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PubMed1993

Regularities in interaction patterns of globular proteins.

The description of protein structure in the language of side chain contact maps is shown to offer many advantages over more traditional approaches. Because it focuses on side chain interactions, it aids in the discovery, study and classification of similarities between interactions defining particular protein folds and offers new insights into the rules of protein structure. For example, there is a small number of characteristic patterns of interactions between protein supersecondary structural fragments, which can be seen in various non-related proteins. Furthermore, the overlap of the side chain contact maps of two proteins provides a new measure of protein structure similarity. As shown in several examples, alignments based on contact map overlaps are a powerful alternative to other structure-based alignments.

Computer Simulation↗

PubMed2000

Giraffe strain of pestivirus: its taxonomic status based on the 5'-untranslated region.

The 5'-untranslated region (5'-UTR) of the 'Giraffe' strain of pestivirus was sequenced for comparison with those of other pestiviruses from cattle, sheep, goats, and swine. A phylogenetic tree constructed with these strains suggested that the 'Giraffe' strain was allocated to a new taxon. This observation was also confirmed by a newly proposed method based on palindromic nucleotide substitutions (PNS) at the three variable regions in the 5'-UTR. Other reported pestivirus strains isolated from deer were assigned as bovine viral disease virus (BVDV)-1 according to the PNS as well as phylogenetic analysis, suggesting that BVDV-1 strains can cross-infect deer as well as cattle, sheep, goats, and swine, and that wild deer may serve as a reservoir of BVDV-1. We also identified the genovar of a deer isolate, SH9/11, as BVDV-1c by the PNS method.

5' Untranslated Regions↗

PubMed2006

Protein secondary structure prediction for a single-sequence using hidden semi-Markov models.

BACKGROUND: The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of prediction algorithms: Single-sequence prediction algorithms imply that information about other (homologous) proteins is not available, while algorithms of the second type imply that information about homologous proteins is available, and use it intensively. The single-sequence algorithms could make an important contribution to studies of proteins with no detected homologs, however the accuracy of protein secondary structure prediction from a single-sequence is not as high as when the additional evolutionary information is present. RESULTS: In this paper, we further refine and extend the hidden semi-Markov model (HSMM) initially considered in the BSPSS algorithm. We introduce an improved residue dependency model by considering the patterns of statistically significant amino acid correlation at structural segment borders. We also derive models that specialize on different sections of the dependency structure and incorporate them into HSMM. In addition, we implement an iterative training method to refine estimates of HSMM parameters. The three-state-per-residue accuracy and other accuracy measures of the new method, IPSSP, are shown to be comparable or better than ones for BSPSS as well as for PSIPRED, tested under the single-sequence condition. CONCLUSIONS: We have shown that new dependency models and training methods bring further improvements to single-sequence protein secondary structure prediction. The results are obtained under cross-validation conditions using a dataset with no pair of sequences having significant sequence similarity. As new sequences are added to the database it is possible to augment the dependency structure and obtain even higher accuracy. Current and future advances should contribute to the improvement of function prediction for orphan proteins inscrutable to current similarity search methods.

Algorithms↗

PubMed2003

[Mutation of envelop protein V3 loop in HIV-1 epidemic in Liaoning province].

OBJECTIVE: To study the characteristics of human immunodeficiency virus (HIV-1) V3 loop amino acid mutations among HIV-1 infected people in Liaoning province. METHODS: The whole blood samples of the HIV carriers and AIDS patients were collected in Liaoning province, China and were extracted PBMC genome DNA. HIV-1 V3 and flanking region sequences were amplified by nest-polymerase chain reaction (nest-PCR) with env specific primers: ED5/ED12 and ED31/ED33. Products were sequenced directly and sequences were aligned, translated and analyzed. RESULTS: In AIDS group, some amino acid mutations at specific position of V3 loop: S to R at position 11, H to S, T and N at position 13, A to V at position 19, F to Y at position 20, Q or D to N at position 25 and 29, were found and all common mutations were associated with T tropic/SI phenotype. The frequency of such amino acid mutations in specific positions was higher in AIDS group than that of the asymptomatic infection group (P < 0.05). In addition, we found some unusual tetramer compositions on the tip of V3 loop: GQGR, APGR and RPGA, GLGR, RPGA in addition to some rare mutations, such as: N to H at position 5 and H to S, F at position 34. CONCLUSION: The amino acid mutations on the V3 loop of HIV-1 epidemic in Liaoning province were in agreement with the results of subtype B, but we observed some rare mutations and unusual tetramer compositions on the tip of V3 loop.

