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A. Tramontano - Computational Analysis of the gene products of the Plasmodium falciparum genome
consistent with most of the experimental data reported
in the literature, and can be a starting point to
unravel the specificities and the mechanisms adopted
by P. falciparum proteins to invade the erythrocytes.
GPA has no detectable similarity with any protein of
known structure and therefore the standard homology-modeling
protocols cannot be applied in this case.
An analysis of the predicted secondary structure
(PSIPRED) and of the disordered regions (DISO-
PRED) of such proteins did not reveal the presence
of unstructured or disordered regions. Therefore
we decided to adopt a de novo strategy to predict the
three-dimensional structure of the proteins. To this
aim we used the Rosetta suite with the following
strategy:
1. We generated 10.000 decoys for each protein (de
novo modeling followed by a full-atom “relax”
refinement);
2. selected the 1.000 decoys with the lowest score;
3. clustered the 1.000 decoy subset,
4. Selected the lowest-scoring decoy in the largest
cluster as a structural candidate.
This strategy produced excellent result for GPB. We
found a very large cluster (250 decoys, RMSD of
1.72 Å) with several low-score decoys. In the Figure
we report the lowest score model, which is a single
beta sheet formed by three antiparallel strands. This
model is coherent with literature data (most of the
glycosilation sites are located on loops and exposed
to the solvent) and the deleted region (with respect
to GPA) is on the loop that connects the second and
the third strands.
Fig. 1 - Predicted structure of GPA
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The same protocol, when applied to GPA, did not
produce a single, reliable model. No cluster could be
detected with the given threshold, so we decided to
analyze the three lowest-score models. Even though
some of the strands identified in GPB are conserved,
there are regions of the GPA models without
a clear secondary structure. Such a big difference
between the models for the two proteins was
unexpected, given the high sequence identity
between GPA and GPB, the short dimension of the
insertion present in GPA (approx. 30 residues) and
the quality of the GPB model prediction and
deserves further studies.
Selected publications
Cozzetto D, Kryshtafovych A, Ceriani M,
Tramontano A. Assessment of predictions in the
model quality assessment category. Proteins 2007,
8:175-83.
Montanari A, Besagni C, De Luca C, Morea V, Oliva
R, Tramontano A, Bolotin-Fukuhara M, Frontali L,
Francisci S. Yeast as a model of human mitochondrial
tRNA base substitutions: Investigation of the
molecular basis of respiratory defects. RNA 2008,
14:275-83.
Soro S, Orecchia A, Morbidelli L, Lacal PM, Morea
V, Ballmer-Hofer K, Ruffini F, Ziche M, D'Atri S,
Zambruno G, Tramontano A, Failla CM. A proangiogenic
peptide derived from vascular endothelial
growth factor receptor-1 acts through alpha5beta1
integrin. Blood 2008, 111:3479-88.