Structural and Functional Discrimination of Membrane Proteins - Ion Channels and Their Inhibitors - page 8

Table 2 Web servers for
transmembrane helix
prediction

Name URL

ALOM http://psort.nibb.ac.jp/form.html

MPEx http://blanco.biomol.uci.edu/mpex/

KD plot http://fasta.bioch.virginia.edu/fasta/grease.htm

http://www.ch.embnet.org/software/
TMPRED_form.html TMpred

SPLIT http://split.pmfst.hr/split/

TopPred http://www.sbc.su.se/~erikw/toppred2/

PRED-TMR http://o2.biol.uoa.gr/PRED-TMR/

http://sosui.proteome.bio.tuat.ac.jp/
sosuiframe0.html SOSUI

MEMSAT http://bioinf.cs.ucl.ac.uk/psipred/psiform.html

PHDhtm http://cubic.bioc.columbia.edu/predictprotein/

TMAP http://bioinfo.limbo.ifm.liu.se/tmap/

DAS http://www.sbc.su.se/~miklos/DAS/

HMMTOP http://www.enzim.hu/hmmtop/

TMHMM http://www.cbs.dtu.dk/services/TMHMM/

CoPreTHi http://athina.biol.uoa.gr/CoPreTHi/

http://linzer.blm.cs.cmu.edu/tmpro/
http://flan.blm.cs.cmu.edu/tmpro/

TMpro

3.3 Transmembrane Strand Proteins: Features

Schultz [ 39 ] analyzed the structures of -barrel membrane proteins and derived ten

basic rules for understanding their folding and stability.

b

1. The number of b strands is even and the N and C termini are at the periplasmic

barrel end.
2. The

-strand tilt is always around 45 and corresponds to the common

-sheet
twist. Only one of the two possible tilt directions is assumed, and the other one
is an energetically disfavored mirror image.
3. The shear number of an n-stranded barrel is positive and around n + 2, in
agreement with the observed tilt.
4. All

b b

strands are antiparallel and connected locally to their next neighbors
along the chain, resulting in a maximum neighborhood correlation.
5. The strand connections at the periplasmic barrel end are short turns of a couple
of residues.
6. At the external barrel end, the strand connections are usually long loops.
7. The

b

-barrel surface contacting the nonpolar membrane interior consists of
aliphatic side chains forming a nonpolar ribbon with a width of about 22 ˚ .
8. The aliphatic ribbon is lined by two girdles of aromatic side chains, which have
intermediate polarity and contact the two nonpolar-polar interface layers of the
membrane.

b