Acquired Immunodeficiency Syndrome↗

PubMed2000

Covariance analysis of protein families: the case of the variable domains of antibodies.

A nonrestrictive method for identifying covariance in protein families is described and applied to human and mouse germline Vkappa and VH sequence alignments. Amino acids that occur at each position in a sequence alignment are divided into two sets, called a word, by generating all possible combinations of alternative amino acids. Each word is associated with a pattern of changes. Words with identical patterns identify covariant positions. In antibody variable domains, the number of words generated ranged between 1103 and 2195 depending on the alignment, of which 4 to 12 % occurred in covariant pairs. Despite the nonrestrictive character of pattern generation, covariant residues did not reflect a random selection with respect to the nature of amino acid changes and/or their spatial proximity in a reference crystallographic structure. This approach allowed the identification of a covariance signal for positions with high variability, mostly located in the outer part of the common structural framework of antibody variable domains. Covariance in these regions may reflect the existence of alternative and mutually exclusive atomic arrangements that are compatible with antibody function. The method may be of general applicability to rationalize residue variability in protein families.

Algorithms↗

PubMed2003

Globin and linker sequences of the giant extracellular hemoglobin from the leech Macrobdella decora.

A detailed electrospray ionization mass spectrometric study of the approximately 3.5-MDa hexagonal bilayer hemoglobin (HBL Hb) from the pond leech Macrobdella decora has shown it to consist of at least six approximately 17-kDa globin chains, of which two are monomeric and the remaining four occur as disulfide-bonded heterodimers, and three approximately 24-kDa nonglobin linker chains (Weber et al., J. Mol. Biol. 251: 703-720, 1995). The cDNA sequences of the five major constituent chains, globin chains IIA, IIB, B, and C and linker chain L1, are reported here. The globins and linkers share 30%-50% and 20%-30% identity, respectively, with other annelid sequences. Furthermore, IIB and C align with strain A of annelid sequences, whereas IIA and B align with the strain B sequences. Although chains B and C are monomeric, chains IIA and IIB form the main disulfide-bonded dimer. They also have some unusual features: the distal His (E7) is replaced by Phe in IIA, and the highly conserved CD1Phe is replaced by Leu in IIB. In spite of these unusual features, the functional properties of Macrobdella Hb are comparable to those of other HBL Hbs. A phylogenetic analysis of the globin sequences from Macrobdella, the polychaete Tylorrhynchus, the oligochaete Lumbricus, and the vestimentiferan Lamellibrachia, indicates that the two strains originated by gene duplication followed by additional duplication of each of the two strains. The mutation rate of the linkers appeared to be faster than that of the globin chains. The phylogenetic trees constructed using the Maximum Likelihood, Neighbor-Joining and Fitch methods showed the Macrobdella globin sequences to be closest to Lumbricus, in agreement with a view of annelid evolution in which the divergence of the polychaetes occurred before the divergence of the leeches from oligochaetes.

Amino Acid Sequence↗

PubMed2003

Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection.

