PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences

Annotation of any newly determined protein sequence depends on the pairwise sequence identity with known sequences. However, for the twilight zone sequences which have only 15–25% identity, the pair-wise comparison methods are inadequate and the annotation becomes a challenging task. Such sequences can be annotated by using methods that recognize their fold. Bowie et al. described a 3D1D profile method in which the amino acid sequences that fold into a known 3D structure are identified by their compatibility to that known 3D structure. We have improved the above method by using the predicted secondary structure information and employ it for fold recognition from the twilight zone sequences. In our Protein Secondary Structure 3D1D (PSS-3D1D) method, a score (w) for the predicted secondary structure of the query sequence is included in finding the compatibility of the query sequence to the known fold 3D structures. In the benchmarks, the PSS-3D1D method shows a maximum of 21% improvement in predicting correctly the α + β class of folds from the sequences with twilight zone level of identity, when compared with the 3D1D profile method. Hence, the PSS-3D1D method could offer more clues than the 3D1D method for the annotation of twilight zone sequences. The web based PSS-3D1D method is freely available in the PredictFold server at .     

Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model

The problem of protein structure prediction in the hydrophobic-polar (HP) lattice model is the prediction of protein tertiary structure. This problem is usually referred to as the protein folding problem. This paper presents a method for the application of an enhanced hybrid search algorithm to the problem of protein folding prediction, using the three dimensional (3D) HP lattice model. The enhanced hybrid search algorithm is a combination of the particle swarm optimizer (PSO) and tabu search (TS) algorithms. Since the PSO algorithm entraps local minimum in later evolution extremely easily, we combined PSO with the TS algorithm, which has properties of global optimization. Since the technologies of crossover and mutation are applied many times to PSO and TS algorithms, so enhanced hybrid search algorithm is called the MCMPSO-TS (multiple crossover and mutation PSO-TS) algorithm. Experimental results show that the MCMPSO-TS algorithm can find the best solutions so far for the listed benchmarks, which will help comparison with any future paper approach. Moreover, real protein sequences and Fibonacci sequences are verified in the 3D HP lattice model for the first time. Compared with the previous evolutionary algorithms, the new hybrid search algorithm is novel, and can be used effectively to predict 3D protein folding structure. With continuous development and changes in amino acids sequences, the new algorithm will also make a contribution to the study of new protein sequences.     

C-curve: A novel 3D graphical representation of DNA sequence based on codons

In this paper, a novel 3D graphical representation of DNA sequence based on codons is proposed. Since there is not loss of information due to overlapping and containing loops, this representation will be useful for comparison of different DNA sequences. This 3D curve will be convenient for DNA mutations comparison specially. In continues we give a numerical characterization of DNA sequences based on the new 3D curve. This characterization facilitates quantitative comparisons of similarities/dissimilarities analysis of DNA sequences based on codons.     

Genes encoding human killer-cell Ig-like receptors with D1 and D2 extracellular domains all contain untranslated pseudoexons encoding a third Ig-like domain

Human killer-cell immunoglobulin-like receptors (KIR) show three types of organization of their extracellular domains: D0-D1-D2 in KIR3D, D1-D2 in the majority of KIR2D, and D0-D2 in KIR2DL4 and the novel KIR2DL5. The gene for a KIR2DL3 variant, which has a D1-D2 structure, has been shown previously to have a nonexpressed region (pseudoexon 3) that is paralogous to the exon encoding the D0 domain of other KIR. This pseudoexon is not expressed because it is skipped during splicing of pre-mRNA. In this study, we demonstrate that all eight genes encoding human KIR with D1-D2 configuration (KIR2DL1-KIR2DL3, KIR2DS1-KIR2DS5) have similarly untranslated pseudoexons. Whereas the pseudoexons of four of these KIR genes bear nonsense mutations and/or altered splicing sites, the pseudoexons in the other four KIR genes have no major structural abnormalities, indicating that other mechanisms are responsible for inactivation of their exons 3. A comparison of the sequences on pseudoexons 3 with the paralogous expressed exons suggests that an exonic splicing enhancer may be necessary for the expression of exon 3 in KIR genes.     

