1
Introduction
1.1
Why Study Membranes and Membrane Proteins?
Biological membranes and membrane proteins, responsible for numerous
exciting biological processes, present one of the paramount challenges
in biophysics today. Membranes are present in great number and variety
in all organisms. They form the boundary between the inside and outside
for any bacterium or cell, and they delimit the host of organelles
that make up their inner subunits. Each biological membrane is made
up of dozens of different types of lipids and sterols, and any particular
type of membrane has a characteristic content of these different constituents.
As a very basic example, we mention that prokaryotic membranes contain
a notable component of negatively charged lipids but almost no cholesterol,
while eukaryotic membranes are mostly zwitterionic but have a significant
amount of cholesterol. Since the driving biophysical principles of
membrane formation are very simple—they lie in the amphipathic
properties of any lipid molecule—a single lipid type is sufficient
to form membrane-like bilayers in an aqueous environment. Such model
membranes are used extensively to study biophysical properties that
are representative for most membrane systems. A particularly interesting
effect is observed when detergent molecules are added to lipid bilayer
samples: the detergents solubilize the bilayers, and in certain regimes
so-called bilayered mixed micelles or “bicelles” are
formed. In the simplest case, they can be described as microscopic
disks where a bilayer patch is encircled by a “rim”
of detergent molecules. Bicelles represent a new instance of lipid
morphology and are extensively applicable to structural studies of
lipid membranes and protein structure.
1
Membranes delimit any cell and all of its compartments. They
form natural borders for metabolic substances and signaling molecules.
Membrane proteins are the porters and gatekeepers that make sure that
only proper molecules or signals make it across the membrane. Since
membrane proteins perform numerous key functions in cell metabolism
and signaling, they contribute over 30% of the genes in typical eukaryotic
genomes,
2
and they form the targets for
over 50% of drugs in use today.
3
The number
of elucidated structures of membrane proteins has grown exponentially
after the first structure was published in 1985, thus equaling the
rate at which structure determination of soluble proteins emerged
early on.
4
Still, the number of available
high-resolution structures of membrane proteins is limited. There
are Internet sites that keep track of newly published structures of
membrane proteins. The crystallography-oriented Web site of Dr. Stephen
White [http://blanco.biomol.uci.edu/mpstruc] has recently
been joined by another site maintained by Dr. Dror Warschawski that
is dedicated to structures of membrane proteins elucidated by nuclear
magnetic resonance (NMR) spectroscopy [www.drorlist.com/nmr/MPNMR.html]. Another equally
important site of Dr. Hartmut Michel [www.mpibp-frankfurt.mpg.de/michel/public/memprotstruct.html]
with an emphasis on crystallization conditions is no longer updated,
but states that access is still enabled.
In this review article,
we aim to give a general overview of lipid
bicelles as employed in the study of protein structure. Recent advances
in the field of protein structural biology that have been made possible
by exploiting the unique properties of lipid bicelles, in both solution and solid-state
NMR spectroscopy, will be discussed. During
the last five years, review contributions have presented bicelles
either within the far more general context of reconstitution media
for solution NMR studies (see section 1.4) or have focused on macroscopically aligned
bicelles as used for
solid-state NMR studies.
5,6
One very recent contribution
has tackled the formidable task of reviewing all membrane
mimetics employed in both solution and solid-state NMR studies.
7
As mentioned above, we will limit the contents
of this review article to applications of lipid bicelles, but will
cover both the isotropic and the aligned bicelles as used in NMR studies.
Some parts of this article can be viewed as an update on the review
articles of Opella and Marassi,
8
Marcotte
and Auger,
9
and Prosser et al.
10
In addition, some of our own recent research
involving bicelles is presented in detail.
1.2
Understanding Atomistic-Level Structures Is
Important
The intrinsic properties of a cell membrane originate
from interactions among molecules like amphipathic lipids, polysaccharides,
cholesterol, proteins, and water. Since the chemical and physical
properties of these molecules differ considerably, the minimum free
energy of mixing corresponds to a heterogeneous cell membrane. Domains
rich in protein, cholesterol and anionic lipids, and rafts have been
reported to play important roles in biological activities of cells
which have direct implications in viral infection, bacterial infection,
amyloid toxicity related to aging diseases, and cancer.
11−13
For example, the presence of charged lipids in bacterial cell membranes
and their absence in mammalian cell membranes are one of the key factors
in the selectivity of antimicrobial peptides. Likewise, cholesterol
present in mammalian and absent in bacterial cell membranes has been
shown to have a similar influence on the selectivity of antimicrobial
peptides.
14
In addition, the process of
folding, misfolding or refolding, and aggregation of amyloidogenic
proteins in cell membranes is different from that in solution, and
also depends on the composition of the cell membrane.
15
Needless to mention that the secondary and tertiary structures
of proteins can be different when they associate with the cell membrane.
Therefore, high-resolution structure of individual molecules and their
orientation in a membrane environment could reveal the factors that
drive the molecular association and their function in this heterogeneous
membrane environment. While solving the atomic-level structure of
a membrane protein still remains a big challenge for most biophysical
techniques, the increasing number of structures determined by X-ray
and NMR studies continue to shed light on the functional aspects of
membrane proteins. For example, the reported high-resolution structure
of the potassium channel forming membrane protein
16−18
has provided
insights into the geometry of the channel, ion selectivity, interactions
between lipids and the protein, and the role of individual amino acids
in the transportation of potassium ions.
1.3
NMR Is an Ideal Technique to Measure Structure
and Dynamics
NMR spectroscopy has played a pivotal role in
the structure determination of a host of biomacromolecules, ranging
from proteins to nucleic acids. Importantly, NMR spectroscopy has
provided scientists with detailed structural and dynamical information
that is inaccessible through other biophysical means. First and foremost,
X-ray crystallography has elucidated a tremendous number of protein
structures in high resolution. The environment of a protein crystal,
however, is far from physiological and may shadow important aspects,
especially of protein dynamics. In this respect, NMR spectroscopy
is both an alternative as well as a complement to X-ray crystallography.
The branch of NMR spectroscopy that deals with molecules in solution
is known as solution-state NMR spectroscopy. It offers varied, well-tested,
and sophisticated tools,
19−25
to routinely deal with any soluble protein that does not exceed
a certain molecular weight. The upper limit for molecular weight is
currently around 100 kDa
26
and is continually
pushed higher. Lipid membranes are typically not amenable to be studied
by solution-state NMR spectroscopy, since they are well above the
molecular weight limit. It is often possible, though, to study the
structure of membrane proteins when they are solubilized by properly
chosen detergents.
27
Membrane proteins
are notoriously hard to study since their highly hydrophobic nature
routinely causes misfolding and aggregation, making it very hard to
crystallize them in sufficient quality for X-ray diffraction.
28
In addition, their slow reorientation in a membrane
environment prohibits the use of well-established solution-state NMR
methodology. The branch of solid-state NMR spectroscopy is rapidly
evolving to deal with membrane proteins that are beyond the size limit
for solution-state NMR spectroscopy.
Since the NMR observables
chemical shift anisotropy and dipolar coupling are sensitive to both
the chemical environment and molecular motions, they can be used to
probe molecular structure and dynamics associated with biological
processes such as ligand binding, conformational exchange and protein–protein
interactions. One of the unique advantages of NMR spectroscopy is
its ability to interrogate molecular dynamics over a wide range of
time scales. Through NMR, motions from nanosecond to microsecond time
scales can be probed via measuring different NMR parameters such as
spin–lattice relaxation (T
1), spin–spin
relaxation (T
2), relaxation in the rotating
frame (T
1ρ), residual dipolar couplings,
and quadrupolar coupling (for nuclei with spin > 1/2). Thus, NMR
spectroscopy
is able to paint a very detailed picture of a system, where structure
and dynamics as well as function can be correlated. Membrane proteins
exhibit a broad time scale of dynamics and these motions highly influence
the function of the protein: The residues in transmembrane segments
generally undergo restricted motion on a fast time scale (picosecond-nanosecond),
while soluble domains show large amplitude motions with slower correlation
times. Loop regions move with intermediate amplitudes on intermediate
time scales since they are anchored at transmembrane segments. The
entirety of domains may perform collective motions like conformational
changes at very slow time scales (microsecond). Typical dynamic properties
of different regions were quantified on bacteriorhodopsin by extensive 13C NMR studies.