MOTIVATION: Experimental methods capable of generating sets of co-regulated genes have become commonplace, however, recognizing the regulatory motifs responsible for this regulation remains difficult. As a result, computational detection of transcription factor binding sites in such data sets has been an active area of research. Most approaches have utilized either Gibbs sampling or greedy strategies to identify such elements in sets of sequences. These existing methods have varying degrees of success depending on the strength and length of the signals and the number of available sequences. We present a new deterministic iterative algorithm for regulatory element detection based on a Markov chain background. As in other methods, sequences in the entire genome and the training set are taken into account in order to discriminate against commonly occurring signals and produce patterns, which are significant in the training set. RESULTS: The results of the algorithm compare favorably with existing tools on previously known and newly compiled data sets. The iteration based search appears rather rigorous, not only finding the binding sites, but also showing how the binding site stands out from genomic background. The approach used to score the results is critical and a discussion of various scoring schemes and options is also presented. Benchmarking of several methods shows that while most tools are good at detecting strong signals, Gibbs sampling algorithms give inconsistent results when the regulatory element signal becomes weak. A Markov chain based background model alleviates the drawbacks of MAP (maximum a posteriori log likelihood) scores. AVAILABILITY: Available on request from the authors. SUPPLEMENTARY INFORMATION: Data and the results presented in this paper are available on the web at http://compbio.ornl.gov/mira/index.html

Algorithms↗

PubMed1999

Protalign: a 3-dimensional protein alignment assessment tool.

Protein fold recognition (sometimes called threading) is the prediction of a protein's 3-dimensional shape based on its similarity to a protein of known structure. Fold predictions are low resolution; that is, no effort is made to rotate the protein's component amino acid side chains into their correct spatial orientations. The goal is simply to recognize the protein family member that most closely resembles the target sequence of unknown structure and to create a sensible alignment of the target to the known structure (i.e., a structure-sequence alignment). To facilitate this type of structure prediction, we have designed a low resolution molecular graphics tool. ProtAlign introduces the ability to interact with and edit alignments directly in the 3-dimensional structure as well as in the usual 2-dimensional layout. It also contains several functions and features to help the user assess areas within the alignment. ProtAlign implements an open pipe architecture to allow other programs to access its molecular graphics capabilities. In addition, it is capable of "driving" other programs. Because amino acid side chain orientation is not relevant in fold recognition, we represent amino acid residues as abstract shapes or glyphs much like Lego (tm) blocks and we borrow techniques from comparative flow visualization using streamlines to provide clean depictions of the entire protein model. By creating a low resolution representation of protein structure, we are able to at least double the amount of information on the screen. At the same time, we create a view that is not as busy as the corresponding representations using traditional high resolution visualization methods which show detailed atomic structure. This eliminates distracting and possibly misleading visual clutter resulting from the mapping of protein alignment information onto a high resolution display of the known structure. This molecular graphics program is implemented in Open GL to facilitate porting to other platforms.

Amino Acid Sequence↗

PubMed1999

Crystal structure at 1.8 A resolution and proposed amino acid sequence of a thermostable xylanase from Thermoascus aurantiacus.

Thermoascus aurantiacus xylanase is a thermostable enzyme which hydrolyses xylan, a major hemicellulose component in the biosphere. Crystals belonging to P21 space group with a=41.7 A, b=68.1 A, c=51. 4 A and beta=113.6 degrees, Z=2 were grown that could diffract to better than 1.8 A resolution. The structure was solved by molecular replacement method using the Streptomyces lividans xylanase model. The amino acid sequence was determined from the electron density map aided by multiple alignment of related xylanase sequences. The sequence thus obtained provides a correction to the sequence reported earlier based on biochemical methods. The final refined protein model at 1.8 A resolution with 301 amino acid residues and 266 water molecules has an R-factor of 16.0 % and free R of 21.1 % with good stereochemistry. The single polypeptide chain assumes (alpha/beta)8 TIM-barrel fold and belongs to F/10 family of glycoside hydrolases. The active site consists of two glutamate residues located at the C terminus end of the beta-barrel, conforming to the double displacement mechanism for the enzyme action. A disulphide bond and more than ten salt bridges have been identified. In particular, the salt bridge Arg124-Glu232 which is almost buried, bridges the beta-strands beta4 and beta7 where the catalytic glutamate residues reside, and it may play a key role in the stability and activity at elevated temperature. To our knowledge, for the first time in the F/10 family xylanases, we observe a proline residue in the middle of the alpha-helix alpha6 which may be contributing to better packing. Earlier studies show that the enzyme retains its activity even at 70 degrees C. The refined protein model has allowed a detailed comparison with the other known structures in the F/10 family of enzymes. The possible causative factors for thermostability are discussed.

