Introduction Features Methods and Definitions Precision Classification Comparision with experimental data Comparision with other computational methods Topology definitions Acknowledgements

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	Method^a
Protein, organism	PDB id	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.