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Search for fucose binding domains in recently sequenced hypothetical proteins using molecular modeling techniques and structural analysis

IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata

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Title Search for fucose binding domains in recently sequenced hypothetical proteins using molecular modeling techniques and structural analysis
 
Creator Majumder, Sujata
Patra, Madhumita
Mandal, Chhabinath
 
Subject Drug Development/Diagnostics & Biotechnology
 
Description The crystal structure of a fucose-binding lectin from the bacteria Pseudomonas aeruginosa in complex with α-L-fucose has been recently determined. It is a tetramer; each monomer displays a nine-stranded, antiparallel, β- sandwiched arrangement and contains two calcium ions that mediate the binding of fucose in a recognition mode unique among protein-carbohydrate interactions. In search of this type of unique interactions in other newly discovered protein sequences, we have used molecular modeling techniques to predict and analyze the 3-D structures of some proteins, which exhibited reasonable degree of homology with the amino acid sequence of the bacterial protein. A BLAST search with the sequence of Pseudomonas aeruginosa as query in the non-redundant sequence database identified four proteins from different species, three organisms from bacteria and one from archaea.We have modeled the structures of these proteins as well as those of the complexes with carbohydrates and studied the nature of physicochemical forces involved in the complex formation both in presence and absence of calcium. The calcium-binding loops have been found to be highly conserved both in terms of primary and tertiary structures in these proteins, although a less acidic character is observed in Photorhabdus lectin due to the absence of two aspartic acid residues on the calcium-binding loop which also resulted in lower binding affinity. All these structures exhibited highly negative electrostatic environment in the vicinity of the calcium-binding loops whichwas essential for neutralizing the positive charges of two closely situated Ca+2 ions. The comparison of the binding affinities of some
 
Date 2006
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://www.eprints.iicb.res.in/462/1/GLYCOCONJUGATE_JOURNAL%2C__23(_3%2D4)%2C__251%2D257_[91].pdf
Majumder, Sujata and Patra, Madhumita and Mandal, Chhabinath (2006) Search for fucose binding domains in recently sequenced hypothetical proteins using molecular modeling techniques and structural analysis. Glycoconj J, 23 (3-4). pp. 251-257.
 
Relation htpp://dx.doi.org/10.1007/s10719-006-7930-6
http://www.eprints.iicb.res.in/462/