Biomedical Engineering Reference
In-Depth Information
Table 1 List of databases related with membrane protein structure and function
Name
URL
PDB, Protein Data Bank
http://www.rcsb.org/
MPtopo
http://blanco.biomol.uci.edu/mptopo
TMPDB
http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/
PDBTM
http://pdbtm.enzim.hu/
TMBETA-GENOME
http://tmbeta-genome.cbrc.jp/annotation/
OMPdb
http://bioinformatics.biol.uoa.gr/OMPdb
TCDB
http://www.tcdb.org/
Ion channels
http://www.ionchannels.org/
TMFunction
http://tmbeta-genome.cbrc.jp/TMFunction/
based on the secondary structures, number of membrane spanning segments and
keywords. In Table
1
, we list the databases for the structure and function of
membrane proteins.
3 Structural Discrimination of Membrane Proteins
3.1 Transmembrane Helical Proteins: Features
The folding environment of TMH proteins differs from that of soluble globular
proteins due to the presence of relatively long hydrophobic helical segments that
traverse the membrane matrix, around which the interaction of water is almost
absent. The TMH proteins generally follow specific rules as listed below (1) the
length of membrane spanning helices is about 20-30 residues, corresponding to the
width of the apolar part of the membrane, (2) globular regions between membrane
helices are generally short, (3) they have a specific distribution of positive charged
amino acid residues known as “positive-inside rule” [
10
], (4) loop regions inside the
membrane have more positive charged residues than that on outside, and (5) long
globular regions follow inside-out topology, which is defined by the orientation of
the helices with respect to the lipid bilayer. If the upper part of the helix is located in the
periplasm and the lower part is located in cytoplasm, then the topology is “out” [
11
].
3.2 Discrimination of TMH Proteins and Predicting
Their Membrane Spanning Regions
The analysis of protein three-dimensional structures in PDB shows that only 2% of
protein structures are membrane proteins. This urges the necessity of developing
methods to predict the three-dimensional structures of membrane proteins to bridge
the gap between the number of solved structures of membrane proteins and their