29,30
Therefore, NMR techniques
are well suited to study the dynamical structures of membrane proteins.
Another unique advantage of NMR spectroscopy is that it can determine
the orientation of a membrane protein relative to the lipid bilayer.
In the context of NMR studies of membrane proteins, lipid bicelles
have opened completely new ways of preparing samples for NMR studies.
This is mostly because the size of lipid bicelles can be custom-tailored
for specific tasks. An additional unique property of certain bicelle
preparations is their propensity to macroscopically align when brought
into an external magnetic field. As a consequence, bicelles disobey
the traditional classification of NMR experiments and notoriously
cross the border between solution-state and solid-state NMR spectroscopy.
Figure 1 gives a graphic overview of the position
of lipid bicelles in NMR studies of membrane proteins. Care must be
taken to prepare a well-behaved sample for successful structural studies
using NMR spectroscopy. As is the case in the study of any membrane
protein, the protein needs to be supplied in sufficient amount and
purity, needs to have a specific isotope labeling scheme, and needs
to be properly folded and reconstituted. Only then can it be taken
into formulations that are suitable for NMR spectroscopy. Typically,
those have been detergent micelles for solution NMR studies, and multilamellar
vesicles (MLVs) of lipid for solid-state NMR studies. Lipid bicelles
open a middle ground between these two model membranes, namely, micelles
and MLVs. Since their size can be chosen to be small enough to tumble
quickly on the NMR time scale, small bicelles (also known as isotropic
bicelles) can be investigated using solution NMR experiments. Larger
bicelles, especially when aligned macroscopically, are amenable to
static solid-state NMR spectroscopy. In addition, magic angle spinning
(MAS) NMR experiments can be applied to lipid bicelles.
Figure 1
A schematic overview
of the use of lipid bicelles in the study
of structure and dynamics of membrane proteins using NMR spectroscopy.
1.4
Need for Excellent Model Membranes
The overall architecture of membrane proteins shows little variation:
integral membrane proteins transverse the lipid bilayer of the cell
membrane either as a single α-helix, or as a bundle of α-helices,
or they form β-barrels. Since the differences in membrane protein
architecture responsible for a specific function are often subtle,
excellent model membrane systems are needed. In addition, the secondary
and tertiary structures, folding, aggregation, dynamics, stability,
orientation, and function of a membrane protein highly depend on the
nature of the membrane environment. This is true even if membrane
proteins are intrinsically tolerant to changes in the composition
of the surrounding membrane.
31
For example,
the choice of a good detergent system was found crucial in studies
of the enzyme PagP, an integral membrane protein forming a β-barrel.
The detergent used initially was found to deactivate the enzyme because
its structure is too similar to the substrate. Only with a more distinct
detergent could an active enzyme be studied.
32
Likewise, specific polyunsaturated side chains are present at high
molar ratios in the lipids of rod outer segment disk membranes and
accumulate near rhodopsin, an integral α-helical membrane protein.
33,34
In the case of the antimicrobial peptide gramicidin A, suitable
conditions had to be established to distinguish the physiologically
relevant conformation from other conformations.
35,36
The general awareness of the distinction between physiologically
relevant and other conformations has obviously faded recently and
had to be called back to mind.
37
Different types of model membranes have been used for NMR studies.
The use of TFE/water mixtures is no longer considered to be a good
model membrane. Detergent micelles and lipid vesicles have commonly
been used in solution and solid-state NMR applications, respectively.
While the use of micelles enables the applications of well-established
solution NMR techniques, the potential impact of the curvature of
micelles on the structural folding remains a concern. Therefore, a
planar lipid bilayer is considered to be a better model membrane than
a micelle. As mentioned earlier, bicelles that are devoid of acute
curvature like a micelle are considered to be a more suitable model
membrane for NMR studies. Nevertheless, micelles have been found to
be useful in trapping transiently lived helical structures of amyloid
proteins that otherwise rapidly convert into β-sheet structures
in a lipid bilayer.
38,39
The importance of detergents
in the study of solubilized membrane
proteins has been reviewed,
40
at times
under imaginative titles referring to detergents as “French
swimwear”
41
or denying that they
are part of a soap opera.
42
In view of
the advantageous properties of bicelles over detergent micelles, another
review title states that “small is beautiful, but sometimes
bigger is better.”
43
Two other review
contributions have reported on bicelles in the context of membrane
mimetics and solubilizing agents for solution NMR spectroscopy.
26,44
These reviews cover micelle-forming detergents as well as innovative
solubilizing approaches other than bicelles, such as in situ NMR,
45
amphipols,
46
or nanodisks
47,48
which are not within
the scope of the current review. A comparison of NMR spectra acquired
on different membrane proteins in bicelles and nanodisks, both isotropic
and aligned, has been performed.
49
Bicelles
were investigated as novel surfactants in the context of cell-free
expression of membrane proteins.
50
Cell-free
production of integral membrane proteins in bicelles was compared
to production in lipid protein nanodisks as well as micelles and liposomes.
51
Subunits a and c of ATP-synthase have been produced
by cell-free synthesis in the presence of bicelles; subunit a was
shown to have a similar fold to native protein extracted from bacterial
cell walls.
52
2
What Are Bicelles?
When detergent molecules
were combined with phospholipids, phases
with completely new morphology were found.
53
The microscopic details of these morphologies have been researched
extensively, and phase diagrams have been established. With the help
of small-angle neutron scattering, detailed descriptions have been
given for all morphologies.
9,54
It was demonstrated
that short-chain phospholipids can be used as detergent, giving formulations
that consist purely of phospholipids.
55
To date, the combination of dimyristoylphosphatidylcholine (DMPC)
as long-chain, bilayer-forming component with dihexanoylphophatidylcholine
(DHPC) as detergent component has remained the most popular choice
for bicelle formulations. The most important descriptor of bicelle
preparations is the molar ratio of long-chain to short-chain component.
It is usually denoted as q, and in the most common
case, it is q = [DMPC]/[DHPC].
The specific
values of q, hydration level, temperature,
ionic strength, etc. determine the microscopic morphology. Figure 2 gives schematic
models for important morphologies.
The long-chain lipid component alone can form MLVs (Figure 2A). An addition of a detergent
results in defects
within the MLVs
56
(Figure 2B) since miscibility between lipid and detergent is low. When
increasing the detergent content, the vesicles break up and extended
lamellae (Figure 2C) or chiral nematic ribbons
(Figure 2D) are formed. Both have the propensity
for magnetic alignment, usually with the membrane normal directed
perpendicular to the external magnetic field direction of an NMR spectrometer
(which would be the vertical z-axis in Figure 2). At even higher concentrations of
the detergent,
aggregates are formed that have a flat, disk-like geometry and tumble
isotropically (Figure 2E). It is important
to note that the long-chain component in this geometry is still separated
from the detergent and forms a lipid bilayer. Pure detergent will
form isotropically tumbling detergent micelles (Figure 2F). The term “bicelle” has
been introduced to
generally denote the phases of long-chain and short-chain components
that are separated in bilayer and “rim” or pore portions,
respectively.
57
The term is regularly understood
in a more narrow sense to denote only the disk-like, isotropically
tumbling aggregates (Figure 2E).
Figure 2
Schematic models for
the morphology of bicellar phases with increasing
detergent content: multilamellar vesicles (A), with toroidal pores
lined up by detergents (B), extended lamellae showing magnetic-alignment
(C), chiral nematic “worm-like” ribbons, also magnetically
alignable (D), flat disk-like aggregates tumbling isotropically (E),
and detergent micelles (F).
Numerous modifications of bicelles have been developed
to make
them more closely resemble native biological membranes. The influence
of q, hydration level, and temperature on bilayer
properties of bicelles has been studied.
