Table 1.2 Properties of the cytosolic and membrane environments that are relevant to protein folding and
association.
Property
Cytosol
Plasma membrane
a
Solvent chemical homogeneity
Yes
No
Chemical groups available
HOH, ions, ÀSH
ÀCH 3 , ÀCH 2 À ¼ CHÀ
Isotropy
~Yes
b
No
pH gradient
No
Yes
c
Electric field (VÁm
À1
)
~ 0
b
~2 Â l0
c
Pressure gradient
No
Yes
Dielectric constant gradient
No
Yes
Redox potential gradient
No
Yes
c
Volume or surface occupancy [protein/solvent (%)]
d
~17
~35
e
Separation between two proteins
Distance (A)
~50
~30–35
Intervening solvent molecules
~15–20
~4
Exchange time between solvent molecules(s)
f
~10
À11
~10
À7
Viscosity at 20
C (η; N.s.m
À2
)
0.001
0.1
Dimensions
3
~2
Translational diffusion
g
D lat (m
2
Ás
À1
)
~10
À10
~10
À11
Average range explored in 1 μs ( x ; Å)
~250
~50
Dielectric constant (ε)
8 0
~ 2
h
ΔG
(kcalÁmol
À1
) for:
Breaking a main chain H-bond
~0
+4–6
i
Deprotonating a Glu side chain (pH7)
À4
>30
j
Opening a salt bridge
<1
60
k
Exposing one Å
2 of hydrophobic surface
+0.025
l
~0
Exposing a Leu side chain to the solvent
+2.8
j
~0
Associating two 50-kDa proteins (TΔS at 20
C)
8
m
5
m
The table and its annotations are from Popot and Engelman (2000)
a For properties that vary as a function of the depth in the membrane, the data correspond to those at the
membrane center
b
Note, however, that the cytosol is heavily encumbered (cf. Goodsell 1991, and Fig. 1.15, left)
c In most but not all membranes
d
Estimated from data compiled by Goodsell (1991) for the cytosol and plasma membrane of an E. coli cell;
calculations for the cytosol are based on Goodsell’s estimates for the average size of a soluble protein and
assume a 1:2.5 w/w ratio of RNA to protein (Alberts et al. 2015); calculations for the plasma membrane
assume the average integral protein (often an oligomer) to comprise ~12 transmembrane helices and to
have about half of its volume buried into the membrane (cf. Popot and de Vitry 1990); estimates published
in the literature vary from 17% to 50% (reviewed in Saxton 1989; see also Lavergne et al. 1992)
e Note that the percolation threshold for short-range diffusion of small molecules in the membrane plane is
~50% (see Saxton 1989; Lavergne et al. 1992)
f
In pure solvent
g
For a middle-sized protein (~50 kDa) in either pure water or pure lipids; in the cytosol and in real
membranes, diffusion coefficients vary with the distance range considered; see Peters (1986); Saxton
(1989); Lavergne et al. (1992)
h
From Dilger et al. (1982)
i
From Allen (1975)
j
Based on Engelman and Steitz (1981)
k
From Honig and Hubbell (1984)
l
From Reynolds et al. (1974)
m
Based on Amzel (1997)
1.3 Membrane Protein Functions
9
association.
Property
Cytosol
Plasma membrane
a
Solvent chemical homogeneity
Yes
No
Chemical groups available
HOH, ions, ÀSH
ÀCH 3 , ÀCH 2 À ¼ CHÀ
Isotropy
~Yes
b
No
pH gradient
No
Yes
c
Electric field (VÁm
À1
)
~ 0
b
~2 Â l0
c
Pressure gradient
No
Yes
Dielectric constant gradient
No
Yes
Redox potential gradient
No
Yes
c
Volume or surface occupancy [protein/solvent (%)]
d
~17
~35
e
Separation between two proteins
Distance (A)
~50
~30–35
Intervening solvent molecules
~15–20
~4
Exchange time between solvent molecules(s)
f
~10
À11
~10
À7
Viscosity at 20
C (η; N.s.m
À2
)
0.001
0.1
Dimensions
3
~2
Translational diffusion
g
D lat (m
2
Ás
À1
)
~10
À10
~10
À11
Average range explored in 1 μs ( x ; Å)
~250
~50
Dielectric constant (ε)
8 0
~ 2
h
ΔG
(kcalÁmol
À1
) for:
Breaking a main chain H-bond
~0
+4–6
i
Deprotonating a Glu side chain (pH7)
À4
>30
j
Opening a salt bridge
<1
60
k
Exposing one Å
2 of hydrophobic surface
+0.025
l
~0
Exposing a Leu side chain to the solvent
+2.8
j
~0
Associating two 50-kDa proteins (TΔS at 20
C)
8
m
5
m
The table and its annotations are from Popot and Engelman (2000)
a For properties that vary as a function of the depth in the membrane, the data correspond to those at the
membrane center
b
Note, however, that the cytosol is heavily encumbered (cf. Goodsell 1991, and Fig. 1.15, left)
c In most but not all membranes
d
Estimated from data compiled by Goodsell (1991) for the cytosol and plasma membrane of an E. coli cell;
calculations for the cytosol are based on Goodsell’s estimates for the average size of a soluble protein and
assume a 1:2.5 w/w ratio of RNA to protein (Alberts et al. 2015); calculations for the plasma membrane
assume the average integral protein (often an oligomer) to comprise ~12 transmembrane helices and to
have about half of its volume buried into the membrane (cf. Popot and de Vitry 1990); estimates published
in the literature vary from 17% to 50% (reviewed in Saxton 1989; see also Lavergne et al. 1992)
e Note that the percolation threshold for short-range diffusion of small molecules in the membrane plane is
~50% (see Saxton 1989; Lavergne et al. 1992)
f
In pure solvent
g
For a middle-sized protein (~50 kDa) in either pure water or pure lipids; in the cytosol and in real
membranes, diffusion coefficients vary with the distance range considered; see Peters (1986); Saxton
(1989); Lavergne et al. (1992)
h
From Dilger et al. (1982)
i
From Allen (1975)
j
Based on Engelman and Steitz (1981)
k
From Honig and Hubbell (1984)
l
From Reynolds et al. (1974)
m
Based on Amzel (1997)
1.3 Membrane Protein Functions
9