Aligning protein structures

Special issue paper PAR-3D-BLAST: A parallel tool for searching and aligning protein structures present a parallel tool, parallel 3D-BLAST (PAR-  3D-BLAST), which lists the similar structures to the query protein. Each protein in the result list has a  structural similarity score and an alignment to the query structure. The presented tool is implemented to fit  both the standalone multi-core computers and clusters of multi-core nodes. The achieved speedup is linear  and scalable.

10p ducla78 30-07-2015 38 2   Download

The Rv0948c gene fromMycobacterium tuberculosisH37Rv encodes a 90 amino acid protein as the natural gene product with chorismate mutase (CM) activity. The protein, 90-MtCM, exhibits Michaelis–Menten kinetics with akcat of 5.5 ± 0.2 s )1 and a Kmof 1500 ± 100lmat 37C and pH 7.5. The 2.0 A˚ X-ray structure shows that 90-MtCM is an alla-helical homodimer (Protein Data Bank ID: 2QBV) with the topology ofEscheri-chia coliCM (EcCM), and that both protomers contribute to each catalytic site.

12p research12 29-04-2013 37 2   Download

The description of globular protein structures as an ensem-ble of contiguous
closed loops or
tightened end fragments reveals fold elements crucial for the formation of stable structures and for navigating the very process of protein folding. These are the ends of the loops, which are spatially close to each other but are situated apart in the polypeptide chain by 25–30 residues. They also correlate with the loca-tions of highly conserved hydrophobic residues (referred to as topohydrophobic), in a structural alignment of the members of a protein family....

0p awards 05-04-2013 48 2   Download

Spinocerebellar ataxia types 2 (SCA2) and 3 (SCA3) are autosomal-dominantly inherited, neurodegenerative dis-eases caused by CAG repeat expansions in the coding regions of the genes encoding ataxin-2 and ataxin-3, respectively. To provide a rationale for further functional experiments, we explored the proteinarchitectures of ataxin-2 and ataxin-3. Using structure-based multiple sequence alignments of homologous proteins, we investigated domains, sequence motifs, and interaction partners.

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A homologue of interleukin 18 has been identified from rainbow trout,Oncorhynchus mykiss. The trout IL-18gene spans 3.7 kb and consists of six exons and five introns, sharing the same gene organization with its human coun-terpart. The putative translated protein is 199 amino acids in length with no predicted signal peptide. Analysis of the multiple sequence alignment reveals a conserved ICE cut site, resulting in a mature peptide of 162 amino acids. The trout IL-18 shares 41–45% similarity with known IL-18 molecules and contains an IL-1 family signature motif....

11p dell39 03-04-2013 51 2   Download

In the postgenomic era it is essential that protein sequences are annotated correctly in order to help in the assignment of their putative functions. Over 1300 proteins in current pro-tein sequence databases are predicted to contain a PAS domainbaseduponaminoacid sequence alignments.Oneof theproblemswith the current annotationof thePASdomain is that this domain exhibits limited similarity at the amino acid sequence level.

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Placental protein 13 (PP13) was cloned from human term placenta. As sequence analyses, alignments and computa-tional modelling showed its conserved structural and func-tional homologyto members of the galectin family, the protein was designated galectin-13. Similar to human eosi-nophil Charcot–Leyden crystal protein/galectin-10 but not other galectins, its weak lysophospholipase activity was confirmed by 31 P-NMR. In this study, recombinant PP13/ galectin-13 was expressed and specific monoclonal antibody to PP13 was developed. ...

14p dell39 03-04-2013 25 2   Download

In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.[1] Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.

29p trautuongquan 25-02-2013 50 6   Download

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: FlexSnap: Flexible Non-sequential Protein Structure Alignment Research...

13p hoami_2511 21-10-2011 50 3   Download

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Protein sequence and structure alignments within one framework...

12p hoami_2511 21-10-2011 48 4   Download

Do đó, các nghiên cứu trong ngành sinh học tính toán (computational biology) thường trùng lặp với sinh học hệ thống (systems biology). Những lĩnh vực nghiên cứu chính của nó bao gồm bắt cặp trình tự (sequence alignment), bắt cặp cấu trúc protein (protein structural alignment), dự đoán cấu trúc protein (protein structure prediction), dự đoán biểu hiện gene (gene expression) và tương tác protein - protein (protein-protein interactions), và mô hình hóa quá trình tiến hoá. ...

6p poseidon05 26-07-2011 105 33   Download