Sequencing and computer time.
Explore the source record for details and available documents.
Databases, Factual↗
Biomedical subjects
W R Taylor
Publications and source records attributed to W R Taylor.
A new approach to protein fold recognition.
The prediction of protein tertiary structure from sequence using molecular energy calculations has not yet been successful; an alternative strategy of recognizing known motifs or folds in sequences looks more promising. We present here a new approach to fold recognition, whereby sequences are fitted directly onto the backbone coordinates of known protein structures. Our method for protein fold recognition involves automatic modelling of protein structures using a given sequence, and is based on the frameworks of known protein folds. The plausibility of each model, and hence the degree of compatibility between the sequence and the proposed structure, is evaluated by means of a set of empirical potentials derived from proteins of known structure. The novel aspect of our approach is that the matching of sequences to backbone coordinates is performed in full three-dimensional space, incorporating specific pair interactions explicitly.
Algorithms↗
Fast structure alignment for protein databank searching.
A fast method is described for searching and analyzing the protein structure databank. It uses secondary structure followed by residue matching to compare protein structures and is developed from a previous structural alignment method based on dynamic programming. Linear representations of secondary structures are derived and their features compared to identify equivalent elements in two proteins. The secondary structure alignment then constrains the residue alignment, which compares only residues within aligned secondary structures and with similar buried areas and torsional angles. The initial secondary structure alignment improves accuracy and provides a means of filtering out unrelated proteins before the slower residue alignment stage. It is possible to search or sort the protein structure databank very quickly using just secondary structure comparisons. A search through 720 structures with a probe protein of 10 secondary structures required 1.7 CPU hours on a Sun 4/280. Alternatively, combined secondary structure and residue alignments, with a cutoff on the secondary structure score to remove pairs of unrelated proteins from further analysis, took 10.1 CPU hours. The method was applied in searches on different classes of proteins and to cluster a subset of the databank into structurally related groups. Relationships were consistent with known families of protein structure.
Amino Acid Sequence↗
The rapid generation of mutation data matrices from protein sequences.
An efficient means for generating mutation data matrices from large numbers of protein sequences is presented here. By means of an approximate peptide-based sequence comparison algorithm, the set sequences are clustered at the 85% identity level. The closest relating pairs of sequences are aligned, and observed amino acid exchanges tallied in a matrix. The raw mutation frequency matrix is processed in a similar way to that described by Dayhoff et al. (1978), and so the resulting matrices may be easily used in current sequence analysis applications, in place of the standard mutation data matrices, which have not been updated for 13 years. The method is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fast enough to generate a matrix from a specific family or class of proteins in minutes. Differences observed between our 250 PAM mutation data matrix and the matrix calculated by Dayhoff et al. are briefly discussed.
Algorithms↗
Childhood chronic illness: prevalence, severity, and impact.
BACKGROUND: Using data from the 1988 National Health Interview Survey, this article presents national estimates of the prevalence and impact of childhood chronic conditions. METHODS: Proxy responses to a checklist of child health conditions administered for 17,110 children under 18 years of age were used. Conditions were classified as chronic if they were first noticed more than 3 months prior to the interview or if they were the type that would ordinarily be of extended duration, such as arthritis. RESULTS: An estimated 31% of children were affected by chronic conditions. Among these children, highly prevalent conditions included respiratory allergies 9.7 per 100, repeated ear infections 8.3 per 100 and asthma 4.3 per 100. These children can be divided into three groups: 66% with mild conditions that result in little or no bother or activity limitation; 29% with conditions of moderate severity that result in some bother or limitation of activity, but not both; and 5% with severe conditions that cause frequent bother and limitation of activity. The 5% with severe conditions accounted for 19% of physician contacts and 33% of hospital days related to chronic illness. CONCLUSIONS: Childhood chronic conditions have highly variable impacts on children's activities and use of health care.
Activities of Daily Living↗
Impact of childhood asthma on health.
In 1988, the National Health Interview Survey contained a supplemental questionnaire on childhood conditions that included asthma. The authors used these data from 17,110 households to determine the disease burden resulting from asthma and to determine the functional status of children with and without asthma by linking information from the core and supplemental questionnaires. The prevalence of asthma in children younger than 18 years of age in the United States as reported by an adult in the household was 4.3% in 1988 and was 3.2% in 1981, the last time a comparable questionnaire was used in the National Health Interview Survey. The difference between the prevalences of asthma was statistically significant (95% confidence interval for the difference was 0.7% to 1.5%). An estimated 2.7 million children younger than 18 years were reported by an adult in the household to have had asthma in the past year. The added burden of illness experienced by children with asthma compared with children without asthma was an additional 10.1 million days missed from school, 12.9 million contacts with medical doctors, and 200,000 hospitalizations. Almost 30% of children with asthma had some limitation in activity, compared with only 5% of children without asthma. A greater proportion of black children experienced more severe functional disability and had more frequent hospitalizations than white children with asthma. Ten percent of children with asthma had severe disease as measured by frequency of bother and limitations in function; these children accounted for 35% of hospitalizations for asthma and 77% of the days in the hospital.(ABSTRACT TRUNCATED AT 250 WORDS)
Adolescent↗
The treatment of adult hyperglycaemia in an African rural hospital.