Primary structure of the two (4 Fe-4 S) clusters ferredoxin from Desulfovibrio desulfuricans (strain Norway 4)

The primary structure of a ferredoxin isolated from D. desulfuricans Norway strain, which we called ferredoxin II (Fd II) has been elucidated. This ferredoxin is a dimer constituted of two identical subunits of molecular weight 6000. In ferredoxin II two (4 Fe-4 S) centers are present per subunit instead of one (Fe-S) center as is the case for the other ferredoxins isolated from Desulfovibrio and for Fd I from the same organism. The comparison of amino-acid sequences shows that ferredoxin II presents more homologies with clostridial type ferredoxin than with the ferredoxins from D. gigas and D. africanus.     

The nucleotide and deduced amino acid structures of sheep and pig fetuin. Common structural features of the mammalian fetuin family.

This study was initiated to gain further insight into the structural features of the mammalian fetuin family. The cDNA structures of sheep and pig fetuin were determined. The cDNA insert encoding sheep (pig) fetuin comprised 1550 (1470) nucleotides, including 54 (46) nucleotides encoding a signal peptide of 18 (15) residues and 1038 (1041) nucleotides encoding the 346 (347) amino acids of the mature plasma protein. The predicted amino-terminal sequence of the mature pig fetuin was confirmed by the amino-terminal sequence of the purified protein. However, two alternative sheep amino-terminal sequences were found in fetuin purified from the plasma of a single sheep fetus; the minor product was the one predicted by comparison with other fetuin sequences while the major product was two amino acids longer. Comparison of the deduced amino acid sequences of sheep and pig fetuin showed an extensive sequence identity between them (75%) and with other proteins of the mammalian fetuin family, i.e. human alpha 2-HS glycoprotein, and bovine and rat fetuins. Twelve cysteine residues were found at invariant positions in all fetuin sequences, suggesting strongly that the arrangement of disulphide bridges identified in human alpha 2-HS glycoprotein is common to the members of the family. Further sequence comparisons revealed that the structures of mammalian fetuins are organised in three domains: two cystatin-like domains (D1 and D2) and a complex carboxyl-terminal domain (D3). The proposed three-domain structure of the protein is reflected in the organisation of the rat fetuin structural gene which has recently been published.     

Molecular and morphometric evidence for separate species of Uncinaria (Nematoda: Ancylostomatidae) in California sea lions and northern fur seals: hypothesis testing supplants verification

California sea lions (Zalophus californianus) and northern fur seals (Callorhinus ursinus) are each believed to host distinct hookworm species (Uncinaria spp.). However, a recent morphometric analysis suggested that a single species parasitizes multiple pinniped hosts, and that the observed differences are host-induced. To explore the systematics of these hookworms and test these competing hypotheses, we obtained nucleotide sequences of nuclear ribosomal DNA (D2/D3 28S, D18/D19 28S, and internal transcribed spacer [ITS] regions) from 20 individual hookworms parasitizing California sea lion and northern fur seal pups where their breeding grounds are sympatric. Five individuals from an allopatric population of California sea lions were also sampled for ITS-1 and D18/D19 28S sequences. The 28S D2/D3 sequences showed no diagnostic differences among hookworms sampled from individual sea lions and fur seals, whereas the 28S D18/D19 sequences had one derived (apomorphic) character demarcating hookworms from northern fur seals. ITS sequences were variable for 7 characters, with 4 derived (apomorphic) states in ITS-1 demarcating hookworms from California sea lions. Multivariate analysis of morphometric data also revealed significant differences between nematodes representing these 2 host-associated lineages. These results indicate that these hookworms represent 2 species that are not distributed indiscriminately between these host species, but instead exhibit host fidelity, evolving independently with each respective host species. This evolutionary approach to analyzing sequence data for species delimitation is contrasted with similarity-based methods that have been applied to numerous diagnostic studies of nematode parasites.     

