Biomedical Engineering Reference
In-Depth Information
Further, databases have been developed specifically for ion channels. Ion
channels are transmembrane pores, which allow the passage of ions (charged
particles) into and out of a cell down the electrochemical gradient. There are
hundreds of different ion channels, and they are distinguished based upon their ion
selectivity, gating mechanism, and sequence similarity. Ion channels can be voltage
gated, ligand gated, pH gated, or mechanically gated. These gating criteria along
with a combination of sequence similarity and ion selectivity further subdivide ion
channels into several subtypes, voltage-gated potassium channels, voltage-gated
sodium channels, voltage-gated calcium channels, chloride channels, ligand-gated
channels, and so on. The ion channel activity for several genomes has been depos-
ited in ion channels database, and it is available at
http://www.ionchannels.org/
.
4.2 Discrimination of Transporters from Other Globular
and Membrane Proteins
The functional discrimination of membrane transporter proteins requires the knowl-
edge about a query protein whether it is a transporter or a nontransporter. Hence, it
is necessary to develop a method to discriminate transporters from other proteins.
Several features have been tried for the discrimination and the important parameters
are amino acid occurrence, amino acid properties and PSSM profiles. The amino
acid occurrence could discriminate a set of 3,336 membrane nontransporters and
1,718 transporters with the fivefold cross-validation accuracy of 79.1% using
k-nearest neighbor methods [
78
]. The sensitivity and specificity are 69.2 and
84.2%, respectively. Further a set of 5,048 proteins including membrane
transporters, membrane nontransporters and globular proteins are discriminated
with an accuracy of 78.7%. The method was also tested with equal number of
transporters and nontransporters, which showed the accuracy in the range of
82-85%. We have developed a web server for discriminating transporters from
other proteins and its utility is illustrated in Fig.
7
. The server takes the amino acid
sequence as input (Fig.
7a
) and predicts the type of the protein as transporter or
nontransporter using k-nearest neighbor (Fig.
7b
). Li et al. [
79
] employed tradi-
tional homology-based methods to detect the transporters in a set of completed
genomes and showed a recall and precision of 81.8% in yeast proteome.
4.3 Characteristic Features of Amino Acid Residues in Different
Classes of Transporters
The three major classes of transporters are channels/pores, electrochemical and
active transporters [
5
]. Channels/pores catalyze facilitated diffusion (by an energy-
independent process) by passage through a transmembrane aqueous pore or channel
