Bioinformatics Storing Databases

An exceptional branch of data that requires huge databases has been shown lately from genome sequencing projects which is a field that employs computational approaches to answer biological questions. With this huge sequence of information that is available for researchers, bioinformatics plays a big role in studying basic medical-biological problems. The challenge that faces bioinformatical scientists is to help in discovering genes and designing molecular models, site-directed mutagenesis, and other experiments that reveal the unknown relationships concerning the structure and function of genes and proteins. This become a big challenge especially with the huge amount of data that is generated using the human genome and other systematic sequencing efforts up till now. Bioinformatics solves biological problems depending on available data. It is concerned with creating databases and predicting the outcome of lab experiments.

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Chitosanase from Streptomyces sp. strain N174: a comparative review of its structure and function

Biochemistry and Cell Biology ◽

10.1139/o97-079 ◽

1997 ◽

Vol 75 (6) ◽

pp. 687-696 ◽

Cited By ~ 20

Author(s):

Tamo Fukamizo ◽

Ryszard Brzezinski

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Substrate Binding ◽

Structure And Function ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Amino Acid Residues ◽

Streptomyces Sp ◽

Binding Cleft ◽

And Function

Novel information on the structure and function of chitosanase, which hydrolyzes the beta -1,4-glycosidic linkage of chitosan, has accumulated in recent years. The cloning of the chitosanase gene from Streptomyces sp. strain N174 and the establishment of an efficient expression system using Streptomyces lividans TK24 have contributed to these advances. Amino acid sequence comparisons of the chitosanases that have been sequenced to date revealed a significant homology in the N-terminal module. From energy minimization based on the X-ray crystal structure of Streptomyces sp. strain N174 chitosanase, the substrate binding cleft of this enzyme was estimated to be composed of six monosaccharide binding subsites. The hydrolytic reaction takes place at the center of the binding cleft with an inverting mechanism. Site-directed mutagenesis of the carboxylic amino acid residues that are conserved revealed that Glu-22 and Asp-40 are the catalytic residues. The tryptophan residues in the chitosanase do not participate directly in the substrate binding but stabilize the protein structure by interacting with hydrophobic and carboxylic side chains of the other amino acid residues. Structural and functional similarities were found between chitosanase, barley chitinase, bacteriophage T4 lysozyme, and goose egg white lysozyme, even though these proteins share no sequence similarities. This information can be helpful for the design of new chitinolytic enzymes that can be applied to carbohydrate engineering, biological control of phytopathogens, and other fields including chitinous polysaccharide degradation. Key words: chitosanase, amino acid sequence, overexpression system, reaction mechanism, site-directed mutagenesis.

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Bacterial Overexpression and Site-directed Mutagenesis of the PS2 Manganese Stabilizing Protein: Progress in Elucidation of Structure and Function

Photosynthesis: Mechanisms and Effects ◽

10.1007/978-94-011-3953-3_297 ◽

1998 ◽

pp. 1253-1258

Author(s):

N. Lydakis-Simantiris ◽

R. S. Hutchison ◽

S. D. Betts ◽

B. A. Barry ◽

C. F. Yocum

Keyword(s):

Structure And Function ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Manganese Stabilizing Protein ◽

And Function

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The Study of Collagen Structure and Function by Site-Directed Mutagenesis of Collagen Genes

Annals of the New York Academy of Sciences ◽

10.1111/j.1749-6632.1990.tb17941.x ◽

1990 ◽

Vol 580 (1 Structure, Mo) ◽

pp. 324-329 ◽

Cited By ~ 3

Author(s):

JOHN F. BATEMAN ◽

THOMAS MASCARA ◽

WILLIAM G. COLE ◽

ALEX STACEY ◽

RUDOLF JAENISCH

Keyword(s):

Structure And Function ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Collagen Structure ◽

And Function ◽

Collagen Genes

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Studies on the structure and function of the carp gonadotropin a subunit by site-directed mutagenesis

International journal of peptide & protein research ◽

10.1111/j.1399-3011.1995.tb00591.x ◽

2009 ◽

Vol 46 (3-4) ◽

pp. 209-213 ◽

Cited By ~ 1

Author(s):