From analysis of protein structural alignments toward a novel approach to align protein sequences

Alignment of protein sequences is a key step in most computational methods for prediction of protein function and homology-based modeling of three-dimensional (3D)-structure. We investigated correspondence between "gold standard" alignments of 3D protein structures and the sequence alignments produced by the Smith-Waterman algorithm, currently the most sensitive method for pair-wise alignment of sequences. The results of this analysis enabled development of a novel method to align a pair of protein sequences. The comparison of the Smith-Waterman and structure alignments focused on their inner structure and especially on the continuous ungapped alignment segments, "islands" between gaps. Approximately one third of the islands in the gold standard alignments have negative or low positive score, and their recognition is below the sensitivity limit of the Smith-Waterman algorithm. From the alignment accuracy perspective, the time spent by the algorithm while working in these unalignable regions is unnecessary. We considered features of the standard similarity scoring function responsible for this phenomenon and suggested an alternative hierarchical algorithm, which explicitly addresses high scoring regions. This algorithm is considerably faster than the Smith-Waterman algorithm, whereas resulting alignments are in average of the same quality with respect to the gold standard. This finding shows that the decrease of alignment accuracy is not necessarily a price for the computational efficiency.     

Digital signal processing methods for biosequence comparison.

A method is discussed for DNA or protein sequence comparison using a finite field fast Fourier transform, a digital signal processing technique; and statistical methods are discussed for analyzing the output of this algorithm. This method compares two sequences of length N in computing time proportional to N log N compared to N2 for methods currently used. This method makes it feasible to compare very long sequences. An example is given to show that the method correctly identifies sites of known homology.     

Comparison of conformation and antimicrobial activity of synthetic analogs of gramicidin S: Stereochemical consideration of the role of D-phenylalanine in the antibiotic.

In order to study the role of D -amino acid residues in keeping the stable β-sheet conformation and in the antimicrobial activity of gramicidin S (GS), the four analogs of GS containing D -Ala, L -Ala, Gly, and Aib (α-aminoisobutyric acid) in place of D -Phe were synthesized. D -Ala-and Gly-containing analogs showed antimicrobial activity, while those containing L -Ala and Aib showed no activity. Conformation of these analogs and their derivatives were studied by comparison of ORD and CD spectra and by slective methylation method. It is concluded that the biologically active analogs have β-sheet conformation while inactive analogs have a much different conformation from that of GS. This indicates that D -Ala-Pro and Gly-Pro sequences favor taking a β-bend form but L -Ala-Pro and Aib-Pro sequences do not because the presence of L -side methyl group on the α-carbon atom of L Ala and Aib residues destabilizes the β-bend form. This would explain why the inactive analogs which take a different conformation from that of the active ones result in the loss of activity.     

一株具有从头合成单萜能力的葡萄酒复膜孢酵母

从中国湖南省刺葡萄果实表面分离到一株产香酵母LA24。对其进行了详细的形态特征描述,提供了显微镜的观察结果;通过对大亚基rRNA基因（LSU rDNA）D1/D2区序列进行PCR扩增,测序,并与NCBI数据库比对确定该菌为葡萄酒复膜孢酵母Saccharomycopsis vini。GC-QQQ鉴定该酵母能以葡萄糖为原料合成香叶醇、香茅醇和微量的α-松油醇和芳樟醇等单萜类物质。该菌株为首次报道具有合成单萜类能力的葡萄酒复膜孢酵母,为微生物合成单萜类生物途径的研究提供独特材料。     

General methods of sequence comparison

Mathematical methods for comparison of nucleic acid sequences are reviewed. There are two major methods of sequence comparison: dynamic programming and a method referred to here as the regions method. The problem types discussed are comparison of two sequences, location of long matching segments, efficient database searches and comparison of several sequences. This work was supported by a grant from the System Development Foundation.     

