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PubMed1986

Retro-all-D and retro isomers of a formyl-methionyl peptide chemoattractant: an insight into the mode of binding at the receptor on rabbit neutrophils.

The retro-all-D analog and retro isomer of the formyl-methionyl-carboxamide-tripeptide chemoattractant, CHO-L-Met-L-Leu-L-Phe-NH2, namely CHO-D-Phe-D-Leu-D-Met-NH2 and CHO-L-Phe-L-Leu-L-Met-NH2, respectively, have been synthesized in solution by classical methods and fully characterized. The tetrapeptide CHO-L-Phe-Gly-L-Leu-L-Met-NH2, representing the C-terminal portion of the tachykinin, Substance P, and resembling the sequence of the retro isomer, has also been synthesized and characterized. The three N alpha-formylated tripeptide amides, prepared in order to obtain a deeper insight into the model of binding at the formyl peptide chemotactic receptor on rabbit neutrophils, have been tested for their ability to induce granule enzyme secretion from rabbit peritoneal neutrophils. The retro isomer, CHO-L-Phe-L-Leu-L-Met-NH2 is approximately 100-fold less active, the retro-all-D analog, CHO-D-Phe-D-Leu-D-Met-NH2 approximately 10,000-fold less active and the Substance P analog CHO-L-Phe-Gly-L-Leu-L-Met-NH2 1000-fold less active than the parent formyl peptide chemoattractant, CHO-L-Met-L-Leu-L-Phe-NH2. We interpret these results to indicate that a precise alignment of amino acid side chains as well as backbone amide bonds is an important factor involved in the receptor recognition of the formyl tripeptide chemoattractant.

Animals↗

PubMed2002

Phylogenetic relationships of Indian caecilians (Amphibia: Gymnophiona) inferred from mitochondrial rRNA gene sequences.

India has a diverse caecilian fauna, including representatives of three of the six currently recognized families, the Caeciliidae, Ichthyophiidae, the endemic Uraeotyphlidae, but previous molecular phylogenetic studies of caecilians have not included sequences for any Indian caecilians. Partial 12S and 16S mitochondrial gene sequences were obtained for a single representative of each of the caecilian families found in India and aligned against previously reported sequences for 13 caecilian species. The resulting alignment (16 taxa, 1200 sites, of which 288 cannot be aligned unambiguously) was analyzed using parsimony, maximum-likelihood, and distance methods. As judged by bootstrap proportions, decay indices, and leaf stabilities, well-supported relationships of the Indian caecilians are recovered from the alignment. The data (1) corroborate the hypothesis, based on morphology, that the Uraeotyphlidae and Ichthyophiidae are sister taxa, (2) recover a monophyletic Ichthyophiidae, including Indian and South East Asian representatives, and (3) place the Indian caeciliid Gegeneophis ramaswamii as the sister group of the caeciliid caecilians of the Seychelles. Rough estimates of divergence times suggest an origin of the Uraeotyphlidae and Ichthyophiidae while India was isolated from Laurasia and Africa and are most consistent with an Indian origin of these families and subsequent dispersal of ichthyophiids into South East Asia.

Amphibians↗

PubMed2006

High-resolution magnetic resonance imaging sinc-interpolation-based subvoxel registration and semi-automated quantitative lateral ventricular morphology employing threshold computation and binary image creation in the study of fatty acid interventions in schizophrenia, depression, chronic fatigue syndrome and Huntington's disease.

