Biomedical Engineering Reference
In-Depth Information
Structural and Functional Discrimination
of Membrane Proteins
M. Michael Gromiha, Yu-Yen Ou, and Shu-An Chen
Contents
1
Introduction . ..................................................................................
2
2 Databases for Membrane Proteins Based
on Their Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3
3 Structural Discrimination of Membrane Proteins ...........................................
4
3.1 Transmembrane Helical Proteins: Features . . . ........................................
4
3.2 Discrimination of TMH Proteins and Predicting
Their Membrane Spanning Regions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4
3.3 Transmembrane Strand Proteins: Features . ...........................................
8
3.4 Discrimination of
b
-Barrel Membrane Proteins . ......................................
9
-Strand Segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
4 Functional Discrimination of Membrane Proteins .......................................... 18
4.1 Databases for Membrane Transporters and Functionally Important Residues
in Membrane Proteins . . . . . ............................................................. 18
4.2 Discrimination of Transporters from Other Globular and Membrane Proteins . . . . . . 21
4.3 Characteristic Features of Amino Acid Residues in Different
Classes of Transporters ................................................................. 21
4.4 Discrimination of Transporters Based on Different Classes and Families . . . ........ 23
4.5 Channels and Pores ..................................................................... 25
4.6 Discrimination of Different Classes of Ion Channel Proteins . . . ..................... 26
5 Drug-Target Interactions ..................................................................... 26
6 Conclusions ................................................................................... 27
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.5 Prediction of Membrane Spanning
b
Abstract Membrane proteins perform diverse functions inside the cell including
transporters, receptors, and channels. Ion channels are integral membrane proteins
that regulate the flow of ions across the membranes and are categorized as a part of
membrane transport proteins. In this article, we briefly outline the structure and