Amino Acid Sequence↗

PubMed1994

Nucleotide sequence of the 3' terminal region of the RNA of two filamentous grapevine viruses.

The 3' terminal region of grapevine virus A (GVA) and grapevine virus B (GVB), encompassing 1883 and 2136 nucleotides, respectively, was sequenced by the deoxynucleotide chain termination method. Three putative open reading frames (ORF) were identified in both genomic viral RNAs, denoted 1 to 3 in the 5' to 3' direction. ORF 1 encoded a polypeptide with estimated M(r) of 31 kDa (GVA) and 36.5 kDa (GVB), possessing the G/D motif of the "30 K superfamily" movement proteins, and showing good alignments with putative movement proteins of trichoviruses and capilloviruses. ORF 2 was identified as the coat protein (CP) cistron, coding for polypeptides with an estimated M(r) of 21.5 kDa (GVA) and 21.6 kDa (GVB). These CPs showed substantial sequence homology with one another and with CPs of tricho- and capilloviruses, but not of closteroviruses. ORF 3 potentially coded for two small polypeptides with estimated M(r) of 10 kDa (GVA) and 14 kDa (GVB). The ORF 3 product of GVB (14 K), but not that of GVA, shared some homology with the 3' terminal polypeptides of different plant viruses that exhibit the "zinc finger domain" of proteins with nucleic acid-binding properties. GVA and GVB have many properties in common with trichoviruses but possess an extra open reading frame (ORF 3). Whether this finding may have a bearing on the classification of these viruses is unclear. However, until the taxonomic significance of this difference in genome structure is established, it seems plausible to include GVA and GVB as tentative species in the Trichovirus genus.

Amino Acid Sequence↗

PubMed2003

Ordered reactive nanomembranes/nanotemplates from thin films of block copolymer supramolecular assembly.

We report on a unique, very simple method of preparation of reactive membranes and nanotemplates with nanoscopic cylindrical channels on the surface of various inorganic and polymeric substrates. Well-ordered nanostructured thin polymer films have been fabricated from the supramolecular assembly of poly(styrene-block-4-vinylpyridine) (PS-PVP) and 2-(4'-hydroxybenzeneazo)benzoic acid (HABA), consisting of cylindrical nanodomains formed by PVP-HABA associates surrounded by PS. Alignment of the domains has been shown to be switched upon exposure to vapors of different solvents from the parallel to perpendicular orientation to the confining surface and vice versa. The alignment of the cylindrical nanodomains is insensitive to the composition of the confining surface due to the self-adaptive behavior of the supramolecular PVP-HABA assembly. Extraction of HABA with selective solvent results in nanomembranes with a hexagonal lattice (24 nm in the period) of hollow channels of 8 nm in the diameter crossing the membrane from the top to the bottom. The walls of the channels are constituted from reactive PVP chains. The channels were filled with Ni clusters via the electrodeposition method to fabricate the ordered array of metallic nanodots of 1.2 tera per cm(2).

Journal Article↗

PubMed2001

Identification of slide coagulase positive, tube coagulase negative Staphylococcus aureus by 16S ribosomal RNA gene sequencing.

