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Glycobiology Advance Access published online on July 11, 2006
Glycobiology, doi:10.1093/glycob/cwl021
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© The Author 2006. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Received March 8, 2006
Revised June 21, 2006
Accepted July 9, 2006

Article

Search for glucose/galactose binding proteins in newly discovered protein sequences using molecular modeling techniques and structural analysis

Madhumita Patra 1 and Chhabinath Mandal 1 *

1 Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata - 700032, INDIA

* To whom correspondence should be addressed.
Chhabinath Mandal, E-mail: cnmandal{at}iicb.res.in


  Abstract

Sugar moieties serve as specificity markers in a wide variety of biochemical functions and periplasmic glucose/galactose binding proteins serve as the primary receptors for transport and chemotaxis. Recently, complete genome sequencing projects have revealed a number of open reading frames for such receptors. Based on 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 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. Calculation of free energies of binding of the modeled structures to glucose and galactose in presence of water suggested that two out of four putative proteins can form complexes with dissociation constants in the micro-molar range (1-10 µM). 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.

Keywords: galactose/glucose/modeling/receptor/structure.
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