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Signal Peptides 303
peptides are thought to be inserted into the membrane in a helix–beak–helix conformation
consistent with the classical helical hairpin hypothesis. 101,102 At this process,
the length of the hydrophobic region of signal peptides seems to play an
important role. 103 The interaction between their positively charged N termini and the
anionic phospholipids is also important for determining the orientation of insertion.
104 Namely, positively charged residues are not favored for transportation across
the membrane; this seems to be the major determinant of the topology of membrane
proteins (the positive-inside rule). 105,106
In another study, the proton motive force (pmf), which renders the cytoplasm
basic and the periplasm acidic, was shown to inhibit membrane translocation of
positively charged residues within membrane proteins. 107,108 However, the determinants
of the positive-inside rule seem still to be controversial. 109 Negatively charged
residues are also likely to be involved in the translocation. 110 When there are no
charged amino acids around the signal peptide, anionic lipids stimulate its translocation
in a direction opposite to the positive-inside rule, possibly because of its helix
dipole moment. 111 Factors that influence the efficiency and specificity of signal
peptides will be discussed in Section 14.4.3.1.
14.3 PROTEIN SECRETION PATHWAYS IN EUKARYOTES
In eukaryotes, it is quite established that proteins transported through the secretory
pathway have a signal peptide, including an uncleavable signal anchor, on their N
terminus and are first transported to the ER, although there are some exceptions.
Unlike the bacterial system, most of the signal peptides are cotranslationally recognized
by SRP, although some proteins are transported through the post-translational
pathway, especially in yeast. In addition, chloroplasts (and mitochondria) seem to
have their own transport system directed by signal peptide-related signals. Here,
eukaryote-specific topics are briefly summarized. 4,5,112-117 Translocation via signal
peptide-like signals within mitochondria and chloroplasts is reviewed elsewhere.
52,118-120
14.3.1 COTRANSLATIONAL PATHWAY
14.3.1.1 Targeting to the ER
Mammalian SRP consists of 6 proteins and 1 RNA (7S RNA). All known SRPrelated
sequences are maintained in a public database (SRPDB). 121 SRP54, a
homolog of bacterial Ffh, recognizes signal peptides and has GTPase activity.
Although still controversial, the nascent polypeptide-associated complex (NAC),
which is an abundant cytosolic heterodimer, has been proposed to first contact the
nascent polypeptide chain emerging from the ribosome and to strengthen the specificity
of SRP for binding signal peptides and for targeting to the ER. 122-124 Although
ribosome–nascent chain (RNC) complexes can be targeted and bind to the ER
membrane without the aid of SRP, the binding of RNC complexes with SRP gives
it a competitive advantage. 125