Protein Structure and Function: Application of Bioinformatics Methods - John Rigden 2014
Prediction of membrane protein structure
Characteristics of membrane protein crystallization
Isolating TM Proteins, whose surfaces contain both hydrophobic and hydrophilic regions, is considerably more challenging than working with Water-soluble proteins. During extraction, the native membrane environment of the protein is disrupted and replaced by detergent molecules, making it crucial to prevent Protein Denaturation. Despite significant efforts in this field, high-resolution crystallographic structures are currently available for only a relatively small number of TM proteins. While TM proteins are estimated to comprise about 30% of the proteome, they are vastly underrepresented in structural Databases such as PDB (Bernstein et al. 2004), accounting for merely 1% of all deposited structures there (White 2004). Tables 4.1 and 4.2 list the transmembrane a-helices and ß-barrels for which crystallographic structures have been solved to date (Lomize et al. 2006b). With the development and increasing accessibility of advanced Research Methods, such as synchrotron X-ray Cell/15.html">Microscopy, it has become possible to investigate Protein Structure using X-Ray Diffraction Analysis with tiny protein crystals as research samples. Combined with cutting-edge crystallization techniques—such as using Antibodies to enhance Protein solubility and employing lipid phases as a crystallization medium—these studies are likely to yield notable progress in determining TM protein structures over the next few years.
Class="center">Table 4.1. Superfamilies of a-helical transmembrane proteins from the OPM database (Lomize et al. 2006b)
Function |
Superfamily |
Light-driven transporters |
Rhodopsin-like proteins |
Oxidoreduction transporters |
Photosynthetic Reaction Centers and Photosystems |
Voltage-gated transporters |
|
Phosphate-dependent transporters |
Transmembrane cytochrome b-like proteins |
Porters (uniporters, symporters, antiporters) |
Cytochrome c oxidases |
Channels, including Ion Channels |
Multiheme Cytochromes |
F/V/A-type proton- or sodium-translocating ATPases |
|
Proteins with alpha-helical transmembrane anchors |
P-type ATPases |
Vitamin B12 transporter-like ABC Transporters Single-helix ATPase regulators Lipid flippase-like ABC transporters Molybdopterin uptake ABC transporter General secretory pathway (Sec) Mitochondrial carrier Major facilitator superfamily Resistance-Nodulation-Cell Division Dicarboxylate/amino acid:cation symporter Monovalent cation/proton antiporter Sodium-neurotransmitter symporter Ammonium transporter (Amt) Metabolite transporter Voltage-gated channels Large conductance mechanosensitive ion channel (MscL) Small conductance mechanosensitive ion channel (MscS) CorA metal ion transporter Ligand-gated ion channel of neurotransmitter receptors Chloride channel Additional outer Membrane Proteins Epithelial sodium channel Magnesium ion transporter (MgtE) Major intrinsic protein (MIP) Methane monooxygenase Rhomboid proteins Disulfide oxidoreductase B (DsbB) T-cell receptor transmembrane dimerization domain Steryl-sulfate sulfohydrolase Stannin Inovirus major coat protein Pilus subunits Pulmonary surfactant-associated protein |
Table 4.2. Superfamilies of transmembrane proteins with a ß-barrel structure from the OPM database (Lomize et al. 2006b)
Source |
Superfamily |
Outer membrane of Gram-negative Bacteria |
OMPA-like |
Oligomeric Beta-barrels of Gram-positive bacteria |
OMPT-like |
Autotransporter (AT) Trimeric autotransporter OM phospholipase Nucleoside-specific channel-forming outer membrane porin FadL outer membrane protein (FadL) OmpG porin Trimeric porins Sugar porins Omp85-TpsB transporters Ligand-gated protein channels Outer membrane factor (OMF) Leukocidin-like |
Last update: 06/08/2026
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