Construction and analysis of a profile library characterizing groups of structurally known proteins

Ogiwara, Atsushi; Uchiyama, Ikuo; Takagi, Toshihisa; Kanehisa, Minoru

doi:10.1002/pro.5560051005

Cited by 27 publications

(13 citation statements)

References 20 publications

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“…Predicted transmembrane segments were analysed by TSEG (http://www.genome.ad.jp/SIT/tseg.html) (Kihara et al, 1998) and SOSUI (http://www.genome.ad.jp/SOSui/index.html) (Hirokawa et al, 1998). Protein motif searching was done by MOTIF (http://motif.genome.ad.jp/MOTIF.html) (Ogiwara et al, 1996).…”

Section: Methodsmentioning

confidence: 99%

Regulation of the aerobic respiratory chain in the facultatively aerobic and hyperthermophilic archaeon Pyrobaculum oguniense

et al. 2003

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Section: Methodsmentioning

confidence: 99%

Regulation of the aerobic respiratory chain in the facultatively aerobic and hyperthermophilic archaeon Pyrobaculum oguniense

et al. 2003

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“…This scheme, adapted here to the computation of pair‐wise amino acid residue similarities, consists of the computation of a mutation matrix, D ij 17 Figure 1. shows an arbitrary string of g i scores evolved by the GA and used in that calculation of the similarity matrix S (a,b) for a pair of amino acids i and j using the expression:…”

Section: Methodsmentioning

confidence: 99%

A combined bioinformatic approach oriented to the analysis and design of peptides with high affinity to MHC class I molecules

et al. 2002

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A combined bioinformatic approach oriented to the analysis and design of peptides with high affinity to MHC class I molecules C A R L O S A D E L C A R P I O , T A B E A H E N N I G , S I M O N E T T A F I C K E L a n d A T S U S H I Y O S H I M O R I Laboratory for Bioinformatics, Department of Ecological Engineering, Toyohashi University of Technology, Tempaku, Toyohashi, JapanSummary We report on a new method to compute the antigenic degree of peptides from available experimental data on peptide binding affinity to class I MHC molecules. The methodology is a combination of two strategies at different levels of information. The first, at the primary structure level, consists in expressing the peptides binding activity as a profile of amino acid contributions, amino acid similarity being accounted for by their characteristic physicochemical properties and their position within the sequence. The higher level of the strategy is based on a meticulous analysis of the contact interface of the peptides with the cleft constituting the receptor region of a particular class I MHC molecule. Interaction interfaces are inferred by docking the peptide onto the receptor groove of the MHC molecule; evaluation of the affinity of the peptide to the receptor is then performed by analysis of the electrostatic and hydrophobic energies on points of the interaction interface.The result is a robust system for analysis of peptide affinity to class I MHC molecules since while the first analysis dictates the composition of active sequences at the amino acid level, the second translates this information to the atomic level, where the molecular interaction can be analyzed in terms of the intrinsic interatomic forces and energies. Evaluation results for the methodology are encouraging since high affinity peptides are reflected by high scores at both levels of information, and are proportionally lower for peptides of medium and lower affinity for which interaction surfaces show relatively lower electrostatic complementarity and hydrophobic correlation than for the former.

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“…The TutH protein sequence was also subjected to a Motif analysis (21). Amino acids 47 to 54 were identified as a putative ATP/GTP binding domain, a region that is conserved in the NorQ and NirQ proteins.…”

Section: Vol 66 2000mentioning

confidence: 99%

Transcriptional Analysis of the tutE tutFDGH Gene Cluster from Thauera aromatica Strain T1

Coschigano

2000

Appl Environ Microbiol

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The denitrifying strain T1, identified as Thauera aromatica, is able to grow with toluene serving as its sole carbon source. Previous work identified two genes, tutD and tutE, that are involved in toluene metabolism. Two small open reading frames, tutF and tutG, which may also play a role in toluene metabolism, were also identified. The present work examines the transcriptional organization and regulation of these toluene utilization genes. Northern analysis indicates that the four genes are organized into two operons, tutE and tutFDG, and that both operons are regulated in response to toluene. Primer extension analysis has identified major transcriptional start sites located 177 bp upstream of the tutE translational start and 76 bp upstream of the tutF translational start. Furthermore, a fifth gene, tutH, has been identified immediately downstream of tutG. It is transcribed from the same start site as tutFDG and is predicted to code for a 286-amino-acid protein with a calculated molecular mass of about 31,800 Da. The TutH protein is predicted to have an ATP/GTP binding domain and is similar to the NorQ/NirQ family of proteins.Toluene is a hazardous substance that poses health risks to humans. A number of microorganisms that are able to metabolize this aromatic hydrocarbon under denitrifying conditions have been isolated and include Thauera aromatica K172 (27), Azoarcus sp. strain T (11, 17), and T. aromatica T1 (formerly known as strain T1) (12,28). Biochemical studies with cell extracts of T. aromatica K172 and Azoarcus sp. strain T have shown that the first step in anaerobic toluene metabolism in these two organisms is the enzymatic formation of benzylsuccinate from toluene and fumarate (4, 6). This is a highly stereospecific reaction carried out by benzylsuccinate synthase, an enzyme recently isolated from T. aromatica K172 (4-6, 19). This purified enzyme has been shown to be an ␣ 2 ␤ 2 ␥ 2 complex consisting of two subunits each of the BssA, BssB, and BssC proteins (19).The genes coding for the benzylsuccinate synthase protein subunits have been cloned from T. aromatica K172 and designated bssCAB (19). Highly similar genes cloned from T. aromatica T1 and designated tutFDG (Fig. 1) most likely also code for a benzylsuccinate synthase (8). Based on similarities of the BssA and TutD proteins with pyruvate formate-lyase, and based on the reported mechanism for pyruvate formate-lyase (23,24,29), it has been proposed that these enzymes function by formation of a glycine free radical (8,19). Biochemical work with the benzylsuccinate synthase enzyme from T. aromatica K172 and mutagenesis studies of the tutD gene of T. aromatica T1 support this mechanism of action (8,19).In addition to the bssA and tutD genes encoding benzylsuccinate synthase and its likely homologue, genes coding for a proposed benzylsuccinate synthase-activating enzyme have also been cloned from T. aromatica K172 and T. aromatica T1 and designated bssD and tutE, respectively (8, 19). The proposed function is based on the similarities of these gene...

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Construction and analysis of a profile library characterizing groups of structurally known proteins

Cited by 27 publications

References 20 publications

Regulation of the aerobic respiratory chain in the facultatively aerobic and hyperthermophilic archaeon Pyrobaculum oguniense

Regulation of the aerobic respiratory chain in the facultatively aerobic and hyperthermophilic archaeon Pyrobaculum oguniense

A combined bioinformatic approach oriented to the analysis and design of peptides with high affinity to MHC class I molecules

Transcriptional Analysis of the tutE tutFDGH Gene Cluster from Thauera aromatica Strain T1

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