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

BACKGROUND: 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.
RESULTS: It was determined that two hydrophobic clusters of residues are
conserved by analysing the ten lipocalin structures and sequences. One cluster is
internal to the barrel, involving all strands and the 310 helix. The other is
external, involving four strands and the helix lying parallel to the barrel
surface. These clusters are also present in RaHBP2, a unusual "outlier" lipocalin
from tick Rhipicephalus appendiculatus. This information was used to assess
assignment of LIR2 a protein from Ixodes ricinus and to build a 3D model that
helps to predict function. FTIR data support the lipocalin fold for this protein.
CONCLUSION: By sequence and structural analyzes, two conserved clusters of
hydrophobic residues in interactions have been identified in lipocalins. Since
the residues implicated are not conserved for function, they should provide the
minimal subset necessary to confer the lipocalin fold. This information has been
used to assign LIR2 to lipocalins and to investigate its structure/function
relationship. This study could be applied to other protein families with low
pairwise similarity, such as the structurally related fatty acid binding proteins
or avidins.