download report - Istituto Pasteur

P a r t i c i p a n t s :
Paolo Marcatili, Domenico Cozzetto, post-doc fellows,
Emanuela Giombini, PhD student.
C o l l a b o r a t i o n s :
Istituto Superiore di Sanità, Roma (Dr. Enrica Pizzi, Dr. Pietro
Alano)
Report of activity
The aim of the project is to use computational biology
tools to predict the function and structure of
Plasmodium proteins involved in key biochemical
processes, predict the structure of the malaria and
human proteins involved in erythrocyte invasion,
model their mode of interaction.
In this first year we concentrated on predicting the
interaction of the PfEMP1 Malaria Protein and the
Human ICAM-1 Receptor and on predicting the
structure of human glycophorins A and B, known to
play a role in Plasmodium infection.
Glycophorins are a group of transmembrane sialoglycoproteins
expressed on the surface membrane of
human cells. There are 5 different glycophorins in
humans, all very similar, and likely to derive by
duplications of an ancestral gene.
GPA and GPB are the glycophorins most expressed
on erythrocytes, they are responsible for the different
blood antigen present in different people and are the
proteins more directly involved in the interaction
with plasmodium.
GPA is a protein of 131 aa, while GPB is shorter,
about 91 aa. Both proteins are formed by three structural
domains (an extra-cellular, a transmembrane
and a cytoplasmatic domain) and both undergo posttranslational
modification: the proteolytic cleavage of
a signal peptide of 19 aa and the addition of specific
sugars. GPA has 16 oligosaccharides chain, 15 O-glycosidic
bond linked to threonine/o/serine, and one
linked to asparagine with C-glycosidic bond 3 . It is
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Biology of malaria and other vector-borne diseases - AREA 7
Computational Analysis of the gene products of the Plasmodium
falciparum genome and their interaction with human proteins
Principal investigator: Anna Tramontano
Professor of Biochemistry
Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”
Tel: (+39) 06 49910556; Fax: (+39) 06 49910717
anna.tramontano@uniroma1.it
known that GPA binds EBA-175 (erythrocyte binding
protein-175) a transmembrane protein of plasmodium,
while this is not the case for GPB.
Plasmodium recognition in mediated by the extracellular
region where GPA and GPB are very similar,
except for the 4th exon. It is therefore likely that
binding regions are mostly located in this exon.
Binding of GPA with EBA-175 seems to be mainly
mediated by Sialic Acid, since it is inhibited when
cells are treated with neuramidase, an enzyme that
cleaves the sugar from the protein, however the protein
moiety is expected to be involved in the recognition
process with its fourth exon. There is a crystallographic
structure for the GPA transmembrane
region (PDB id: 1AFO), but this region is clearly not
involved in plasmodium recognition. Clearly the sugars
are the most important players in GPA-EBA-175
binding. Unfortunately, it is very difficult to predict
their precise conformation with our present knowledge.
However, they are bound to the proteic moiety
and a 3D model of the latter can help investigating
the possible modes of interaction. Consequently, we
built 3D models for GPA and GPB.
GPA and GPB three-dimensional models
GPA and GPB, even though sharing a high sequence
identity, show some remarkable differences from a
functional and molecular point of view. We inferred
the three-dimensional structures for GPA and GPB
independently, and then compared them in order to
highlight structural dissimilarities that could at least
partially explain the different behavior of the two
proteins. Solved structures of the cytoplasmatic and
membrane domains of GPA and GPB are available,
so we focused only on the extracellular domain. Most
of the differences between GPA and GPB are located
in this domain, which is responsible for the
EBA175 binding as well.
Using a de novo prediction protocol, we were able to
produce models for both GPA and GPB. These models,
even if with a different degree of reliability, are