Pure multiple RNA secondary structure alignments: a progressive profile approach

In functional, noncoding RNA, structure is often essential to function. While the full 3D structure is very difficult to determine, the 2D structure of an RNA molecule gives good clues to its 3D structure, and for molecules of moderate length, it can be predicted with good reliability. Structure comparison is, in analogy to sequence comparison, the essential technique to infer related function. We provide a method for computing multiple alignments of RNA secondary structures under the tree alignment model, which is suitable to cluster RNA molecules purely on the structural level, i.e., sequence similarity is not required. We give a systematic generalization of the profile alignment method from strings to trees and forests. We introduce a tree profile representation of RNA secondary structure alignments which allows reasonable scoring in structure comparison. Besides the technical aspects, an RNA profile is a useful data structure to represent multiple structures of RNA sequences. Moreover, we propose a visualization of RNA consensus structures that is enriched by the full sequence information.     

Characterization of the complete mitochondrial genome of Diphyllobothrium nihonkaiense (Diphyllobothriidae: Cestoda), and development of molecular markers for differentiating fish tapeworms

We sequenced and characterized the complete mitochondrial genome of the Japanese fish tapeworm D. nihonkaiense. The genome is a circular-DNA molecule of 13607 bp (one nucleotide shorter than that of D. latum mtDNA) containing 12 protein-coding genes (lacking atp8), 22 tRNA genes and two rRNA genes. Gene order and genome content are identical to those of the other cestodes reported thus far, including its congener D. latum. The only exception is Hymenolepis diminuta in which the positions of trnS2 and trnL1 are switched. We tested a PCR-based molecular assay designed to rapidly and accurately differentiate between D. nihonkaiense and D. latum using species-specific primers based on a comparison of their mtDNA sequences. We found the PCR-based system to be very reliable and specific, and suggest that PCR-based identification methods using mtDNA sequences could contribute to the study of the epidemiology and larval ecology of Diphyllobothrium species.     

Optimal alignment between groups of sequences and its application to multiple sequence alignment

Four algorithms, A–D, were developed to align two groupsof biological sequences. Algorithm A is equivalent to the conventionaldynamic programming method widely used for aligning ordinarysequences, whereas algorithms B – D are designed to evaluatethe cost for a deletion/insertion more accurately when internalgaps are present in either or both groups of sequences. Rigorousoptimization of the ‘sum of pairs’ (SP) score isachieved by algorithm D, whose average performance is closeto O(MNL²) where M and N are numbers of sequences included inthe two groups and L is the mean length of the sequences. AlgorithmB uses some app mximations to cope with profile-based operations,whereas algorithm C is a simpler variant of algorithm D. Thesegroup-to-group alignment algorithms were applied to multiplesequence alignment with two iterative strategies: a progressivemethod based on a given binary tree and a randomized grouping-realignmentmethod. The advantages and disadvantages of the four algorithmsare discussed on the basis of the results of exatninations ofseveral protein families.     

Diverse organization of immunoglobulin VH gene loci in a primitive vertebrate.

The immunoglobulin (Ig) heavy chain variable (VH) gene family of Heterodontus francisci (horned shark), a phylogenetically distant vertebrate, is unique in that VH, diversity (DH), joining (JH) and constant region (CH) gene segments are linked closely, in multiple individual clusters. The V regions of 12 genomic (liver and gonad) DNA clones have been sequenced completely and three organization patterns are evident: (i) VH-D1-D2-JH-CH with unique 12/22 and 12/12 spacers in the respective D recombination signal sequences (RSSs); VH and JH segments have 23 nucleotide (nt) spacers, (ii) VHDH-JH-CH, an unusual germline configuration with joined VH and DH segments and (iii) VHDHJH-CH, with all segmental elements being joined. The latter two configurations do not appear to be pseudogenes. Another VH-D1-D2-JH-CH gene possesses a D1 segment that is flanked by RSSs with 12 nt spacers and a D2 segment with 22/12 spacers. Based on the comparison of spleen, VH+ cDNA sequences to a germline consensus, it is evident that both DH segments as well as junctional and N-type diversity account for Ig variability. In this early vertebrate, the Ig genes share unique properties with higher vertebrate T-cell receptor as well as with Ig and may reflect the structure of a common ancestral antigen binding receptor gene.