Serial high-resolution structural magnetic resonance imaging scans of the brain can now be precisely aligned, with six degrees of freedom (three mutually orthogonal translational and three rotational degrees of freedom around three mutually orthogonal axes), using a rigid-body subvoxel registration technique. This is driven by the in-plane point spread function for images acquired in the Fourier domain with data obtained over a bounded region of k-space, namely the sinc interpolation function, where sinc z = (sin z)/z, with z being any complex number (including zero). Computational subtraction of the three-dimensional Cartesian spatial representation matrices of serially acquired scan data allows for the determination of structural cerebral changes with great precision, since voxel signals from unchanged structures are almost completely cancelled. Thus changes readily show up against a background of noise. Furthermore, lateral ventricular changes can now be accurately quantified using a semi-automated method involving contour production, threshold computation, binary image creation and ventricular extraction. These techniques have been applied to the investigation of the effects on cerebral structure of intervention with fatty acids, particularly the long-chain polyunsaturated n-3 fatty acid eicosapentaenoic acid (EPA), in disorders such as schizophrenia, treatment-resistant depression, chronic fatigue syndrome (myalgic encephalomyelitis or ME), and Huntington's disease.

Atrophy↗

PubMed2002

An evaluation of beta-turn prediction methods.

MOTIVATION: beta-turn is an important element of protein structure. In the past three decades, numerous beta-turn prediction methods have been developed based on various strategies. For a detailed discussion about the importance of beta-turns and a systematic introduction of the existing prediction algorithms for beta-turns and their types, please see a recent review (Chou, Analytical Biochemistry, 286, 1-16, 2000). However at present, it is still difficult to say which method is better than the other. This is because of the fact that these methods were developed on different sets of data. Thus, it is important to evaluate the performance of beta-turn prediction methods. RESULTS: We have evaluated the performance of six methods of beta-turn prediction. All the methods have been tested on a set of 426 non-homologous protein chains. It has been observed that the performance of the neural network based method, BTPRED, is significantly better than the statistical methods. One of the reasons for its better performance is that it utilizes the predicted secondary structure information. We have also trained, tested and evaluated the performance of all methods except BTPRED and GORBTURN, on new data set using a 7-fold cross-validation technique. There is a significant improvement in performance of all the methods when secondary structure information is incorporated. Moreover, after incorporating secondary structure information, the Sequence Coupled Model has yielded better results in predicting beta-turns as compared with other methods. In this study, both threshold dependent and independent (ROC) measures have been used for evaluation.

Algorithms↗

PubMed2001

Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set.

MOTIVATION: SAM-T99 is an iterative hidden Markov model-based method for finding proteins similar to a single target sequence and aligning them. One of its main uses is to produce multiple alignments of homologs of the target sequence. Previous tests of SAM-T99 and its predecessors have concentrated on the quality of the searches performed, not on the quality of the multiple alignment. In this paper we report on tests of multiple alignment quality, comparing SAM-T99 to the standard multiple aligner, CLUSTALW. RESULTS: The paper evaluates the multiple-alignment aspect of the SAM-T99 protocol, using the BAliBASE benchmark alignment database. On these benchmarks, SAM-T99 is comparable in accuracy with ClustalW. AVAILABILITY: The SAM-T99 protocol can be run on the web at http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html and the alignment tune-up option described here can be run at http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-tuneup.html. The protocol is also part of the standard SAM suite of tools. http://www.cse.ucsc.edu/research/compbio/sam/

Computational Biology↗

PubMed1999

Discovery of local packing motifs in protein structures.

We present a language for describing structural patterns of residues in protein structures and a method for the discovery of such patterns that recur in a set of protein structures. The patterns impose restrictions on the spatial position of each residue, their order along the amino acid chain, and which amino acids are allowed in each position. Unlike other methods for comparing sets of protein structures, our method is not based on the use of pairwise structure comparisons which is often time consuming and can produce inconsistent results. Instead, the method simultaneously takes into account information from all structures in the search for conserved structure patterns which are potential structure motifs. The method is based on describing the spatial neighborhoods of each residue in each structure as a string and applying a sequence pattern discovery method to find patterns common to subsets of these strings. Finally it is checked whether the similarities between the neighborhood strings correspond to spatially similar substructures. We apply the method to analyze sets of very disparate proteins from the four different protein families: serine proteases, cuprodoxins, cysteine proteinases, and ferredoxins. The motifs found by the method correspond well to the site and motif information given in the annotation of these proteins in PDB, Swiss-Prot, and PROSITE. Furthermore, the motifs are confirmed by using the motif data to constrain the structural alignment of the proteins obtained with the program SAP. This gave the best superposition/alignment of the proteins given the motif assignment.

