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Prediction of Signal Peptides and Signal
Anchors of Cytochrome c Nitrite Reductase
from Desulfovibrio desulfuricans ATCC
27774 Using Bioinformatic Tools
Luisa L. GONÇALVES 1,2,3 , Maria Gabriela ALMEIDA 1,2 , Jorge LAMPREIA 1 , José J.G.
MOURA 1 and Isabel MOURA 1 .
1 REQUIMTE, CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia,
Universidade Nova de Lisboa, 2829-516 Monte de Caparica, Portugal.
2 Instituto Superior de Ciências da Saúde-Sul, Campus Universitário - Quinta da Granja,
2825-511 Caparica, Portugal.
3 Present Adress: Faculty of Pharmacy, Room #514, 19 Russel Street, Toronto, Ontario
M5S 2S2, Canada.
Abstract. The cytocrome c nitrite reductase (ccNir) isolated from the sulphate-
reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is a hetero-oligomeric
complex composed by two subunits (61 KDa and 19 KDa), encoded by genes nrfA
and nrfH, respectively. We report the use of bioinformatic predictive models in
order to access of ccNir most relevant topological characteristics, namely signal
peptides and signal anchors. We made used of a combined method of SignalP V2.0
(SignalP-HMM and Signal-NN) in association with TMHMM 2.0 for the prediction
of the presence and location of signal peptide cleavage sites, to discriminate between
cleavable signal peptides and N-terminal transmembrane anchors segments and, to
predict of transmembrane helices.
Introduction
Sub cellular protein sorting, i.e. the processes through which proteins are routed to their
final destination within a cell, is a fundamental attribute of cellular life. In general, sorting
depends on “signals” that can already be identified by looking at the primary structure of a
protein. N-terminal signal peptides (also referred to as signal sequences or leader
sequences) target proteins to the secretory pathway in eukaryotic cells and for translocation
across the cytoplasmatic membrane in bacteria [1]. They have a conserved three-region
design with a positively charged amino-terminal segment (n-region), a central hydrophobic
segment (h-region) and, a more polar c-terminal segment (c-region) that is recognised by
the membrane bound signal peptidase enzyme. The general signal peptide structure is
conserved among different proteins and also across different species [2]. Although general
physiochemical properties are conserved among proteins within the same cellular
localisation, the primary structure is low conserved. Signal peptides (SP) are often cleaved
off of the mature proteins upon arrival at the sub cellular destination site. Otherwise, the
remaining signal peptide anchors the protein to the membrane and is referred to as a “signal
anchor” (SA) [3]. Signal anchors have both an n- and h- region, and no cleavage site.
In bacteria, three types of signal peptidases are known so far [for a review see 4 and
references therein]. The type II signal peptidases (Spase II; EC 3.4.23.36), or proliprotein
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