Comprehensive study on iterative algorithms of multiple sequence alignment

Hirosawa, Makoto; Totoki, Yasushi; Hoshida, Masaki; Ishikawa, Masato

doi:10.1093/bioinformatics/11.1.13

Cited by 77 publications

(60 citation statements)

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“…Amino acid sequence alignment indicated a 61.4% residue identity between the primary structures of the urease enzymes. The three-dimensional model was constructed by copying aligned coordinates of identical residues, building loops, and structural refinement (10). The protein modeling tools available in the computer software package MOE (2000; Chemical Computing Group Inc. Montreal, Quebec, Canada) were used for protein modeling.…”

Section: Methodsmentioning

confidence: 99%

Three-Dimensional Quantitative Structure-Activity Relationship and Comparative Molecular Field Analysis of Dipeptide Hydroxamic Acid Helicobacter pylori Urease Inhibitors

Mishra¹,

Parrill

Williamson

2002

Antimicrob Agents Chemother

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A homology model of Helicobacter pylori urease was developed by using the crystal structure of urease from Klebsiella aerogenes (EC 3.5.1.5) as a template. The acetohydroxamic acid moiety was docked into the active pocket of the enzyme model, followed by relaxation of the complex by use of molecular dynamics. The resulting conformation was used as a template to construct 24 potential dipeptide hydroxamic acid inhibitors with which comparative molecular field analysis (CoMFA) was performed. The resulting model provided a cross-validation correlation coefficient (q 2 L00 ) of 0.610, a conventional r 2 value of 0.988, and an F (Fisher indication of statistical significance) value of 294.88. We were able to validate the CoMFA model by using the 50% inhibitory concentrations of six compounds that were not included in the construction of the model. A very good structural correlation was observed between the amino acids in the model urease's active pocket and the contour maps derived from the CoMFA model. This correlation, accompanied by the validation supplied by use of the CoMFA data, illustrates that the model can aid in the prediction and design of novel H. pylori urease inhibitors.Helicobacter pylori is a gram-negative, spiral bacterium thought to affect about 90% of the world's population (11). It is well accepted that H. pylori infection is etiologically associated with chronic active gastritis, peptic ulcer diseases, mucosa-associated lymphoid tissue-type gastric carcinoma, and other gastric cancers (16). Although H. pylori infection has been implicated as an etiological factor in chronic gastric reflux disease, new studies show that H. pylori infection may provide a protective mechanism against such disease; however, the results of those studies remain controversial (8, 18). Eradication therapy heals gastritis and results in cure of peptic ulcer and the remission of mucosa-associated lymphoid tissue-type gastric carcinomas (22). Although most infections can be controlled by antibiotic therapy (17, 27), H. pylori antibiotic resistance is becoming somewhat commonplace (1). Antibiotic resistance in a microorganism as widespread as H. pylori is a cause for immediate concern and warrants a dedicated search for the discovery of new drug therapies.H. pylori, characterized by its strong urease activity (5), has received a great deal of attention from the scientific community over the past two decades. It is now clear that for survival the organism requires the production of a urease enzyme to help produce ammonia to counteract the strong acidic environment of the stomach (19). It has been estimated that over 5% of the total protein in the cell is represented by this enzyme (12). The urease reaction not only provides an environment with a pH suitable for H. pylori colonization of the stomach mucosal lining but also provides the mechanism for eventual gastric wall damage that increases the overall likelihood and the severity of gastric ulcers (20). Ureases are ubiquitous in nature and are inhibited, in general, by a var...

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Section: Methodsmentioning

confidence: 99%

Three-Dimensional Quantitative Structure-Activity Relationship and Comparative Molecular Field Analysis of Dipeptide Hydroxamic Acid Helicobacter pylori Urease Inhibitors

Mishra¹,

Parrill

Williamson

2002

Antimicrob Agents Chemother

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“…The polymerase chain reaction (PCR) amplification and the sequencing analysis of the PCR products of the SSU-rRNA genes derived from MG-EM-01 and UZG-EC-01 were performed as described previously (Suzuki et al, 2008). Analysis and multiple alignments of the acquired sequences of the SSU-rRNA genes of E. muris (MG-EM-01) and E. coli (UZG-EC-01) were performed by following the Yebis system for DNA Alignment, which uses a treebased round-robin iterative algorithm (Hirosawa et al, 1995). The phylogenetic tree was constructed using PhyML software package version 2.4.5 (Guindon and Gascuel, 2003) using maximum likelihood (ML) analysis and a general time-reversible (GTR) model to calculate genetic distances.…”