AIMS: To ascertain the clinical importance of a strain of slide coagulase positive but tube coagulase negative Staphylococcus species isolated from the blood culture of a 43 year old patient with refractory anaemia with excessive blasts in transformation who had neutropenic fever. METHODS: The isolate was investigated phenotypically by standard biochemical methods using conventional biochemical tests and two commercially available systems, the Vitek (GPI) and API (Staph) systems. Genotypically, the 16S ribosomal RNA (rRNA) gene of the bacteria was amplified by the polymerase chain reaction (PCR) and sequenced. The sequence of the PCR product was compared with known 16S rRNA gene sequences in the GenBank by multiple sequence alignment. RESULTS: Conventional biochemical tests did not reveal a pattern resembling a known Staphylococcus species. The Vitek system (GPI) showed that it was 94% S. simulans and 3% S. haemolyticus, whereas the API system (Staph) showed that it was 86.8% S. aureus and 5.1% S. warneri. 16S rRNA gene sequencing showed that there was a 0 base difference between the isolate and S. aureus, 28 base difference between the isolate and S. lugdunensis, 39 base difference between the isolate and S. schleiferi, 21 base difference between the isolate and S. haemolyticus, 41 base difference between the isolate and S. simulans, and 23 base difference between the isolate and S. warneri, indicating that the isolate was a strain of S. aureus. Vancomycin was subsequently prescribed and blood cultures taken four days after the start of treatment were negative. CONCLUSIONS: 16S rRNA gene sequencing was useful in ascertaining the clinical importance of the strain of slide coagulase positive but tube coagulase negative Staphylococcus species isolated from blood culture and allowing appropriate management.

Adult↗

PubMed2000

Vaccination against gonadotropin-releasing hormone (GnRH) using toxin receptor-binding domain-conjugated GnRH repeats.

A method for the preparation of an immunogen containing multiple copies of a self-peptide in linear alignment was designed in order to overcome the difficulty of inducing an immune response to poorly immunogenic peptide antigens. DNA fragments encoding multiple repeats of the self-peptide were generated by a new technique, termed template-repeated polymerase chain reaction (TR-PCR), which could be subcloned into an expression vector for production of peptide repeats as an immunogen. This approach was tested by constructing fusion proteins containing the receptor-binding domain of Pseudomonas exotoxin A and multiple copies of the 10-residue sequence of the peptide hormone gonadotropin-releasing hormone (GnRH). Immunization of female rabbits with the immunogen that contained the exotoxin receptor-binding domain and 12 copies of GnRH (PEIa-GnRH12) resulted in the generation of high-titer antibodies specific for GnRH. Although at equal molar basis of the GnRH moiety, the immunogen that contained single copy of GnRH (PEIa-GnRH1) induced low-titer anti-GnRH antibodies. These observations suggest that the presence of multiple peptide repeats is a key factor in eliciting an immune response. In addition, anti-GnRH antibodies effectively neutralized GnRH activity in vivo, as demonstrated by the degeneration of the ovaries in the injected rabbits. Because anti-GnRH antibody could be functionally analogous to GnRH antagonist, which has been used to treat patients with ovarian cancer, vaccination of PEIa-GnRH12 presents a potential therapeutic application for the treatment of GnRH-sensitive ovarian cancer.

ADP Ribose Transferases↗

PubMed1991

Detection of common three-dimensional substructures in proteins.

We present a fully automatic algorithm for three-dimensional alignment of protein structures and for the detection of common substructures and structural repeats. Given two proteins, the algorithm first identifies all pairs of structurally similar fragments and subsequently clusters into larger units pairs of fragments that are compatible in three dimensions. The detection of similar substructures is independent of insertion/deletion penalties and can be chosen to be independent of the topology of loop connections and to allow for reversal of chain direction. Using distance geometry filters and other approximations, the algorithm, implemented in the WHAT IF program, is so fast that structural comparison of a single protein with the entire database of known protein structures can be performed routinely on a workstation. The method reproduces known non-trivial superpositions such as plastocyanin on azurin. In addition, we report surprising structural similarity between ubiquitin and a (2Fe-2S) ferredoxin.

Algorithms↗

PubMed1998

Single-particle selection and alignment with heavy atom cluster-antibody conjugates.

