Analysis of Bitopic Proteins

Table. Bitopic proteins from different biological membranes can be classified into three types based on characteristics of their TM domains: length of TM segments, hydrophobic thickness (D), transfer energy of an α-helix from water to the lipid environment (ΔGαtransf), and folding energy of an α-helix in membrane relative to coil in water (ΔGfold).




Membrane type


Length of TM segment (aa)

D (Å)


ΔGαtransf (kcal/mol)

ΔGfold (kcal/mol)

Protein count

Type I

Eukaryotes: Plasma membrane

26.0±2.8

35.0±2.6

-25.5±5.1

-19.5±5.9

2210

Endosomal membrane

24.1±2.6

31.8±1.9

-25.3±4.3

-19.6±5.1

27

Lysosomal membrane

25.6±3.4

33.4±3.2

-24.7±5.0

-18.2±6.2

24

Vacuolar membrane

23.7±2.1

32.8±2.5

-24.3±4.1

-18.7±5.0

45

Vesicular membranes

24.0±2.9

32.4±2.7

-24.0±5.4

-18.0±6.7

91

Type II

E. coli: inner membrane

22.9±2.7

31.6±2.0

-21.6±4.5

-14.5±5.2

196

M. jannaschii: plasma membrane

23.0±2.5

31.2±2.4

-22.4±4.7

-15.0±6.0

70

Endoplasmic reticulum membrane

22.6±2.6

31.4±2.2

-22.0±4.2

-14.4±4.6

880

Golgi apparatus membrane

22.7±2.2

31.5±2.1

-22.0±4.2

-14.4±4.6

638

Nucleus membranes

22.6±2.3

31.2±1.8

-20.9±4.3

-12.8±5.8

114

Chloroplast&thylakoid membranes

22.9±2.1

31.3±2.2

-19.8±4.6

-10.8±5.1

76

Type III

Mitochondrial inner membrane

21.8±2.5

29.6±2.1

-17.1±4.1

-8.5±3.6

229

Mitochondrial outer membrane

22.9±2.4

30.8±2.4

-17.5±4.3

-10.8±4.8

106

Peroxisomal membrane

22.2±1.9

30.1±1.7

-17.9±3.7

-9.8±4.3

38







Figure 9. Distributions of hydrophobic thicknesses of TM α-helices of bitopic proteins from different membrane types: prokaryotic plasma membranes (A), eukaryotic plasma membrane (B), membranes of endoplasmic reticulum (C), Goldgi apparatus (D), mitochondrial inner (E) and outer (F) membranes. Number of proteins assigned to each membrane type are indicated in parentheses. Distributions demonstate presence of multiple maxima with a major maximum at ~35 Å for eukaryotic plasma membane proteins, ~31 Å for proteins from prokaryotic cell membrane, endoplasmic reticulum and Golgi apparatus membranes, and ~29 Å for proteins from mitochondrial membranes.

Figure 10. Distributions of folding energies (dashed line) and transfer energies (solid line) of TM α-helices of bitopic proteins from different membrane types: prokaryotic plasma membranes (A), eukaryotic plasma membrane (B), membranes of endoplasmic reticulum (C), Goldgi apparatus (D), mitochondrial inner (E) and outer (F) membranes. Numbers of proteins assigned to each membrane type are indicated in parentheses. Distributions demonstrate that TM helices of plasma proteins are more stable and hydrophobic than helices from other membranes, especially from mitochondria.