical residues within the peptide sequence was consistent with the central core, of approximately eight amino acids, adopting a helical conformation. The terminal residues were less constrained and might not be part of a regular conformation. Increasing the helical propensity of the determinant, by simply acetylating and amidating the peptide, resulted in an analogue that was able to stimulate a specific T cell clone at significantly lower concentrations than the natural sequence. A potential location for the peptide in the binding site was postulated based on the presence of complementary amino acids in the class II molecule and supported by screening a large number of peptide analogues for their ability either to bind the restriction element or to stimulate T cell proliferation.

Amino Acid Sequence↗
PubMed1989

A holistic approach to protein structure alignment.

A method of protein structure comparison developed previously is extended to incorporate other aspects of protein structure in addition to the inter-atomic vectors on which it was originally based. Each additional aspect, which induced hydrogen bonding, solvent exposure, torsional angles and sequence, was introduced separately and evaluated for its ability to improve alignment quality. The components were then combined, suitably weighted, to produce a more holistic comparison method. The method was tested on a group of remotely related beta/alpha type proteins that share a common feature in their overall chain fold. The results indicated that while the original inter-atomic vector component was sufficient to give the correct alignment of most pairs of topologically equivalent proteins, the inclusion of hydrogen bonds, torsion angles and a measure of solvent exposure led to improvements in the more difficult comparisons. Consideration of amino acid properties, including hydrophobicity, had no beneficial effect. The failure of the latter component was not unexpected considering the almost total lack of sequence similarity among the proteins considered.

Chemistry, Physical↗
PubMed1989

Temperature dependence of phase response curves for drug-induced phase shifts.

The effectiveness of drugs active in phase-shifting the circadian rhythm of bioluminescent glow in the unicellular dinoflagellate Gonyaulax polyedra differs, depending upon the time of drug exposure (as pulses). For two drugs tested--cycloheximide and anisomycin, both inhibitors of cytosolic protein synthesis--this function, referred to as the drug phase response curve (dPRC), differs, depending upon the ambient temperature. Since dPRCs may differ at different drug concentrations, the effects observed may be attributable to differences in the effectiveness of or recovery from the drugs at different temperatures.

Animals↗
PubMed1988

Structural model of HLA-DR1 restricted T cell antigen recognition.

Two human helper T cell determinants in influenza have been identified, one in the hemagglutinin and the other in the matrix protein (M1). Both were shown to be DR1 restricted by using transfected L cells to present antigen. Comparison of the sequences of the two peptides revealed a similar pattern that could account for their DR1 specificity if the peptides adopt a helical conformation. The model was supported by the demonstration that hybrid peptides, composed of the amino acids that interact with DR1 from one determinant and the residues that interact with the T cell receptor from the other, were recognized by each clone. The generality of the motif was confirmed by the finding that DR1 individuals respond to a ragweed peptide containing the defined pattern.

Allergens↗
PubMed1988

A sequence pattern common to T cell epitopes.

An analysis of the known cytotoxic and helper T cell epitopes has revealed similarity within their primary sequences. These similar motifs, characteristic of the known determinants, have been incorporated into predictive templates that have been used successfully to define eight helper and three cytotoxic epitopes in four different proteins. When the defined epitopes are segregated by restriction element, allele specific subpatterns emerge centering around the general pattern. The presence of similarities argues that the binding of peptide antigens to class I and class II is similar in nature. In addition, these motifs can be used to predict accurately areas within proteins capable of being recognized by individual MHC class I and class II molecules.

Amino Acid Sequence↗
PubMed1988

Measles control efforts in urban Africa complicated by high incidence of measles in the first year of life.

A measles vaccination coverage of between 50 and 60% has been achieved in Kinshasa, Zaire, from 1980-1985. During that interval, the annual number of measles cases and the incidence rate of measles reported by a surveillance system remained similar, and measles epidemics occurred in alternating years. The estimated number of measles cases in Kinshasa is 87,600 per year. Of reported measles cases, 27% occurred in children under nine months of age, younger than the recommended age at vaccination. Two results expected in a partially vaccinated population, a reduction in measles incidence greater than the level of vaccination coverage and a shift in the age distribution of measles to older children, have not been observed. Measles control in Kinshasa will require a vaccination coverage of higher than 60%. In addition, given the age-specific risk of measles infection here, a measles vaccine that would be effective when given before nine months of age would be an important element in controlling measles transmission. Because the epidemiology of measles in Kinshasa is a likely consequence of its urban environment, such a vaccine would represent a significant advance toward the control of measles in urban Africa.

Age Factors↗