This paper describes the treatment of adult diabetic ketoacidosis in an African rural hospital in which there were only rudimentary diagnostic facilities. It is intended to be a practical guide to doctors working under similar conditions. It also deals with some of the pathophysiological mechanisms underlying diabetic ketoacidosis but emphasises the use of clinical skills in patient assessment and management.
Blood Glucose↗
Evidence for synergistic interactions between ras, myc and a mutant form of p53 in cellular transformation and tumor dissemination.
Mouse 10T1/2 cells were transfected with combinations of T24 H-ras, human c-myc and the proline 193 mutant form of p53. The three-gene ras/myc/p53 combination was significantly more efficient than single genes or double gene combinations in inducing transformed foci in vitro. An analysis of cell lines isolated after transfections with ras, ras/myc, ras/p53 and ras/myc/p53 indicated that the last combination contained significantly higher levels of ras protein than the other combinations, produced tumors in syngeneic mice with a shorter latency period, and exhibited an increased ability to form lung tumors in an in vivo experimental metastasis assay. Synergistic interactions between ras, myc and mutant p53 genes were observed in focus formation and metastasis assays, suggesting that the action of the three oncogenes in malignant transformation occurs along separate but interactive pathways. These results support a working model of oncogene cooperativity in which alterations in myc and p53 permit elevated expression of ras, which is important in a mechanism affecting both cellular transformation in vitro and tumor dissemination in vivo.
Animals↗
An extension of secondary structure prediction towards the prediction of tertiary structure.
Secondary structure prediction parameters and optimised decision constants for use with the method of Garnier et al. [(1978) J. Mol. Biol. 120, 97-120] have been derived for two new and distinct substates of beta-structure. These we term internal and external on the basis of their hydrogen bonding patterns. The profiles of the amino acids for several of the parameters are considerably different in the two substates. Predictions using the new parameters attempt to distinguish the strands at the core of the beta-sheet from those at its edges and so restrict the possible topologies in tertiary structure prediction. The potential application of these parameters is illustrated for the class of beta/alpha proteins.
Adenylate Kinase↗
A hypothetical model for the peptide binding domain of hsp70 based on the peptide binding domain of HLA.
The sequences of the peptide binding domains of 33 70 kd heat shock proteins (hsp70) have been aligned and a consensus secondary structure has been deduced. Individual members showed no significant deviation from the consensus, which showed a beta 4 alpha motif repeated twice, followed by two further helices and a terminus rich in Pro and Gly. The repeated motif could be aligned with the secondary structure of the functionally equivalent peptide binding domain of human leucocyte antigen (HLA) class I maintaining equivalent residues in structurally important positions in the two families and a model was built based on this alignment. The interaction of this domain with the ATP domain is considered. The overall model is shown to be consistent with the properties of products of chymotryptic cleavage.
Adenosine Triphosphate↗
Visualization of structural similarity in proteins.
Two new methods for the visualization of structural similarity in proteins with known three-dimensional structures are presented. They are based on the degree of equivalence of alpha-carbon pairs in two proteins. The quantitative measure for residue equivalence is the comparison score generated using the sequence and structure alignment method of Taylor and Orengo, which is based on the comparison of interatomic distances (and other properties that can be defined on a residue basis). The first method uses information on corresponding alpha-carbon positions to display vectors joining these structurally equivalent residues. These vectors can be defined as target constraints, and their minimization "bends" the two proteins toward a common average structure. In the average structure the corresponding residues virtually superpose, while insertions and deletions become clearly visible. The second method uses the comparison scores to perform a weighted least-squares fit of the two structures. It is further used to color code the two structures according to the score value, i.e., their similarity, on a continuous scale from red to blue. Examples of the methods for the comparison of flavodoxin, chemotaxis Y protein and L-arabinose-binding protein are given.
Amino Acid Sequence↗
Towards protein tertiary fold prediction using distance and motif constraints.
Based on a simplified model of the all-alpha class of protein, all packing arrangements of alpha-helices were generated and assessed by both general and specific structural rules. The method was applied to myoglobin and parvalbumin, which were both ranked in the top 4% of folds under the general packing constraints. Incorporation of the restrictions implied by the EF-hand motifs of parvalbumin were sufficient to select the correct fold as one of two (equal scoring) possibilities. Myoglobin scored well under the general packing constraints and the addition of a single distance constraint, implied by haem binding, was sufficient to select the correct fold as one of several candidates. Incorporation of a score for complementary hydrophobic packing between helices further selected myoglobin as a unique fold but did not improve the ranking of parvalbumin. For both proteins, the alpha-helices were predicted from multiply aligned sequences using pattern-matching methods and no specific aspect of the known X-ray structures influenced this or the prediction of the correct folds. Although the method is currently of limited generality, its further applications and extension to a more detailed structural level are discussed.
Amino Acid Sequence↗
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↗
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↗
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↗
Occult ischemic necrosis of skeletal muscle.
Explore the source record for details and available documents.
Acute Disease↗
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↗
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↗