CHANG-JEN HUANG ◽

FORE-LIEN HUANG ◽

GEEN-DONG CHANG ◽

YEA-SHA CHANG ◽

TUNG-BIN LO

Keyword(s):

Structure And Function ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

A Subunit ◽

And Function

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Structure and function analysis of Polygonatum cyrtonema lectin by site-directed mutagenesis

Acta Biochimica et Biophysica Sinica ◽

10.1093/abbs/gmx116 ◽

2017 ◽

Vol 49 (12) ◽

pp. 1099-1111 ◽

Cited By ~ 1

Author(s):

Yuyu Chen ◽

Kaimin Lu ◽

Jianzong Li ◽

Danfeng Liang ◽

Hao luo ◽

...

Keyword(s):

Function Analysis ◽

Structure And Function ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

And Function

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Structure and Function of Prostanoid Receptors as Revealed by Site-Directed Mutagenesis

Advances in Experimental Medicine and Biology - Eicosanoids and other Bioactive Lipids in Cancer, Inflammation, and Radiation Injury 3 ◽

10.1007/978-1-4899-1813-0_31 ◽

1997 ◽

pp. 205-209 ◽

Cited By ~ 4

Author(s):

Hsin-Hsiung Tai ◽

Chifu Huang ◽

Nan Chiang

Keyword(s):

Structure And Function ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Prostanoid Receptors ◽

And Function

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Structure and Function of ras p21: Studies BY Site-Directed Mutagenesis

The Guanine — Nucleotide Binding Proteins ◽

10.1007/978-1-4757-2037-2_22 ◽

1989 ◽

pp. 229-239 ◽

Cited By ~ 1

Author(s):

Thomas Y. Shih ◽

David J. Clanton ◽

Pothana Saikumar ◽

Linda S. Ulsh ◽

Seisuke Hattori

Keyword(s):

Structure And Function ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Ras P21 ◽

And Function

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Identification of a Claudin-4 Residue Important for Mediating the Host Cell Binding and Action of Clostridium perfringens Enterotoxin

Infection and Immunity ◽

10.1128/iai.00778-09 ◽

2009 ◽

Vol 78 (1) ◽

pp. 505-517 ◽

Cited By ~ 47

Author(s):

Susan L. Robertson ◽

James G. Smedley ◽

Bruce A. McClane

Keyword(s):

Host Cell ◽

Clostridium Perfringens ◽

Normal Structure ◽

Structure And Function ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Extracellular Loop ◽

Cell Binding ◽

Clostridium Perfringens Enterotoxin ◽

And Function

ABSTRACT The 24-member claudin protein family plays a key role in maintaining the normal structure and function of epithelial tight junctions. Previous studies with fibroblast transfectants and naturally sensitive Caco-2 cells have also implicated certain claudins (e.g., Claudin-4) as receptors for Clostridium perfringens enterotoxin (CPE). The present study first provided evidence that the second extracellular loop (ECL-2) of claudins is specifically important for mediating the host cell binding and cytotoxicity of native CPE. Rat fibroblast transfectants expressing a Claudin-4 chimera, where the natural ECL-2 was replaced by ECL-2 from Claudin-2, exhibited no CPE-induced cytotoxicity. Conversely, CPE bound to, and killed, CPE-treated transfectants expressing a Claudin-2 chimera with a substituted ECL-2 from Claudin-4. Site-directed mutagenesis was then used to alter an ECL-2 residue that invariably aligns as N in claudins known to bind native CPE but as D or S in claudins that cannot bind CPE. Transfectants expressing a Claudin-4N149D mutant lost the ability to bind or respond to CPE, while transfectants expressing a Claudin-1 mutant with the corresponding ECL-2 residue changed from D to N acquired CPE binding and sensitivity. Identifying carriage of this N residue in ECL-2 as being important for native CPE binding helps to explain why only certain claudins can serve as CPE receptors. Finally, preincubating CPE with soluble recombinant Claudin-4, or Claudin-4 fragments containing ECL-2 specifically blocked the cytotoxicity on Caco-2 cells. This result opens the possibility of using receptor claudins as therapeutic decoys to ameliorate CPE-mediated intestinal disease.

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