Algorithms↗

PubMed2005

Serial analysis of gene expression in the silkworm, Bombyx mori.

The silkworm Bombyx mori is one of the most economically important insects and serves as a model for Lepidoptera insects. We used serial analysis of gene expression (SAGE) to derive profiles of expressed genes during the developmental life cycle of the silkworm and to create a reference for understanding silkworm metamorphosis. We generated four SAGE libraries, one from each of the four developmental stages of the silkworm. In total we obtained 257,964 SAGE tags, of which 39,485 were unique tags. Sorted by copy number, 14.1% of the unique tags were detected at a median to high level (five or more copies), 24.2% at lower levels (two to four copies), and 61.7% as single copies. Using a basic local alignment search tool on the EST database, 35% of the tags matched known silkworm expressed sequence tags. SAGE demonstrated that a number of the genes were up- or down-regulated during the four developmental phases of the egg, larva, pupa, and adult. Furthermore, we found that the generation of longer cDNA fragments from SAGE tags constituted the most efficient method of gene identification, which facilitated the analysis of a large number of unknown genes.

Animals↗

PubMed2001

Identification and tissue distribution of two differentially spliced variants of the rat carnitine transporter OCTN2.

In this paper we show that the only known Na(+) dependent transporter of carnitine in mammals, organic cation transporter number 2 (OCTN2), is subject to differential splicing. Cloning of OCTN2 in different rat tissues identified two splicing variants. We have developed a real time quantitative polymerase chain reaction method for quantification of these splice variants. Both splice variants could be detected in all tissues examined with a relative abundance of 0.1-1% of the full length transcript. We also draw attention to the previously described mutations in clinical examples of primary carnitine deficiency in humans where the described mutations appear to be those of a splicing or mis-splicing event.

Alternative Splicing↗

PubMed1999

Conformational flexibility in calcitonin: the dynamic properties of human and salmon calcitonin in solution.

We have studied the dynamic properties of human (h) and salmon (s) calcitonin (CT) in solution. For both hormones, distance geometry in torsion-angle space has been used to generate three-dimensional structures consistent with NMR data obtained in sodium dodecyl sulfate micelles. For sCT and hCT we used, respectively, 356 and 275 interproton distances together with hydrogen-bonds as restraints. To better characterize their flexibility and dynamic properties two fully unrestrained 1100-ps molecular dynamics (MD) simulations in methanol were performed on the lowest-energy structures of both hormones. Statistical analyses of average geometric parameters and of their fluctuations performed in the last 1000 ps of the MD run show typical helical values for residues 9-19 of sCT during the whole trajectory. For hCT a shorter helix was observed involving residues 13-21, with a constant helical region in the range 13-19. Angular order parameters S(phi) and S(psi) indicate that hCT exhibits a higher flexibility, distributed along the whole chain, including the helix, while the only flexible amino acid residues in sCT connect three well-defined domains. Finally, our study shows that simulated annealing in torsion-angle space can efficiently be extended to NMR-based three-dimensional structure calculations of helical polypeptides. Furthermore, provided that a sufficient number of NMR restraints describes the system, the method allows the detection of equilibria in solution. This identification occurs through the generation of 'spurious' high-energy structures, which, for right-handed alpha-helices, are likely to be represented by left-handed alpha-helices.

Amino Acid Sequence↗

PubMed1995

Isolation and characterization of the first simian immunodeficiency virus from a feral sooty mangabey (Cercocebus atys) in West Africa.