58
For spectroscopic purposes, it is advantageous to flip magnetically
aligned bicelles to make their membrane normal line up with the external
magnetic field axis. This can be achieved by adding lanthanide ions
59,60
or by using lipids with a biphenyl group in one of their acyl chains.
61,62
Two very recent studies demonstrated that incorporation of Cu2+ in a lipid by means
of the chelating agent 14:0-PE-DTPA
can shorten the T1 relaxation and therefore faster data
acquisition is feasible; this approach is attractive as an NMR experiment
can be completed faster and therefore a sensitive membrane protein
can be preserved from RF-pulse induced sample heating.
63,64
The magnetic-alignment of bicelles can be influenced by the embedded
protein, as was shown for gramicidin A, which causes alignment when
embedded in small bicelles that would tumble isotropically in the
absence of the protein.
65
Ether-lipids
can be used to increase sample stability,
66
but have recently been found to alter the structure of an antimicrobial
peptide novicidin.
67
Hybrid bicelles covered
with a siloxane ceramic layer were recently shown to increase the
stability.
68
Domain formation could be
modeled in bicelle formulations containing unsaturated lipids and
cholesterol.
69
Considerable effort
has been invested to establish bicelles as
a membrane mimetic for studies using electron paramagnetic resonance
(EPR) spectroscopy. Alignment can be achieved even at a weak magnetic
field strength used in X-band EPR measurements.
70,71
Structural and dynamic properties of the necessary nitroxide spin
labels were investigated
72
and a systematic
comparison with NMR results was performed.
73
The conformation of a nitroxide spin label in the homodimeric protein
CylR2 was compared in NMR, EPR, and X-ray crystallographic conditions.
74
Other innovative applications of bicelles
outside of NMR spectroscopy
include the crystallization of membrane proteins from bicelle formulations,
75−78
the use of bicelles as delivery vehicles for membrane proteins to
oocyte membranes,
79
and the use of bicelles
as templates for the synthesis of platinum nanowheels.
80,81
Today, the term “bicelle” has become so popular that
it was even applied to flat, disk-like aggregates formed by linear
peptide copolymers with different length hydrophobic and hydrophilic
portions.
82
The potential pharmaceutical
application of bicellar formulations to the skin has been investigated
in detail and has been reviewed.
83
A study
involving the drug diclofenac has investigated bicelles as drug carriers
in dermal applications.
84
3
An Overview of the Use of Bicelles in the Structural
Studies of Proteins
Bicelles are used in a number of ways
in the study of proteins,
be it a globular or a membrane protein. Figure 3 gives a cartoon overview of the different
approaches. In general,
both isotropically tumbling as well as magnetically aligned bicelles
are valuable tools to study proteins. Membrane proteins can be embedded
in both isotropic (Figure 3C) and aligned bicelles
(Figure 3A), enabling their study by methods
of solution-state or solid-state NMR spectroscopy, respectively. Globular
proteins are often studied in the presence of magnetically aligned
bicelles (Figure 3B). The aligned bicelles
impose a weak orientational preference onto the proteins which can
be detected in suitable solution-state NMR spectra. Furthermore, membrane
interaction of soluble proteins can be studied in the presence of
isotropic bicelles (Figure 3D).
Figure 3
Proteins can be studied
in numerous ways employing bicelles. Membrane
proteins can be macroscopically oriented using magnetically aligned
bicelles (A). Magnetically aligned bicelles can also be used to give
a residual preferential orientation to globular proteins (B). Membrane
proteins can be studied in isotropically tumbling bicelles (C). The
combination of isotropic bicelles and globular proteins can be used
to study membrane binding (D).
The following sections will review each approach. Section 4 and section 5 deal
with
soluble proteins in the presence of aligned or isotropic bicelles,
respectively. Section 6 introduces the special
situation of integral membrane proteins in bicelles in general terms
and section 7 describes the technical preparation
of such samples. Section 8 presents results
obtained on integral membrane proteins in isotropic bicelles, section 9 the same in
magnetically aligned bicelles.
The remaining sections report on the use of magic-angle spinning (section 10) and
the study of protein–lipid
interactions (section 11).
4
Bicelles as an Alignment Medium for Structural
Studies on Soluble Proteins
Globular proteins in solution
tumble isotropically, at a rate that
is usually fast on the NMR time scale. Hence, the anisotropic nuclear
spin interactions, namely, dipolar coupling, chemical shift anisotropy,
and quadrupolar interaction, are usually not observable for soluble
proteins. An average value is observed instead, which is zero in the
cases of dipolar and quadrupolar interactions, and gives the isotropic
chemical shift in the case of chemical shift anisotropy. Partly reintroducing
an anisotropic interaction, most often dipolar coupling, is a popular
and fruitful approach to gain structural information on biomolecules.
Dipolar coupling can be partly reintroduced by a large variety of
anisotropic ordering media. Magnetically aligned bicelles are often
used as an ordering medium. Figure 3B gives
a schematic idea of such a sample. The bicelles show macroscopic order
that is induced by the magnetic field of the NMR spectrometer. A soluble
biomolecule is restricted in its mobility by the presence of oriented
bicelles, which basically form “walls” that hinder the
reorientation of the investigated molecule. In some cases, a globular
protein can have a partial interaction with the head groups of lipids
and detergents of bicelles. Other alignment media may also show electrostatic
interaction with the molecule under investigation. As a consequence,
the investigated molecule is not fully free in its reorientation,
but shows a weak preference for a certain induced orientation. The
described weak alignment results in a weak dipolar splitting on the
order of Hz to several tens of Hz. Since the full magnitude of the
dipolar coupling is far larger—for example its value in an
amide 15N–1H bond is around 15 kHz
85,86
—these weak induced dipolar couplings are termed “residual
dipolar couplings” (RDCs). RDCs are invaluable parameters in
biomolecular structure determination, since they contain information
on global molecular structure as well as dynamic information.
RDC measurement was successfully utilized in the study of protein
structure using solution NMR experiments.
87
It was soon demonstrated that RDCs can be used to determine the
relative orientation of domains in multidomain proteins.
88
Since then, this field has expanded, and the
utilization of RDC data has been applied widely. An especially intriguing
application of RDC studies is in the study of dynamics of biomolecules
such as proteins and RNA.
89−91
A comprehensive overview of pulse
sequences used to measure RDCs can be found in the literature.
92
RDCs are most commonly recorded for amide protons
of folded proteins, but can also be determined and utilized for methyl
and methylene groups
93
and in unfolded
proteins.
94
A software dedicated to the
analysis of RDC data in structural terms is available.
95,96
Prediction of the alignment that a given molecular structure will
experience in a particular ordering medium has been achieved for purely
steric interaction
97
as well as steric
and electrostatic interactions with the ordering medium.
98
A dedicated software for prediction of alignment
from structure (PALES) has been developed.
99
Some studies have reported specific effects when bicelles
were
used to collect RDC values. It was found that the presence of two
transmembrane domains of the human glycine receptor GlyR in low-q bicelles—which in
the absence of protein would
tumble isotropically—impose a weak alignment and made the measurement
of RDCs possible. Magic angle spinning (MAS) was used to compare these
values to isotropic values.
100
RDCs could
even be measured on a peptide embedded in isotropic bicelles that
were aligned in stretched polyacrylamide gels.
101
However, exposing some proteins to bicelles as alignment
medium may have adverse effects. For example, in SDF-1/CXCL12, a cardioprotective
chemokine, the presence of aligned bicelles for RDC collection was
found to favor the presumably inactive dimeric state of the protein.
102
Magnetically aligned bicelles represent
one of the many alignment
media used in the study of RDCs. Other orienting media include bacterial
phages, stretched polyacrylamide gels, CmEn/n-hexanol mixtures, and liquid crystals.
Covalently attached
paramagnetic tags provide another option to weakly align molecules.
Tabulated overviews of alignment media are given in Prestegard et
al.
92
and Tolman and Ruan.
89
The parallel use of different alignment media can give
additional insight, allowing for the resolution of ambiguities and
the determination of generalized order parameters. Using 18 different
independent ordering media, recognition dynamics on time scales up
to μs could be observed in ubiquitin.