Section: Ementioning

confidence: 99%

Establishment of a continuous culture system forEntamoeba murisand analysis of the small subunit rRNA gene

2009

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Summary :We established a culture system for Entamoeba muris (MG-EM-01 strain isolated from a Mongolian gerbil) using a modified Balamuth's egg yolk infusion medium supplemented with 4 % adult bovine serum and Bacteroides fragilis cocultured with Escherichia coli. Further, encystation was observed in the culture medium. The morphological characteristics of E. muris are similar to those of Entamoeba coli (E. coli); moreover, the malic isoenzyme electrophoretic band, which shows species-specific electrophoretic mobility, of E. muris had almost the same mobility as that observed with the malic isoenzyme electrophorectic band of E. coli (UZG-EC-01 strain isolated from a gorilla). We determined the small subunit rRNA (SSU-rRNA) gene sequence of the MG-EM-01 strain, and this sequence was observed to show 82.7 % homology with that of the UZG-EC-01 strain. Further, the resultant phylogenetic tree for molecular taxonomy based on the SSU-rRNA genes of the 21 strains of the intestinal parasitic amoeba species indicated that the MG-EM-01 strain was most closely related to E. coli. E ntamoeba muris is a highly contagious intestinal protozoan parasite of laboratory mice, rats and other rodents; this species is morphologically similar to Entamoeba coli (E. coli) (Neal, 1950) and primarily proliferates and encysts in the caecum of mice (Lin, 1971). In vitro culture of E. muris has been attempted (Neal, 1950;Simitch & Petrovitch, 1951;Smith et al., 1985); however, trials to achieve successive culture have not been successful. In the present study, we established a system for the stable and successive culture of an E. muris strain. Further, we attempted phylogenetic analysis of this strain to help in investigating its molecular taxonomy. Résumé MATERIALS AND METHODS E.muris (strain MG-EM-01) isolated from a Mongolian gerbil spontaneously infected in our laboratory was used to establish the culture system. An E. coli strain (UZG-EC-01) isolated from a gorilla in a zoo in Tokyo, Japan, was used as a reference. Escherichia coli and Bacteroides fragilis strains were isolated from the stool of a primate [DeBrazza's guenon (Cercopithecus neglectus)] and fresh human stool samples from a patient with intestinal amoebic colitis, respectively. The E. coli strains were maintained in a chemically defined medium (R medium) (Robinson, 1968), and the B. fragilis strains were maintained on trypticase, yeast extract and iron (TYI) broth (Diamond et al., 1978); these strains were used as supplements for the culture system of E. muris.Article available at http://www.parasite-journal.org or http://dx.doi.org/10.1051/parasite/2009162135The egg yolk infusion medium of Balamuth's medium (Balamuth, 1946) was replaced with infusion of a liver concentrate with 4 % preheat-treated adult bovine serum (56°C for three hours). At least one day prior to E. muris culture, 0.1 ml of E. coli maintained in the R suspension was added from the stock culture preserved at 4°C (used within one month); however, 0.2 ml of a 1-to 3-day culture of B. fragilis maintained in ...

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“…These include tabu search [200], Monte Carlo optimizaton [201], methods based on genetic algorithms [202], relaxation methods [203], simulated annealing [204], iterative algorithms [205] and parallel simulated annealing [206].…”

Section: Optimization In Bioinformaticsmentioning

confidence: 99%

Machine Learning in Bioinformatics

Mohammed¹,

Mohammed²

2008

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Comprehensive study on iterative algorithms of multiple sequence alignment

Cited by 77 publications

References 0 publications

Three-Dimensional Quantitative Structure-Activity Relationship and Comparative Molecular Field Analysis of Dipeptide Hydroxamic Acid Helicobacter pylori Urease Inhibitors

Three-Dimensional Quantitative Structure-Activity Relationship and Comparative Molecular Field Analysis of Dipeptide Hydroxamic Acid Helicobacter pylori Urease Inhibitors

Establishment of a continuous culture system forEntamoeba murisand analysis of the small subunit rRNA gene

Machine Learning in Bioinformatics

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