A method is proposed for selecting and aligning images of single biological particles to obtain high-resolution structural information by cryoelectron microscopy. The particles will be labeled with multiple heavy atom clusters to permit the precise determination of particle locations and relative orientations even when imaged close to focus with a low electron dose, conditions optimal for recording high-resolution detail. Heavy atom clusters should also allow selection of images free from many kinds of defects, including specimen movement and particle inhomogeneity. Heavy atom clusters may be introduced in a general way by the construction of "adaptor" molecules based on single-chain Fv antibody fragments, consisting of a constant framework region engineered for optimal cluster binding and a variable antigen binding region selected for a specific target. The success of the method depends on the mobility of the heavy atom cluster on the particle, on the precision to which clusters can be located in an image, and on the sufficiency of cluster projections alone to orient and select particles for averaging. The necessary computational algorithms were developed and implemented in simulations that address the feasibility of the method.

Antibodies↗

PubMedDate not supplied

PCR-based ribosomal DNA detection technique for microalga (Heterosigma carterae) causing red tide and its application to a biosensor using labeled probe.

A technique for detecting Raphidophycean, a bloom-forming genus of algae, was developed using a specific DNA probe. The design of the probe was based on a sequence polymorphism within the small subunit (SSU) ribosomal RNA gene (rDNA) of this strain by using fluorescence polarization (FP) analysis and the BIAcore 2000 biosensor, which utilized surface plasmon resonance (SPR). The specific sequence in SSU rDNA for Heterosigma carterae was determined by sequence data analysis. One pair of polymerase chain reaction (PCR) probes was designed for use in making the identification. H. carterae SSU rDNA was amplified by PCR. Using a fluoroscein isothiocyanate-labeled or biotin-labeled oligonucleotide probe, the PCR-amplified rDNA was selectively detected as an FP-intensity change via FP analysis or as a resonance-unit change via SPR. Although total time for final detection after sampling was within 3 hours, specific rDNA could be detected within 10 minutes after PCR through these detection methods.

Base Sequence↗

PubMed1997

Identification of clinically relevant viridans group streptococci to the species level by PCR.

A PCR assay that allows identification of clinically relevant viridans group streptococci (Streptococcus gordonii, S. mitis, S. mutans, S. oralis, S. salivarius, and S. sanguis) to the species level and identification of milleri group streptococci (S. anginosus, S. constellatus, and S. intermedius) to the group level was developed. This assay was based on specific amplification of internal fragments of genes encoding D-alanine:D-alanine ligases which are species specific and ubiquitous in prokaryotes possessing peptidoglycan. The specificity of this assay was tested on 9 reference strains and 91 characterized clinical isolates. This assay offers a specific and rapid alternative to phenotypic or DNA-DNA hybridization methods for identification of clinically relevant viridans group streptococci.

Alanine↗

PubMed2005

An improved reverse transcription-polymerase chain reaction (RT-PCR) assay for the detection of two cherry flexiviruses in Prunus spp.

A one-step reverse transcription-polymerase chain reaction (RT-PCR) procedure was developed to detect Cherry green ring mottle virus (CGRMV) and Cherry necrotic rusty mottle virus (CNRMV) in woody indicators and naturally infected Prunus spp. Viral RNA suitable for RT-PCR was obtained by a simple trapping method that did not require either extraction of double-stranded RNA (dsRNA) or total RNA, availability of virus antibodies, or purification of viral particles. Consensus primers, degenerate primers and virus-specific primers, whose designs were based on alignments of available cherry flexivirus sequences, were tested to amplify viral genomic fragments of six CGRMV isolates and one CNRMV isolate. RT-PCR allowed CGRMV detection in total RNA and viral RNA preparations equivalent to 400mug and 4mug of infected leaf tissue, respectively. CGRMV was detected in tender shoots, leaves, bark and root tips, and the strongest bands were obtained using young leaves. Detection was less consistent in summer when the temperature was elevated and plant tissues were old. A direct comparison of the RT-PCR and grafting assays indicated that the RT-PCR assay is sensitive, rapid and reliable. The method will improve the routine diagnosis of cherry flexiviruses in Prunus spp.

Capsid Proteins↗