91
DMPC/DHPC bicelles with different minute additions of SDS were used
to collect three independent sets of RDCs on three N-terminal domains
of the human factor H complement regulator and characterize interdomain
motions.
103
Since bicelles do not play
a distinctive role of their own in RDC studies, we do not intend to
treat them isolated in the context of the current review article.
Instead, we refer the reader to a wide variety of review articles
that continue to be published on the topic of RDC studies in structural
biology. Excellent review articles can be found on RDC studies in
general,
92,104,105
on proteins,
106−110
and on RNA and DNA.
111−114
The potential of RDC methods in high-throughput studies for structural
genomics has also been pointed out.
115
5
Interaction of Soluble Proteins with Isotropic
Bicelles
The combination of soluble globular proteins with
isotropically
tumbling bicelles (Figure 3D) has been used
repeatedly to study protein–membrane interaction. For example,
solutions of isotropic bicelles modulate the amyloid formation of
full-length prion protein.
116
This study
did not use NMR spectroscopy, but it is in line with the increasing
evidence that lipid membranes play an important role in the formation
of amyloid fibrils.
117
In an NMR study
of an enzyme, cobra venom phospholipase A2, isotropic bicelles
were used as substrate to monitor enzyme function.
118
Binding of the cytosolic domain of rhomboid protease to
isotropic bicelles has been studied.
119
IFABP, a soluble shuttle protein that transfers hydrophobic ligands
to and from membranes, was investigated in the presence of isotropic
bicelles, and the potential to map out the membrane binding region
was reported.
120
For Arf1, ADP-ribosylation
factor 1, measurements of effective rotational correlation time were
used to characterize the binding of myristoylated and nonmyristoylated
Arf1 to bicelles with q ranging from 0.75 to 3.5.
121
The structure of the N-terminal activation
domain of Formin C was determined (pdb-id 2L1A).
122
The structure
of this regulatory domain was found to change significantly in the
presence of DPC micelles containing negatively charged phosphoinositides,
but not in the presence of phosphatidylcholine micelles and isotropic
bicelles. For each HAMP signaling domain of four different proteins,
two α-helical segments were structurally characterized in the
presence of bicelles and strong differences were found in α-helical
propensities, hinting at possible regulatory dimerization mechanisms.
123
BclXL, extra-large apoptotic repressor protein,
was investigated in q = 0.5 bicelles to study dimerization
in the presence of ligand and lipid bilayers.
124
Membrane binding and phosphatidic acid interaction of the
FRB domain of human TOR was probed in different neutral and negatively
charged membrane mimetics, including bicelles.
125
6
Are Bicelles Suitable to Study Membrane Proteins?
Today, almost 20 years after the first description of bilayered
oriented aggregates consisting purely of phospholipids in 1992
55
and the introduction of the term “bicelle”
in 1995,
57
this question has to be seen
as purely rhetorical. In a large number of instances, bicelle environments
have been found superior to micelle preparations.
It was realized
very early on that the enzyme diacylglycerol kinase
(DAGK) is active in bicelles, while activity is lost in micelles.
57
DAGK activity was quantified under a large number
of conditions.
126
HIV envelope peptide
was studied in bicelle and micelle samples, which were both weakly
aligned in a strained gel. In this study, structure determination
using RDCs revealed that micelles induce a curvature in the peptide
that is not present in a more natural bicelle environment.
101
Similarly, structural differences between micelles
and isotropic bicelles were found for BtuB, a 22-stranded β-barrel
protein, by site-directed spin labeling and EPR spectroscopy. It was
shown here that oriented bicelles preserve structure even better than
isotropic bicelles.
127
The protein Smr,
staphylococcal multidrug resistance pump, binds substrate in isotropic
bicelles, but shows only reduced or unspecific binding in a number
of detergent systems. High quality solution-state NMR spectra were
recorded and unambiguous assignments of 55% of the amide and Cα positions were possible.
128,43
The authors
point out the importance of a functional assay to unambiguously identify
the functional state of a protein. In their study, Smr was shown to
be functional in bicelles. Then, protein spectra recorded in bicelles
were taken as a point of reference to identify detergent systems that
support function.
43
In the case of MerF,
a bacterial mercury transporter, where no assay for protein function
is easily available, the similarity of micelle spectra to bicelle
spectra was taken as a criterion for proper refolding.
129
Bicelles where found to be superior to
micelles in another respect:
For lipolytic enzymes, in this case cobra venom phospholipase A2, the phospholipids
in the bicelle can act as substrate and
give insight in enzymatic mechanism. Here, short- and long-chain phospholipids
were found to be hydrolyzed with similar efficiency.
118
This application and the examples presented previously
clearly prove that bicelles have established their place in the structural
study of membrane proteins and are regularly found to give superior
results.
7
Protocols for Reconstitution of Proteins into
Lipid Bicelles
It has to be noted that the quality of the
achievable results depends
primarily on the quality of the bicelle sample that is to be investigated.
Especially in the case of membrane proteins, this may prove to be
very difficult. Whenever a membrane protein is to be embedded in bicelles,
there are multiple ways in which these bicelles can be prepared.
130,131
Figure 4 gives a schematic overview
of preparation
protocols. (A) Detergent may be added to preformed proteoliposomes,
containing the reconstituted membrane protein of interest. This may
be done gradually, resulting in a “q-titration”
and subsequently investigating aligned and isotropic bicelles. (B)
Detergent-solubilized protein may be brought in contact with lipid
vesicles, disrupting the vesicles and at the same time inserting the
membrane protein. (C) In cases were protein can be solubilized without
a detergent, pure protein may spontaneously insert into preformed
bicelles. (D) For membrane proteins that have an extraordinarily stable
fold, it may be possible to prepare a lyophilized mixture of protein,
lipid, and detergent, which forms a bicelle sample upon addition of
buffer.
Figure 4
Preparation protocols for a bicelle containing membrane proteins
can be chosen from a variety of possible pathways. Red, dark green,
and light green colors denote protein, lipid bilayer, and detergent,
respectively.
A comparison of different preparation protocols
and optimization
of all parameters may critically improve the quality of the resulting
NMR sample. Optimization of q-ratio in isotropically
tumbling bicelles can differentiate between mobile and structured
residues in embedded proteins, as demonstrated for seven membrane
proteins consisting of one to seven α-helices.
132
Protocols for the production and reconstitution of G protein-coupled
receptors for structural biology studies have recently been reviewed.
133,134
8
Solution NMR Studies of Membrane-Associated
Peptides and Proteins in Near-Isotropic Bicelles
Solution-state
NMR spectroscopy is a well-established experimental
technique and offers a tremendous wealth of proven tools to answer
almost any question on the structure and dynamics of small soluble
proteins.
20−23
Solution-state NMR spectra are characterized by nuclear resonances
of very small line width resulting in highly resolved spectra with
the option of resolving site-specific properties. The antimicrobial
peptide mastoparan X was the first biological system to be studied
by solution-state NMR in isotropic bicelles.
135
More and more systems have been studied since then, with amazing
results. In the following, a comprehensive overview of membrane proteins,
protein fragments, and peptides that have been investigated in isotropically
tumbling lipid bicelles is given (Figure 3C).
The use of isotropic bicelles is a necessary criterion and is not
reiterated in each case. Comprehensive galleries of high resolution
structures of membrane proteins solved by solution-state NMR are presented
in two recent review publications.
24,25
8.1
Proteins and Protein Fragments
The
structure of myristoylated Arf1, ADP ribosylation factor 1, was solved
in q = 0.25 bicelles (pdb-id 2KSQ).
136
It makes for a fruitful comparison to an earlier structure
determination with neither bilayer nor detergent present.
121
A novel experiment to measure one- and two-bond
N–C couplings that are complementary to more common RDCs was
developed and introduced in the study of Arf1.
137
A myristoylated N-terminal fragment of the protein has
been studied earlier in isotropic
138
and
aligned bicelles.
139
The structure
of OmpX, a bacterial outer membrane porin that forms an eight-stranded
β-barrel, has been solved, and NOE crosspeaks that report on
contacts between the protein and the DMPC and DHPC molecules in the
bicelle have been observed.
