The N-terminal region of Ncb5or is predicted to be intrinsically
disordered.
The amino acid sequence of the N-terminal region of human Ncb5or is
shown in Figure 1B , and an alignment of this 50-residue
polypeptide with all known Ncb5or examples in animals is included inFigure S1 . The alignment revealed an overall homology, which is
weaker in the first 21 residues than the subsequent 29-residue stretch
which is rich in Arg and Lys residues and contains five invariant
residues (Lys25, Leu28, Gly31, Trp37 and Gly49). Trp37 is part of a
highly conserved motif that has the sequence
L34MDWIRL40 in mammalian orthologs.
The PONDR VL-XT
program28-30predicts that the N-terminal region of Ncb5or is intrinsically
disordered, in sharp contrast to the b5, b5R and CS domains
(Figure S2A ). Secondary structure prediction algorithms
generally gave inconsistent predictions for the N-terminal region, but
several of them indicated a preference for α-helical structure for the
L34MDWIRL40 sequence. This included
PROF31 and
PSIPRED32,
33 (Figure S2B ), as well as
SPINE-X34 (not
shown). The latter two ab initio algorithms (i.e. , those
not utilizing homology modeling) have been shown to yield the most
accurate
predictions.35AGADIR36 , an
algorithm that predicts helical content of peptides on the basis of
helix/coil transition theory, also predicts some helical tendency for
the L34MDWIRL40 sequence, albeit
with a population of less than 10% at pH 7 and 25°C (Figure
S2C ).