Search for Glucose/galactose-binding Proteins in Newly Discovered Protein Sequences Using Molecular Modeling Techniques and Structural Analysis
IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata
View Archive Info| Field | Value | |
| Title |
Search for Glucose/galactose-binding Proteins in Newly Discovered Protein Sequences Using Molecular Modeling Techniques and Structural Analysis
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| Creator |
Patra, Madhumita
Mandal, Chhabinath |
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| Subject |
Structural Biology & Bioinformatics
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| Description |
Sugar moieties serve as specificity markers in a wide variety of biochemical functions, and periplasmic glucose/galactosebinding proteins (GGBPs) serve as the primary receptors for transport and chemotaxis. Recently, complete genome sequencing projects have revealed many open reading frames for such receptors. On the basis of the homology search with the known x-ray structures (PDB ID: 3GBP/1GCA) of a periplasmic receptor protein from Salmonella typhimurium, we selected four putative proteins with amino acid identities between 30 and 48% for the prediction of three-dimensional (3D) structures of the proteins as well as their complexes with glucose and galactose. We could successfully identify the key
residues involved in coordination with calcium ion spanning
over two loop structures. We calculated the ligand-binding
affinities and hydrogen bonding patterns of the modeled
structures and compared with those of the x-ray structures.
The calculation of free energies of binding of the modeled
structures to glucose and galactose in the presence of water
suggested that two of four putative proteins can form complexes with dissociation constants in the micromolar range (1–10 mM). Electrostatic potentials on the surfaces near the sugar and calcium-binding sites of the modeled structures were predominately negative as found in case of the x-ray structure. Taken together, our results suggest that the products of two newly discovered genes would serve as receptors for the transport of glucose and galactose.
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| Date |
2006
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| Type |
Article
PeerReviewed |
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| Format |
application/pdf
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| Identifier |
http://www.eprints.iicb.res.in/455/1/GLYCOBIOLOGY%2C_16(_10)%2C_959%2D968[31].pdf
Patra, Madhumita and Mandal, Chhabinath (2006) Search for Glucose/galactose-binding Proteins in Newly Discovered Protein Sequences Using Molecular Modeling Techniques and Structural Analysis. Glycobiology, 16 (10). pp. 959-968. |
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| Relation |
htpp://dx.doi.org/10.1093/glycob/cwl021
http://www.eprints.iicb.res.in/455/ |
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