140
For BtuB,
a 22-stranded β-barrel protein, an EPR study found that isotropic
bicelles with q = 2.0 do not stabilize the native
fold, but q = 4.0 bicelles do.
127
Other EPR studies have shown that α-synuclein in
bicelles forms a single extended α-helix rather than a helix–turn–helix
structure
141
and picked up typical periodicity
for an α-helical segment of the M2δ subunit of the nicotinic
acetylcholine receptor (AChR).
142
The kinetics
of nitroxide spin label reduction by ascorbic acid has been used to
characterize membrane immersion of the M2δ-peptide of AChR in
EPR experiments.
143
For the seven-helix
transmembrane receptor sensory rhodopsin II,
a solution-state NMR structure was determined in micelles (pdb-id 2KSY). Measurements
in
bicelles were taken as an indication that the micelle structure is
similar to the structure in lipid bilayers.
144
Sensory rhodopsin and its apoprotein, opsin, were investigated in
bicelles of very different q-values. In addition,
phospholipids with varying chain length were used with either DHPC
or CHAPS as solubilizing agents to find optimal conditions to keep
the proteins stable.
145
Opsin was tested
in q = 1.0 bicelles for stability against urea unfolding
in DMPC/DHPC and DMPC/CHAPS formulations. Higher stability was observed
in DMPC/CHAPS bicelles by tryptophan fluorescence and far-UV circular
dichroism.
146
The coupling efficiency of
rhodopsin and transducin was investigated in q =
2.8 bicelles by absorbance measurements and was found to be dramatically
stabilized in bicelles containing 30% anionic lipids.
147
An activated rhodopsin/transducin complex using a constitutively
active mutant of rhodopsin was prepared in q = 0.65
bicelles.
148
It has been shown that
both DMPC/CHAPS and DMPC/DHPC bicelles can
be used to refold bacteriorhodopsin from a denatured state. Increased
DMPC content was found to slow down the formation of a partially folded
intermediate, which is ascribed to increased bending rigidity of the
bilayer portion.
149
The kinetic mechanism
of SDS-denatured bacteriorhodopsin being refolded by stopped-flow
mixing with bicelles was studied by pulsed oxidative labeling and
optical spectroscopy.
150
The successful
stabilization of the seven-helix transmembrane opioid receptor ORL-1
in sterol/detergent micelles was attributed to the bicelle-like geometry
of these mixed micelles.
151
Smr,
the small multidrug-resistance pump from S. aureus, is functional as a homodimer of
four transmembrane α-helices
each. Lipid bicelles were found to stabilize this functional form.
128
A major review on solution NMR of membrane
proteins has presented Smr as a prototypical example.
43
Recently, a backbone assignment of the functional form
was reported.
152
EmrE, a small multidrug
resistance transporter from E. coli known to be highly
sensitive to its environment, was reconstituted into isotropic bicelles
with improved sample stability and expanded lipid composition profile.
153
It forms asymmetric antiparallel homodimers
that were found functional in isotropic bicelles; global conformational
exchange between identical inward- and outward-facing states was found
and exchange rates were measured quantitatively.
154
The protein MerF from the bacterial mercury detoxification
system was investigated in isotropic bicelles and different detergent
micelles. Similarity of micelle to bicelle spectra was used to find
a micelle system supporting native protein fold. SDS micelles were
chosen to solve the structure, which contains two parallel transmembrane
helices.
129
Similarly, for LR11/SorLA,
a binding partner of the human amyloid precursor protein, a 1H–15N-TROSY spectrum
recorded in isotropic bicelles
was used as a ’gold standard’ in screening for a suitable
detergent system.
155
Conformational equilibria
of phospholamban, a single-pass transmembrane protein, were studied
in neutral and negatively charged isotropic bicelles.
156
This is part of a broader effort to combine solution- and
solid-state NMR to investigate phospholamban and sarcolipin inhibition
of Ca2+-ATPase.
157
A structure
determination of the integrin β3 transmembrane
(TM) domain was performed in both detergent micelles and isotropic
bicelles. A kinked α-helical structure was found that was very
similar in bicelles containing long-chain phospholipids varying in
length and also in charged bicelles, but had distinct deviations from
the structure determined from micelles.
158
Similarly, a structure was determined for the integrin αIIb
TM domain.
159
Both integrin TM domains
formed a stable heterodimeric complex whose solution NMR structure
gives insight into integrin TM signaling.
160,161
Methods for efficient construction of covalent TM complexes and
high-throughput selection of membrane mimics were established using
integrin αIIbβ3 as a model system; bicelles were identified
as the best membrane mimic.
162
For
the TM α-helix of BNip3, a prominent representative of
apoptotic Bcl-2 proteins, a homodimeric structure was determined.
163
The structures of several TM segments of receptor
tyrosine kinases have also been elucidated. For the TM region of growth
factor receptor ErbB2, a homodimeric right-handed α-helical
bundle was found. The monomers interact via an N-terminal double GG4-like
motif.
164
The TM regions of ErbB1 and ErbB2
form similar heterodimeric right-handed α-helical bundles by
association of N-terminal GG4-like and glycine zipper motifs.
165
The energetics and kinetics of the weak dimerization
of the ErbB4 transmembrane domain has been investigated in isotropic
bicelles with different protein to lipid ratios.
166
For the TM domain of EphA1, the ephrin receptor tyrosine
kinase, a dimeric right-handed α-helical bundle was found. A
pH-dependent change in conformation was observed.
167
The TM domain of EphA2 dimerizes in a left-handed α-helical
bundle, interacting through an extended heptad repeat motif, indicating
diversity in helix packing among receptor tyrosine kinases of the
same family.
168
A recent review article
provides more details about studies on bitopic membrane proteins.
169
A 25-residue peptide from MARCKS-ED,
the effector domain of the
myristoylated alanine-rich C-kinase substrate, was synthesized. This
segment, which reversibly binds the full-length protein to the membrane-solution
interface, can be switched on and off by phosphorylation and sequesters
phosphoinositol.
170
For an α-helical
fragment from a regulatory lipid glycosyltransferase that is predicted
to bind to membranes, bilayer affinity for zwitterionic and anionic
bilayers was studied.
171
Voltage-gated
sensors in the K+-channels HsapBK and KvAP were found to
form an α-helix on the bilayer surface.
172
A transmembrane orientation was determined for prion protein
residues 110–136.
173
Hydrogen/deuterium
exchange measurement on a fragment (1–30) of mouse prion-like
Doppel protein indicated a transmembrane orientation.
174
Similarly, for the N-terminal fragment (1–30) of
bovine prion protein, a peptide with cell-penetrating properties,
deuterium exchange in isotropic as well as 2H NMR splittings
in oriented bicelles indicate a transmembrane orientation with slight
hydrophobic mismatch.
175
For the mitochondrial
F1β presequence from Nicotinia plumbagigifolia an NMR solution structure was determined,
and differences between
the induced α-helical structure in neutral and acidic bicelles
were described.
176
Relaxation rate measurements
on the influenza hemagglutinin fusion peptide embedded in different
size isotropic bicelles revealed an overall rocking motion of the
membrane-bound peptide.
177
8.2
Peptides
The conformation of methionine-enkephalin
(Menk), a pentapeptide found in the central nervous system, was investigated
in fast-tumbling bicelles. The bound proportion was estimated to be
60% in pulsed field gradient (PFG) experiments. Two different conformers
were found that may be relevant for binding to two different opiate
receptors.
9,178
The structure of the five-residue neuropeptide
leucine enkephalin (Lenk) was determined. Binding was increased in
bicelles containing ganglioside GM1.
179
The membrane interaction of Lenk was studied by monitoring its tyrosine
side chain in ultrafast two-dimensional infrared spectroscopy. It
was concluded that the tyrosine side chain is not embedded in the
hydrophobic core of the lipid bilayer.
180
The partitioning of another neuropeptide, 11-residue substance P,
into isotropic bicelles was studied by PFG methods.
181
A conformational change of substance P was observed when
using bicelles that contain ganglioside GM1.