The lineage of HIV-2-like viruses was studied in feral sooty mangabeys (SMs) by serological and genetic methods. Four feral sooty mangabeys were positive for simian immunodeficiency virus (SIV) antibodies and a new isolate, SIVsmSL92a, was obtained. Genetic analysis of gag genes showed that SIVsmSL92a was highly diverse and a distinct sequence subtype within the SIV sm/HIV-2 family. The results showed that SIVsm is the most diverse group of SIVs found thus far in a single monkey species.

Africa, Western↗

PubMed2001

Identification of deoxynivalenol- and nivalenol-producing chemotypes of Gibberella zeae by using PCR.

Gibberella zeae, a major cause of cereal scab, may be divided into two chemotypes based on production of the trichothecenes deoxynivalenol (DON) and nivalenol (NIV). We cloned and sequenced the gene cluster for trichothecene biosynthesis from each chemotype. G. zeae H-11 is a DON producer isolated from corn, and G. zeae 88-1 is a NIV producer from barley. We sequenced a 23-kb gene cluster from H-11 and a 26-kb cluster from 88-1, along with the unlinked Tri101 genes. Each gene cluster contained 10 Tri gene homologues in the same order and transcriptional directions as those of Fusarium sporotrichioides. Between H-11 and 88-1 all of the Tri homologues except Tri7 were conserved, with identities ranging from 88 to 98% and 82 to 99% at the nucleotide and amino acid levels, respectively. The Tri7 sequences were only 80% identical at the nucleotide level. We aligned the Tri7 genes and found that the Tri7 open reading frame of H-11 carried several mutations and an insertion containing 10 copies of an 11-bp tandem repeat. The Tri7 gene from 88-1 carried neither the repeat nor the mutations. We assayed 100 G. zeae isolates of both chemotypes by PCR amplification with a primer pair derived from the Tri7 gene and could differentiate the chemotypes by polyacrylamide gel electrophoresis. The PCR-based method developed in this study should provide a simple and reliable diagnostic tool for differentiating the two chemotypes of G. zeae.

Cloning, Molecular↗

PubMed1999

Isolation of an IgG monoclonal anti-dnaJ antibody from an immunoglobulin combinatorial library from a patient with rheumatoid arthritis.

OBJECTIVE: Previously, we showed that rheumatoid arthritis (RA) had both antibodies and T cells specific for the QKRAA-encompassing Escherichia coli dnaJ protein. These findings suggest that the bacteria induced anti-dnaJ responses may cross react with the human homolog of bacterial dnaJ in the joint, resulting in tissue damage. METHODS: We used the combinatorial library technique to isolate and characterize an IgG monoclonal anti-dnaJ antibody (designated CG1) from the blood of a patient with RA. RESULTS: Sequence analysis of CG1 revealed that its heavy and light chain V regions were respectively most homologous to the 3d279d VH4 and the O18 Vk1 genes. Interestingly, 3d279d is frequently expressed by B cells stimulated with staphylococcal enterotoxin; and O18 is the main gene employed by the Vk1 IgG antibodies against Haemophilus influenzae. CONCLUSION: The combinatorial immunoglobulin library method represents an interesting model of how to approach the isolation and characterization of antibody-like reagents in the elucidation of autoantigens in RA.

Amino Acid Sequence↗

PubMed1997

Analysis of retinoic acid receptor beta expression in normal and malignant laryngeal mucosa by a sensitive and routine applicable reverse transcription-polymerase chain reaction enzyme-linked immunosorbent assay method.

