PDB ID or protein name

Comparison with other computational methods

Table 5. Comparison of hydrophobic thicknesses (Å) of some TM proteins evaluated “manually” from their crystal structures (Man) and calculated using OPM or other computational methods (IMPALA and PDB_TM).
Protein, organism PDB id Methoda
Man OPM IMPALA PDB_TM
TM β-barrel proteins
Trimeric porin OmpF, Escherichia coli 1hxx 24 24.2±0.8 29 19.0
OmpA, Escherichia coli 1qjp 24 24.9±2.2 28 19.5
OmpX, Escherichia coli 1qj8 24 23.9±1.9 19 28.5
FhuA, Escherichia coli 1qfg 24 23.5±1.0 22 19.0
FepA, Escherichia coli 1fep - 24.5±1.2 20 20.3
OmpLA (dimer), Escherichia coli 1qd6 - 23.2±1.5 18 22.5
Fatty acid transporter FadL Escherichia coli 1t1l - 23.9± 1.5 - 34.0
MspA octameric channel, Mycobacterium smegmatis 1uun 37 43.8±0.9 - 22
TM α-helical proteins
Bacteriorhodopsin, Halobacterium salinarium 1m0l 35 30.0±1.1 28 35.5
Rhodopsin, Bos Taurus 1gzm 35 32.4±1.7 28 31.0
Photosynthetic reaction center, Rhodobacter spaeroides 1rzh 28 30.0±1.2 29 25.5
Photosynthetic reaction center, Rhodopseudomo-nas viridis 1dxr 31 30.5±1.8 - 26.5
Photosynthetic reaction center, Thermochroma-tium tepidum 1eys 28 30.0±1.5 - 25.0
Photosystem I, Synechococcus elongatus 1jb0 32 31.5±0.8 - 21.0
Cytochrome c oxidase, Paracoccus denitrificans 1qle 33 31.2±1.5 - 25.5
Cytochrome c oxidase, Thermus thermophilus 1ehk 31 30.4±1.3 - 27.5
Ubiquinol oxidase, Escherichia coli 1fft 29 29.0±1.2 - 20.8
Bc1 complex, Bos Taurus 1l0l 32 26.8±0.6 - 32.5
Bc1 complex, Saccharomyces cerevisiae 1kb9 28 26.0±0.8 - 34.0
KcsA potassium channel, Streptomyces lividans 1r3j 37 33.1±1.0 32 34.5
MscL mechanosensitive channel, Mycobacterium tuberculosis 1msl 34 26.5±3.8 25 30.0
Clc chloride channel, Escherichia coli 1ots 23 23.4±1.6 - 21.0
Ca2+-ATPase, Oryctolagus cuniculus 1iwo 21 29.0±1.5 - 26.0
Light-harvesting complex, Rhodospirillum molischianum 1lgh 31 28.7±0.9 47 31.0
Integral monotopic proteins
Prostaglandine H2 synthase, Ovis aries 1prh <15 10.0±0.1 36 -

aAll deviations from OPM greater than 4 A are shown by bold. “Manually” estimated thicknesses are taken from Table 1 in Lee (2003) or from original crystallographic publications (prostaglandine synthase (Picot et al. 1994) and MspA channel (Faller et al. 2004)).  Parameters obtained in calculations with IMPALA are taken from Table 1 in Basyn et al (2003) after subtracting thicknesses of interfacial areas (9 Å).  Most recent version of PDB_TM database (2.1) (Tusnady et al. 2004) was used.

References

Basyn, F, Spies, B, Bouffioux, O, Thomas, A, and Brasseur, R. 2003. Insertion of X-ray structures of proteins in membranes. J. Mol. Graph. Model. 22: 11-21.

Faller, M., Niederweis, M., and Schulz, G.E. 2004. The structure of a mycobacterial outer-membrane channel. Science 303: 1189-1192.

Lee, A.G.2003Lipid-protein interactions in biological membranes: a structural perspective. Biochim. Biophys. Acta 1612: 1-40.

Picot, D., Loll, P.J., and Garavito, R.M. 1994. The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1. Nature 367: 243-259.

Tusnady, G.E., Dosztanyi, Z., and Simon, I. 2004. Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics 20: 2964-2972.