Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling

BMC Structural Biology
Benoit AdamLaurence Lins

Abstract

Lipocalins are widely distributed in nature and are found in bacteria, plants, arthropoda and vertebra. In hematophagous arthropods, they are implicated in the successful accomplishment of the blood meal, interfering with platelet aggregation, blood coagulation and inflammation and in the transmission of disease parasites such as Trypanosoma cruzi and Borrelia burgdorferi. The pairwise sequence identity is low among this family, often below 30%, despite a well conserved tertiary structure. Under the 30% identity threshold, alignment methods do not correctly assign and align proteins. The only safe way to assign a sequence to that family is by experimental determination. However, these procedures are long and costly and cannot always be applied. A way to circumvent the experimental approach is sequence and structure analyze. To further help in that task, the residues implicated in the stabilisation of the lipocalin fold were determined. This was done by analyzing the conserved interactions for ten lipocalins having a maximum pairwise identity of 28% and various functions. It was determined that two hydrophobic clusters of residues are conserved by analysing the ten lipocalin structures and sequences. One cluster is internal to t...Continue Reading

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Citations

Mar 5, 2011·The Journal of Organic Chemistry·Richard I DuclosS John Gatley
Oct 3, 2012·Journal of Biomolecular Structure & Dynamics·Xian-Li FengXu-Ri Huang
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Apr 8, 2015·International Journal of Biological Macromolecules·Mohd Akram Kabir-ud-Din

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Methods Mentioned

BETA
X-ray
NMR
PCR

Software Mentioned

PROF
PSI
NPSA
VAST
ClustalW
SignalP
ClustaW
PredictProtein
BLAST
Modeller

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