182
For the neuropeptides dynorphin A and B, ligands to the κ-opioid
receptor with cell penetrating properties, structural properties,
and membrane interaction were studied.
183
The structure of motilin, a 22-residue gastrointestinal peptide
hormone, was solved (pdb-id 1LBJ), and dynamic properties were investigated.
184
Structural properties of peptide hormones and
their binding to peptidergic GPCR have been reviewed.
185
An initial study on antimicrobial peptides (AMP)
in isotropic lipid bicelles used mastoparan X and was already mentioned
above.
135
The solution-state NMR structural
studies of mastoparan X have since been refined and extended to solid-state
NMR methods.
186
The structure of the AMP
alamethicin was solved and compared to results from a molecular dynamics
simulation on a DMPC bilayer. The peptide was found in a transmembrane
configuration, and its high degree of dynamics and heterogeneity could
not be described by a single conformational model.
187
Membrane binding of the magainin-derived AMP MSI-78 has
been studied by 19F-NMR on a variety of fluorine-labeled
analogues of MSI-78.
188−191
For arenicin-2, an AMP from a marine polychaete, a bent β-hairpin
structure was found in solution, which assembles into flat dimers
in DPC micelles and retains this structure in DPC/DMPG bicelles.
192
The structures of three C-terminal analogues
of the human AMP β-defensin-3 showed that dimer formation and
accretion of well-defined structures upon interaction with lipid membranes
contributes to compactization of positive charges within peptide oligomers
and antimicrobial activity. Bicelles with a high bilayer content, q = 3, were used
at low temperature to avoid magnetic alignment
and rather observe solution NMR spectra in isotropically tumbling
bicelles.
193
The relevance and implications
of solution NMR structures for the mode of a peptide’s action
has been critically reviewed for amphibian AMPs, with a special focus
on the synergy of different AMPs.
194
Another
review focuses on the role of membrane lipids in the action of AMPs
as well as pore-forming peptides and proteins in general.
195
Excimer fluorescence spectroscopy on an analogue
of the lipo-AMP daptomycin in a q-titrated bicelle experiment showed
that stochiometric binding of DMPG triggers daptomycin oligomerization.
196
The membrane-induced structure of a bee
venom peptide melittin
was found to be correlated with lipid fluidity.
197
Melittin was also studied in discoidal aggregates formed
when pegylated lipids are added to bilayers.
198
These aggregates have a disk-like morphology similar to isotropic
bicelles,
199
and it has been argued that
they are a superior membrane mimic in partitioning studies.
200
Melittin was bound tightly in comparably large
quantities to the rim of the stable and well-defined PEG-stabilized
disks, which might be exploited for drug delivery purposes.
198
A structural study on a cell-penetrating
peptide (CPP) transportan
bound to neutral bicelles is reported (pdb-id 1SMZ).
201
Transportan was further studied in neutral and partly charged
isotropic bicelles.
202
Penetratin, a cell-penetrating
fragment of the Antennapedia homeodomain protein of Drosophila, was
studied in two different bilayer mimetics.
203
In addition, penetratin’s dynamics and diffusion were studied
using 15N relaxation and PFG NMR experiments.
204
Membrane interactions of CPPs have been reviewed
in a recent review article.
205
For
two model transmembrane peptides, KALP-21 and KALP-23, changes
in lipid dynamics were observed in bicelles with different bilayer
thickness due to different long-chain lipid components, namely, DLPC,
DMPC, and DPPC.
206
The 22-residue model
peptide P16 assumes a transmembrane orientation as determined by amide–water
chemical exchange and lipid NOEs.
207
(A
parallel solid-state investigation on P16
208
is described below.)
9
Solid-State NMR Studies on Magnetically Aligned
Bicelles
Dramatic recent developments in pulse sequences,
instrumentation,
and sample preparations enabled high-resolution structural studies
of biological solids using solid-state NMR spectroscopy. Solid-state
NMR spectra are characterized by nuclear resonances of considerable
line width due to anisotropic interaction which often make site-specific
information hard to observe. However, numerous experimental strategies
are available to overcome these obstacles. Solid-state NMR has been
applied successfully to study a variety of membrane proteins and peptides
in a large number of instances, and today it is fully established
as a standard tool in the study of membrane protein structure, dynamics,
and orientation.
209
Since native membrane
proteins are restricted in their isotropic reorientation by the lipid
bilayer, they naturally display strong anisotropic nuclear spin interactions,
making solid-state NMR the natural approach to study their properties.
Two strategies have been developed to deal with strong anisotropic
interactions. One of the approaches is magic angle spinning (MAS),
which suppresses anisotropic interactions to render “solution-like”
high-resolution spectra of solids. This approach enjoys the benefits
from the use of ultrafast spinning, multidimensional pulse sequences,
recoupling techniques to selectively measure an anisotropic interaction,
homogeneous sample preparation, and low temperature capabilities.
MAS techniques have been applied to proteins embedded in MLVs but
only rarely utilized to study proteins incorporated in bicelles, as
described in section 10. The second strategy
involves the application of static solid-state NMR experiments on
macroscopically aligned samples. Here, aligned bicelles are obviously
a very helpful tool to achieve high-quality macroscopic alignment
(Figure 3A). This section will first give a
quick overview of solid-state NMR techniques that are designed especially
for the study of proteins or peptides aligned in lipid bilayers. In
the following, successful studies of membrane proteins or peptides
embedded in aligned bicelles will be reviewed. Again, the aim of this
section is to give a comprehensive overview of membrane proteins,
protein fragments, and peptides studied in magnetically aligned bicelles.
The use of aligned bicelles is a presupposition for each mentioned
study and not stated explicitly each time.
9.1
Aligned Molecules Enable High-Resolution Molecular
Imaging
Use of Unaligned Lipids
Solid-state NMR studies commonly
utilize unaligned MLVs and aligned lipids under static conditions.
Unaligned lipid bilayers are traditionally characterized using one-dimensional 31P
chemical shift spectral lines as they can distinguish different
phases (gel, lamellar, hexagonal, cubic) of lipids and can measure
the changes in the dynamics and conformation of lipid headgroup. Therefore, 31P NMR
experiments on unaligned MLVs have been well utilized
to study lipid–lipid, lipid–protein/peptide, and lipid-drug
interactions. In addition to 31P NMR, quadrupole coupling
parameters measured from 14N (only from choline-containing
lipids)
210
and 2H (only from
deuterated lipids)
211
NMR spectra have
been useful in probing the electrostatic interactions and dynamics
associated with the lipid headgroup. 2H NMR has also been
used to measure the order/disorder of C-D bonds in different regions
of a lipid in MLVs.
212
While unaligned
MLVs continue to be used in solid-state NMR applications, the use
of aligned samples can provide more site-specific information on lipids
and also from embedded peptides/proteins.
Approaches to Prepare Aligned Lipid Bilayers
Macroscopically
aligned lipid bilayer samples can be prepared using three different
approaches. The first approach uses the mechanical alignment of lipids
between glass plates.
213,214
This approach has been used
in the structural studies of membrane proteins and peptides. The main
advantage of this type of sample is that various combinations of lipids
can be incorporated. But the main disadvatages are (i) it takes more
than a day to prepare samples in spite of using the recently developed
naphthalene procedure
214
to speed up the
hydration process. (ii) The filling factor in the NMR sample coil
is poor as the glass plates occupy most of the space. (iii) A flat-coil
probe is needed to accommodate the glass-plate sandwich sample.
The second approach uses aluminum oxide nanodiscs to mechanically
align lipid bilayers.
215−217
While this approach renders a quick way
to prepare aligned samples, the extent of alignment is small for high-resolution
structural studies on membrane proteins. Nevertheless, this approach
has been well utilized in various applications.
218
The third approach is to use magnetically aligned bicelles
as explained earlier. Some of the main advantages are as follows:
(i) It is easy to prepare well-hydrated bicelles. (ii) Bicelles of
varying sizes can be prepared. (iii) It is devoid of glass plates
and therefore the filling factor is very high. (iv) The presence of
bulk water can enable native-like folding of membrane proteins particularly
those containing large water-soluble domains. As mentioned above,
bicelles are increasingly applied because of these advantages.
