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
View Archive Info| Field | Value | |
| Title |
Search for fucose binding domains in recently sequenced
hypothetical proteins using molecular modeling techniques
and structural analysis
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| Creator |
Majumder, Sujata
Patra, Madhumita Mandal, Chhabinath |
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| Subject |
Drug Development/Diagnostics & Biotechnology
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| 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
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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/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. |
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| Relation |
htpp://dx.doi.org/10.1007/s10719-006-7930-6
http://www.eprints.iicb.res.in/462/ |
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