Retinoic acid receptor beta (RAR-beta) seems to be a useful intermediate marker in trials of retinoids, and the aim of this work was to describe a fast, sensitive, and routine applicable method to measure RAR-beta expression in tumor biopsies. We developed a new technique combining reverse transcription-PCR with a colorimetric ELISA detection of amplification products. The principle of this nonradioactive method is based on digoxigenin labeling of PCR products during amplification. Amplified DNA is hybridized with a biotinylated capture probe. The generated hybrid is immobilized on a streptavidin-coated microtiter plate, and detection is performed with the use of an antidigoxigenin peroxidase conjugate. We applied this method to quantify the expression of RAR-beta and an internal control (beta2 microglobulin) in laryngeal tumors. We found a detection threshold at 50 pg of PCR products, which represents a 100-fold improvement when compared to the detection limit of ethidium bromide detection. The method was reproducible (intra- and interassay reproducibilities at 7 and 5%, respectively). We used this technique for determining RAR-beta expression in 20 patients with laryngeal carcinoma and in 20 patients without cancer. The data show that the value of the RAR-beta:beta2 microglobulin ratio is decreased in tumoral versus nontumoral specimens (P = 0.0012), which is consistent with previously published results.

Adult↗

PubMedDate not supplied

Predicting the phosphorylation sites using hidden Markov models and machine learning methods.

Accurately predicting phosphorylation sites in proteins is an important issue in postgenomics, for which how to efficiently extract the most predictive features from amino acid sequences for modeling is still challenging. Although both the distributed encoding method and the bio-basis function method work well, they still have some limits in use. The distributed encoding method is unable to code the biological content in sequences efficiently, whereas the bio-basis function method is a nonparametric method, which is often computationally expensive. As hidden Markov models (HMMs) can be used to generate one model for one cluster of aligned protein sequences, the aim in this study is to use HMMs to extract features from amino acid sequences, where sequence clusters are determined using available biological knowledge. In this novel method, HMMs are first constructed using functional sequences only. Both functional and nonfunctional training sequences are then inputted into the trained HMMs to generate functional and nonfunctional feature vectors. From this, a machine learning algorithm is used to construct a classifier based on these feature vectors. It is found in this work that (1) this method provides much better prediction accuracy than the use of HMMs only for prediction, and (2) the support vector machines (SVMs) algorithm outperforms decision trees and neural network algorithms when they are constructed on the features extracted using the trained HMMs.

Algorithms↗

PubMed1976

A possible correlation between lipid hydration and lipid activation of the C55-isoprenoid alcohol phosphokinase apoprotein.

1. A direct method for determining the binding of triated water to lipids is described. The experimental conditions were practically identical to those previously employed (1974) in the determination of the cofactor activities of a series of oleyl-lipids in reactivation of the C55-isoprenoid alcohol phosphokinase apoprotein. 2. Active cofactor lipids (dioleyl lecithin, sodium oleate, 1-monoolein, 1-monomyristin)bound between 2.3 and 5.3 nmol 3H2O per nmol lipid, whereas less than 0.14 nmol 3H2O were bound per nmol of the inactive lipids (1,2- and 1,3-diolein, triolein, oleyl alcohol, methyl oleate, cholesteryl oleate). 3. When exposed to 3H2O vapour, the active lipids adsorbed between 1 and 2 nmol 3H2O per nmol lipid, whereas the inactive lipids adsorbed less than 0.1 nmol 3H2O per nmol lipid. 4. The active lipid cofactor, egg lecithin, bound more than twice as much 3H2O as egg phosphatidylethanolamine which was devoid of cofactor activity in the absence of detergent. 5. Appropriately hydrated lipid polar groups are concluded to be required for an alignment with polar amino acid side chains of the enzyme apoprotein in the formation of a mixed micellar lipoprotein complex. The enzyme reaction might occur at the resulting lipoprotein/water interface.

Apoenzymes↗

PubMed2001

Wide variety of genotypes and geographic origins of hepatitis B virus in Belgian children.