Examining the Quality of Aligned Lipid Bilayers
The
quality of alignment of lipids is commonly examined using a 31P chemical shift spectrum.
A well-aligned lipid bilayer sample exhibits
a narrow spectral line revealing the direction of alignment relative
to the external magnetic field. One-dimensional chemical shift spectra
of 1H, 31P, and 13C nuclei from aligned
samples are easy to obtain and therefore commonly used to study lipids
and their interactions with other embedded molecules. Quadrupole coupling
spectra of 14N and 2H nuclei from aligned samples
are also useful to study lipid bilayers as mentioned above. Spectra
of peptides or proteins labeled with 15N, 13C, 2H or 19F embedded in aligned lipid
bilayers
are useful in determining their orientation relative to the lipid
bilayer surface or normal.
9.2
Custom-Tailored NMR Experiments
One-dimensional
static solid-state NMR experiments on aligned lipid bilayers containing
peptides or proteins labeled with 15N, 13C, 2H, or 19F have been well utilized in
various instances.
For example, it has become very common to determine the overall orientation
of an antimicrobial peptide in a lipid bilayer in order to understand
its mode of action.
219−221
However, the spectral resolution rendered
by a 1D spectrum is insufficient to resolve spectral lines arising
from a uniformly labeled membrane protein. On the other hand, a well-equipped
arsenal of solid-state NMR experiments is ready for the study of macroscopically
aligned proteins and peptides. A central role is taken by two-dimensional
separated-local-field (SLF) experiments that correlate 15N chemical shift and 1H–15N
dipolar
coupling, thus reporting on the geometry and alignment of peptide
groups. The prototype of such experiments is the polarization inversion
by spin exchange at the magic angle (PISEMA) experiment.
222−224
PISEMA experiments display characteristic patterns that report on
a molecule’s orientation with respect to the lipid bilayer.
Most notably, α-helices give circular spectral patterns known
as polarity index slant angle (PISA) wheels which can be used to infer
a peptide’s tilt within the bilayer.
225,226
The analysis of PISA wheels requires detailed knowledge of the chemical
shift anisotropy tensor within the geometry of an amide bond.
85,86,227
PISEMA can be improved by using
different mixing schemes in the indirect dimension, e.g., BB-PISEMA,
228
HIMSELF (heteronuclear isotropic mixing spin exchange via local field)
or HERSELF (heteronuclear rotating-frame spin exchange via local field)
229
or SAMMY.
230
Methods to enhance sensitivity in SLF experiments,
231
in heteronuclear correlation spectroscopy,
232
and in proton evolved local field experiments
using Hadamard encoding,
233
all in oriented
systems, have been reported. Cross-polarization can be made more efficient
by performing multiple repetitive contacts.
234
Specific strategies for backbone assignment in oriented samples
have been described, utilizing controlled reintroduction of proton
spin diffusion,
235−237
or mismatched Hartmann–Hahn magnetization
transfer,
238,239
or a previously assigned isotropic
chemical shift spectrum.
240
De
novo sequential assignment was demonstrated for 26 residues
out of the 31-residue membrane protein sarcolipin in uniformly 15N-labeled form.
241
Influence of
orientational and motional narrowing of lineshapes in PISEMA-type
experiments has been investigated theoretically and experimentally
and can potentially yield an additional angular constraint in structure
calculations.
242
Aligned bicelles
have been established for EPR spectroscopy
70,71
and can give similar information on the tilt of transmembrane domains.
The structural and dynamic properties of the necessary spin label
have been characterized.
72
For a transmembrane
α-helical segment of the M2δ subunit of the nicotinic
acetylcholine receptor, a helical tilt of 14° with respect to
the bilayer normal was determined by EPR.
243
It was established experimentally on the M2δ peptide
142
as well as theoretically
244
that unoriented bicelles can be used for the same purpose.
The helical tilt of phospholamban, a regulatory single-pass transmembrane
protein, and its segmental mobility were probed by EPR in oriented
bicelles.
245
9.3
Proteins and Protein Fragments
Solid-state
NMR methodology is routinely applied to membrane proteins and protein
fragments embedded in magnetically aligned bicelles. Among the most
challenging targets for structure elucidation are G-protein coupled
receptors (GPCR) that consist of seven transmembrane α-helices.
A high-resolution structure determination was recently achieved for
a GPCR by solution-state NMR (ref (144) and section 8.1),
and solid-state NMR investigations of GPCR are becoming increasingly
common. The chemokine receptor CXCR1, another GPCR, was successfully
incorporated in aligned bicelles and studied in solid-state NMR.
246
Solution-state NMR assignment experiments could
identify only a limited number of resonances in CXCR1. A combination
of solution- and solid-state NMR experiments was used to characterize
local and global dynamics of this protein
247
and binding to its ligand interleukin-8.
248
The C-terminal domain of human cannabinoid 1 GPCR was found to modulate
the structure of its membrane environment.
249
A reconstitution protocol for Y2, a human GPCR, into
lipid bicelle environment has been described.
250
Reviews are available on the expression, solubilization,
and reconstitution of GPCR in membrane mimetic environments including
bicelles.
133,134
The second transmembrane
domain (TM2) of the α4 subunit of the neuronal α4β2
nicotinic acetylcholine receptor (nAChR) was prepared as a selectively 15N-Leu labeled
peptide. In the presence of unlabeled TM2 from
the β2 subunit, it forms functional (α4)2(β2)3 pentamers, for which the tilt and azimuthal
rotation of the
α2-TM2 subunit could be determined. Structural changes were
observed in the presence of anesthetic drug molecules.
251
The membrane protein p7 from hepatitis
C virus could be expressed
as a fusion protein to give sufficient yield for NMR samples; incorporation
in aligned bicelles was successfully achieved.
252
PISA wheels corresponding to two α-helical transmembrane
segments could be identified with the help of a truncated construct
corresponding to the second transmembrane α-helix.
253
Further experiments including a “q-titration” gave RDC and isotropic NMR data and
helped refine the structural model to define seven distinct structural
regions within the 63-residue protein.
254
The three-dimensional structure of the membrane-spanning domain
of Vpu from HIV-1, consisting of a single α-helix, was solved,
255
and changes were investigated in the presence
of channel-blocking drugs.
256
A review
comparing both viral proteins, p7 and Vpu, is available.
257
The major coat protein of bacteriophage Pf1
was investigated in biphenyl bicelles that orient with their bilayer
normal parallel to the applied magnetic field.
258
A combination of solution- and solid-state NMR yielded
a full structure of the protein in lipid bilayer environment, which
consists of a tilted transmembrane α-helix and a second, orthogonal
α-helix.
259
MerFt, a truncated
construct of the bacterial mercury transport
protein MerF, was found to consist of two membrane-spanning α-helices
and a short loop region.
260
An α-helical
transmembrane segment from the pore forming component TatA of the
twin-arginine translocase was found to have a tilt of 17° with
respect to the bilayer normal.
261
Further
studies on larger fragments revealed that a second adjacent α-helix
is immersed in the phospholipid headgroup region.
262
For tOmpA, the transmembrane portion of bacterial
outer membrane
porin A which spans the membrane as an eight-stranded β-barrel,
successful reconstitution in aligned bicelles was reported.
263
For OmpX, another eight-strandend β-barrel,
orientational constraints from solid-state NMR were combined with
atomic coordinates from X-ray crystallography to give the protein’s
overall orientation within the bilayer.
264
Structural propensities of an exceptionally long linker region
from the human voltage-gated K+ channel hERG were found
to be dependent on bicelle composition, as determined by solution
and solid-state NMR experiments.
265
In
addition, this study used isotropic bicelles to characterize membrane
binding affinity of hERG. The interaction of two different Arg-rich
paddle domains of voltage gated K+ channels with the lipid bilayer
have been characterized in oriented bicelles.
266
The myristoylated 14-residue peptide Cat14 from the catalytic
unit of cAMP-dependent protein kinase A was incorporated in q = 3.5 bicelles to study
interaction with lipids by 2H NMR.
