Biomedical Engineering Reference
In-Depth Information
function of membrane proteins and their classifications. On the structural point of
view, we discuss the available databases and methods for discriminating
a
-helical
and
-barrel membrane proteins from globular proteins. In addition, different
algorithms developed for identifying the membrane spanning segments are
discussed. On the functional aspect, the discrimination of transporters from other
membrane proteins is mentioned. Further, classification of transporters into differ-
ent groups such as channels/pores, electrochemical and active transporters, as well
as their six families is illustrated. The specific features of channels compared with
porins are discussed along with the discrimination of channels and pores and the
classification of channels and drug targets for channel proteins. In addition, a list of
online resources for the databases and classifications of membrane proteins based
on their structure and function is provided.
b
Keywords Channel Function Membrane protein Structure Transporter
Abbreviations
DAS
Dense alignment surface
HMM
Hidden Markov model
OMP
Outer membrane protein
PDB
Protein Data Bank
PSSM
Position-specific scoring matrices
RBF
Radial basis function
TCDB
Transport Classification Database
TMB
Transmembrane
b
-barrel
TMH
Transmembrane helical
TMS
Transmembrane strand
1
Introduction
Membrane proteins, which require to be embedded into the lipid bilayers, have amino
acid sequences that will fold with a hydrophobic surface in contact with the alkane
chains of the lipids and polar surface in contact with the aqueous phases on both sides
of the membrane and the polar head groups of the lipids. Membrane proteins have
become attractive targets for pharmaceutical agents and about 20-30% of protein
sequences in genomes are identified as membrane proteins. On the structural aspect,
they are of two kinds (1) transmembrane helical (TMH) and (2) transmembrane
strand (TMS or outer membrane or transmembrane
b
-barrel, TMB) proteins. TMH
proteins span the cytoplasmic membrane with
-helices [
1
], whereas TMS proteins
traverse the outer membranes of Gram-negative bacteria with
a
b
-strands [
2
].
