Biomedical Engineering Reference
In-Depth Information
TMB finding pipeline
Sequence
Residue pair preference
Weighted average (
σ
TMB-glob
)
Negative
Positive
Globular
Residue pair preference
Weighted average (σ
TMB-TMH
)
Negative
Positive
TMH
Length > 50 residues
No
Short sequence
Yes
SOSUI analysis
Yes
TMH
No
Sequence identity > 40%; Coverage > 80%
Globular/TMH proteins in PDB
Yes
No
Globular/TMH
Sequence identity > 60%
Globular/TMH proteins in SWISS-PROT
Yes
No
Globular/TMH
Predicted TMB
Fig. 2 Pipeline for detecting
b
-barrel membrane proteins in genomic sequences [
61
]
3.5.1 Statistical Methods
Paul and Rosenbusch [
66
] proposed an indirect method to predict transmembrane
b
-strands based on the elimination of turns in membrane. In their procedure, the
amino acid residues have been divided into three groups: turn promoters, turn
indifferent, and turn blockers. Turns have been identified as segments
3 residues,
of which at least one in turn promoting and none in turn blocking. Segments
between turns are considered to be membrane spanning segments and the longer
stretches of residues between 6 and 18 are identified as potential
-strands.
Vogel and Jahnig [
67
] applied the concept of “amphipathicity of
b
b
-strands” to
predict
the transmembrane
b
-strands in TMBs.
In this method,
the mean
