1.6
Dynamics of Transmembrane Regions and the Function
of Membrane Proteins
X-ray data provide us with static structures of MPs, but the presence of disordered regions often hints
at local mobility, particularly in the water-exposed loops or domains. As a matter of fact, one of the
tasks crystallographers frequently have to deal with, as is particularly vividly illustrated by studies of
GPCRs, is to restrict this mobility in order for the protein to organize into well-ordered crystals. Highresolution cryo-EM indeed often reveals the existence of multiple accessible conformations of a given
MP (see Chap. 12). Mobility is often essential to protein function, the movement of domains or loops
relative one to another being a classical feature of catalytic or regulatory mechanisms. In the case of
MPs, conformational changes in the TM regions are generally key elements of transport activity, or of
the transmission of regulatory signals from one side of the membrane to the other. Large β-barrel MPs
can signal the extracellular binding of a ligand by the change of conformation of a protein domain
contained in the lumen of the barrel, which change is detected in the periplasm, initiating the import of
the ligand (see e.g. Locher et al. 1998). In α-helical MPs, relative displacements of helices or groups of
helices are a frequent feature of functional cycles (see e.g. Martfeld et al. 2015).
Depending on the protein, transitions between conformational states in the course of the
functional cycle may involve more or less important rearrangements, and they may or not affect the
membrane-exposed surface of the protein. If they do, conformational changes may be affected or
regulated by the membrane environment the protein is in contact with, e.g. by the lipid composition, or
by interactions with small lipophilic molecules, TM peptides, or other MPs. Some MPs can function as
more or less solid-state devices, e.g. the “antenna” complexes that collect photons and transfer the
resulting excitons to reaction centers in photosynthesis. The functioning of other MPs requires, on the
contrary, extensive conformational changes within the membrane, such as those leading to opening
and closing of mechanosensitive channels. Another case of extensive rearrangement is that of receptors
whose oligomerization state changes upon stimulation, e.g. growth factor receptors, which the binding
of a ligand causes to dimerize. In this process, two monomers whose single TM helix was probably
totally surrounded by lipids will see part of these interactions replaced with protein/protein ones. In
between these two extremes lies a whole gamut of conformational changes that may be more or less
restricted to the core of the protein or affect more or less extensively its lipid-exposed surface.
In the following sections, we will introduce three of the MPs that have served as models in the
course of developing APols and their applications and that will recurrently appear in the upcoming
chapters to illustrate and discuss, in particular, the effects of APols and other surfactants on MP
stability, function, immobilization, or folding. Whereas the basic function of each of these proteins is
simple, the details of their structure and their functional cycle can be quite intricate. In order to keep
this section reasonably short, we will focus on a few selected issues, particularly inasmuch as they are
important to understanding the observations described in the next chapters, and leave out many details,
for which the reader is referred to specialized reviews.
1.6.1
Bacteriorhodopsin
BR is a small MP (~27 kDa), produced by the halophilic archaebacterium H. salinarum, which
functions as a light-driven proton pump (for reviews, see e.g. Lanyi and Luecke 2001; Lanyi 2004;
Andersson et al. 2009; Kandori 2015; Wickstrand et al. 2015; Brown and Ernst 2017). BR comprises
seven TM α-helices linked by short extramembrane loops (Fig. 1.24B). This helix bundle surrounds a
cofactor, retinal (Fig. 1.23A), which is covalently but reversibly bound by a Schiff base (Fig. 1.23B) to
32
1 Membrane Proteins and Their Natural Environment
Dynamics of Transmembrane Regions and the Function
of Membrane Proteins
X-ray data provide us with static structures of MPs, but the presence of disordered regions often hints
at local mobility, particularly in the water-exposed loops or domains. As a matter of fact, one of the
tasks crystallographers frequently have to deal with, as is particularly vividly illustrated by studies of
GPCRs, is to restrict this mobility in order for the protein to organize into well-ordered crystals. Highresolution cryo-EM indeed often reveals the existence of multiple accessible conformations of a given
MP (see Chap. 12). Mobility is often essential to protein function, the movement of domains or loops
relative one to another being a classical feature of catalytic or regulatory mechanisms. In the case of
MPs, conformational changes in the TM regions are generally key elements of transport activity, or of
the transmission of regulatory signals from one side of the membrane to the other. Large β-barrel MPs
can signal the extracellular binding of a ligand by the change of conformation of a protein domain
contained in the lumen of the barrel, which change is detected in the periplasm, initiating the import of
the ligand (see e.g. Locher et al. 1998). In α-helical MPs, relative displacements of helices or groups of
helices are a frequent feature of functional cycles (see e.g. Martfeld et al. 2015).
Depending on the protein, transitions between conformational states in the course of the
functional cycle may involve more or less important rearrangements, and they may or not affect the
membrane-exposed surface of the protein. If they do, conformational changes may be affected or
regulated by the membrane environment the protein is in contact with, e.g. by the lipid composition, or
by interactions with small lipophilic molecules, TM peptides, or other MPs. Some MPs can function as
more or less solid-state devices, e.g. the “antenna” complexes that collect photons and transfer the
resulting excitons to reaction centers in photosynthesis. The functioning of other MPs requires, on the
contrary, extensive conformational changes within the membrane, such as those leading to opening
and closing of mechanosensitive channels. Another case of extensive rearrangement is that of receptors
whose oligomerization state changes upon stimulation, e.g. growth factor receptors, which the binding
of a ligand causes to dimerize. In this process, two monomers whose single TM helix was probably
totally surrounded by lipids will see part of these interactions replaced with protein/protein ones. In
between these two extremes lies a whole gamut of conformational changes that may be more or less
restricted to the core of the protein or affect more or less extensively its lipid-exposed surface.
In the following sections, we will introduce three of the MPs that have served as models in the
course of developing APols and their applications and that will recurrently appear in the upcoming
chapters to illustrate and discuss, in particular, the effects of APols and other surfactants on MP
stability, function, immobilization, or folding. Whereas the basic function of each of these proteins is
simple, the details of their structure and their functional cycle can be quite intricate. In order to keep
this section reasonably short, we will focus on a few selected issues, particularly inasmuch as they are
important to understanding the observations described in the next chapters, and leave out many details,
for which the reader is referred to specialized reviews.
1.6.1
Bacteriorhodopsin
BR is a small MP (~27 kDa), produced by the halophilic archaebacterium H. salinarum, which
functions as a light-driven proton pump (for reviews, see e.g. Lanyi and Luecke 2001; Lanyi 2004;
Andersson et al. 2009; Kandori 2015; Wickstrand et al. 2015; Brown and Ernst 2017). BR comprises
seven TM α-helices linked by short extramembrane loops (Fig. 1.24B). This helix bundle surrounds a
cofactor, retinal (Fig. 1.23A), which is covalently but reversibly bound by a Schiff base (Fig. 1.23B) to
32
1 Membrane Proteins and Their Natural Environment