BACKGROUND: Belgium is a country with low endemicity for hepatitis B virus (HBV) infection. Few data are available on genotypes or serotypes of HBV among infected children. METHODS: The S region of the hepatitis B virus genome was amplified and sequenced in 23 children treated with interferon-alpha in Belgium. Nucleotide sequences were aligned and compared with other known sequences in a phylogenetic analysis. RESULTS: A high stability of the S gene was observed during treatment. Four genotypes were represented in this sample of Belgian patients (A, B, D, and E), reflecting the geographic diversity of origins. CONCLUSIONS: In this series, the wide variety of geographic origins is confirmed by the molecular characteristics of HBV. In Belgium, HBV infection of children is currently essentially an imported infection.

Antiviral Agents↗

PubMed1994

Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility.

Side-chain to side-chain contacts, accessibility, secondary structure and RMS deviation were compared within 607 pairs of proteins having similar three-dimensional (3D) structures. Three types of protein 3D structural similarities were defined: type A having sequence and usually functional similarity; type B having functional, but no sequence similarity; and type C having only 3D structural similarity. Within proteins having little or no sequence similarity (types B and C), structural features frequently had a degree of conservation comparable to dissimilar 3D structures. Despite similar protein folds, as few as 30% of residues within similar protein 3D structures can form a common core. RMS deviations on core C alpha atoms can be as high as 3.2 A. Similar protein structures can have secondary structure identities as low as 41%, which is equivalent to that expected by chance. By defining three categories of amino acid accessibility (buried, half buried and exposed), some similar protein 3D structures have as few as 30% of positions in the same category, making them indistinguishable from pairs of dissimilar protein structures. Similar structures can also have as few as 12% of common side-chain to side-chain contacts, and virtually no similar energetically favourable side-chain to side-chain interactions. Complementary changes are defined as structurally equivalent pairs of interacting residues in two structures with energetically favourable but different side-chain interactions. For many proteins with similar three-dimensional structures, the proportion of complementary changes is near to that expected by chance, suggesting that many similar structures have fundamentally different stabilising interactions. All of the results suggest that proteins having similar 3D structures can have little in common apart from a scaffold of core secondary structures. This has profound implications for methods of protein fold detection, since many of the properties assumed to be conserved across similar protein 3D structures (e.g. accessibility, side-chain to side-chain contacts, etc.) are often unconserved within weakly similar (i.e. type B and C) protein 3D structures. Little difference was found between type B and C similarities suggesting that the structure of similar proteins can evolve beyond recognition even when function is conserved. Our findings suggest that it is more general features of protein structure, such as the requirements for burial of hydrophobic residues and exposure of polar residues, rather than specific residue-residue interactions that determine how well a particular sequence adopts a particular fold.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed1995

Generation of entire human papillomavirus genomes by long PCR: frequency of errors produced during amplification.

Recently, several improvements of traditional PCR techniques have facilitated the amplification of significantly longer DNA target sequences. Here we report an improved method for amplification of entire human papillomavirus (HPV) genomes. Using rTth DNA polymerase, XL (Perkin-Elmer, Foster City CA), and the accompanying XL PCR buffer system, we have successfully amplified 8-kb genomes from approximately 10 copies of input reference strain HPV16 DNA. This long PCR (LPCR) method was subsequently used to amplify the entire HPV16 genome from clinical specimens. The fidelity with which the rTth DNA polymerase XL amplified target sequences under our chosen amplification conditions was estimated by partial sequencing of cloned LPCR products generated from cloned reference strain HPV16 genomes. A region spanning the HPV16 E6, E7, and part of the E1 open reading frames (ORFs) was sequenced in 29 clones. A total of 33 nucleotide substitutions were observed in the 23.5 kb sequenced. This corresponds to an error frequency of approximately one error per 700 bases. Finally, LPCR methods were used to amplify entire, novel HPV genomes from clinical specimens. LPCR primer pairs were designed for amplification of seven potentially novel HPV types. Amplicons of approximately 8 kb were generated from five of the seven HPV types targeted. One of the LPCR-generated novel genomes, CP141, was subsequently cloned and a partial sequence was determined.

Amino Acid Sequence↗