267
A myristoylated N-terminal
14-residue peptide from pp60ν-src was studied
in neutral and acidic bicelles.
268
9.4
Peptides
The effect of bound Menk,
the neuropeptide methionine enkephalin, on different types of lipid
bilayers was investigated using oriented bicelles.
269
Binding and arrangement of aromatic pharmacophores were
investigated for the δ-opiate DPDPE.
270
The neurotoxin pardaxin permeabilizes vesicles more efficiently
by pore formation than by disruption. It assumes a transmembrane orientation
in neutral bicelles, while it is restricted to headgroup contacts
in DMPG-doped bicelles.
271
The binding
of two fragments of rat islet amyloid polypeptide (rIAPP, also known
as rat amylin) to aligned bicelles was investigated. The nontoxic
rIAPP(1–37) binds to the bilayered regions of low curvature,
while the toxic rIAPP(1–19) binds to detergent-rich regions
of high curvature. Neither peptide caused membrane fragmentation.
272
The consequences of hydrophobic mismatch
and peptide sequence were
investigated in the transmembrane model peptide P16.
208
A 21-mer cytotoxic model peptide modified with crown ethers
stabilized bicelle structure and orientation and perturbed the lipid
polar headgroup conformation.
273
For a
similar 14-mer peptide modified with crown ethers, no significant
change in the morphology and orientation of bicelles was found.
274
The antimicrobial peptide (AMP) mastoparan
X was found to orient
perpendicular or parallel to the membrane normal of the bilayer patch
depending on bilayer charge.
186
Various
AMPs found in the skin of Australian amphibians were characterized
in aligned bicelles and compared to results obtained in mechanically
aligned DMPC bilayers.
275
For the AMP novicidin,
significant structural and conformational differences were observed
between ordinary DMPC/DHPC bicelles and bicelles with analogous ether-lipids.
67
This result has a considerable impact, since
ether-lipids are regularly employed to increase sample stability and
lifetime.
66
For lactophorin I and II, two
AMP found in bovine milk, tertiary structure and membrane orientation
were determined.
276
The bee venom peptide
melittin disrupts aligned q = 1.8 bicelles, unless
they are protected by embedded cholesterol.
277
9.5
Cytochrome b
5
The Ramamoorthy laboratory is currently investigating cytochrome b
5, a membrane-anchored protein that is mostly
found in the endoplasmic reticulum of liver cells and plays a supportive
role in the biodegradation of a large number of toxic and drug molecules.
We have given a comprehensive overview of the structure and function
of cytochrome b
5 and its physiological
interaction partners, especially with respect to NMR spectroscopic
investigations.
278
Briefly, cytochrome b
5 supports members of the cytochrome P450 family
of enzymes to oxidize their substrates, which are typically drug or
toxic molecules that need to be prepared for excretion. Cytochrome b
5 accelerates the oxidization process for numerous
cytochrome P450 isozymes, most probably by transferring an electron.
The function of cytochrome b
5 is intimately
linked to its topology, which is represented as a cartoon in Figure 5. A globular
domain contains a heme prosthetic group
which carries electrons that are to be transferred to cytochrome P450.
However, this transfer is not possible unless the globular domain
is attached to the membrane of the endoplasmic reticulum by a membrane
anchor. The membrane anchoring part of cytochrome b
5 consists of a putatively α-helical transmembrane
domain and a flexible linker region. It was shown that the length,
but not the actual amino acid composition of the linker domain is
critical for electron transfer to cytochrome P450.
279
The globular domain of cytochrome b
5 truncated from the holo-protein has been the subject of extensive
structural investigations. Very few structural studies, however, have
been conducted on cytochrome b
5 in its
holo-form of 16.7 kDa molecular weight. This is particularly unsatisfactory
as cytochrome b
5 function is critically
dependent on the presence of its membrane anchor. For this reason,
we decided to investigate holo-cytochrome b
5 in lipid bicelle environment.
Figure 5
Schematic of the topology of full-length
cytochrome b
5 (cyt b
5, yellow). The protein
consists of an α-helical transmembrane domain, a highly flexible
linker region, and a globular domain that carries a prosthetic heme
molecule. Also shown is the bicellar environment used to macroscopically
align cyt b
5 with respect to the external
magnetic field, B
0.
Bicelle samples made from DMPC and DHPC at a q ratio of 3.5 were used to incorporate
full-length rabbit
cytochrome b
5 into a bilayer environment.
280
The quality of the bicellar phase in terms
of orientation
and mosaic spread was monitored by 31P NMR. Figure 6A shows the 31P NMR spectrum of
a pure q = 3.5 DMPC/DHPC bicelle preparation. Two well-separated
resonances originate from the phosphocholine headgroups of DMPC and
DHPC and report on their orientation. The very narrow width of the
lines reflects the high quality of alignment reached in this case.
Upon addition of 1 cytochrome b
5 molecule
per 86 DMPC molecules, there are still two distinct 31P
NMR resonances, shown in Figure 6B. However,
the width and overall shape of the lines indicates that only a very
limited amount of macroscopic orientation is reached. In samples with
a lower ratio of protein per lipid, macroscopic orientation can be
recovered. Figure 6C shows the 31P NMR spectrum of a sample with 170 DMPC molecules
per cytochrome b
5. Macroscopic orientation is recovered, but
the quality of alignment is still poor. A ratio of 212 DMPC molecules
per cytochrome b
5 is necessary to reach
a quality of alignment that is comparable to pure DMPC/DHPC bicelle
samples (see Figure 6D).
Figure 6
Proton-decoupled 31P NMR chemical shift spectra of different
bicelle preparations used in the study of cytochrome b
5. Phosphorus-31 NMR spectra report directly on the quality
of bicelle alignment. (A) Pure q = 3.5 DMPC/DHPC
bicelles. Bicelles in the presence of one cytochrome b
5 molecule per 86 (B), 170 (C), and 212 (D) molecules
of DMPC. (E) Bicelles in the presence of both cytochrome b
5 and cytochrome P450. The resonance observed at approximately
0 ppm originates from phosphate buffer.
After establishing experimental conditions for
oriented bicelle
samples with very low mosaic spread, we used uniformly 15N-labeled cytochrome b
5 to investigate
its molecular structure.
280
Figure 7B shows one-dimensional proton-decoupled 15N NMR chemical shift spectra obtained
using different NMR pulse
schemes. Shown in the figure are cross-polarization (CP) spectra obtained
at contact times of 3.0, 0.8, and 0.1 ms. The CP spectrum at 0.8 ms
contact time shows the strongest overall signal intensity. It displays
intensity in the spectral range around 125 ppm; this range is typical
for isotropic amide 15N chemical shifts. In addition, signal
is observed in a range around 80 ppm, which indicates that the protein
is macroscopically oriented and experiences 15N chemical
shift anisotropy. When the CP contact time is lowered to 0.1 ms, the
intensity in this spectral region stays visible, while it drops severely
in the region around 125 ppm. This is consistent with macroscopically
oriented protein components with high molecular order resulting in
fast and efficient polarization transfer from protons by strong 15N–1H dipolar couplings.
If, on the other
hand, the contact time is increased to 3.0 ms, intensity in the spectral
region around 85 ppm is lost because of increased relaxation due to
strong 1H–1H dipolar couplings. The signal
in the isotropic range around 125 ppm is still visible at 3.0 ms contact
time, indicating that it arises from highly mobile regions of the
molecule. In mobile molecular segments, dipolar coupling is decreased
by motional averaging, resulting in a less efficient cross-polarization
and slower relaxation losses. Remarkably, the spectral intensity around
125 ppm is observable in refocused-INEPT experiments that are usually
applied to soluble proteins in solution-state NMR (see top spectrum
in Figure 7B). We conclude that our bicelle
samples indeed confer macroscopic orientation to cytochrome b
5, and that by different NMR pulse schemes,
we can distinguish domains of cytochrome b
5 that display different degrees of molecular mobility.
Figure 7
Structural observations
on full-length cytochrome b
5 using solid-state 15N NMR spectroscopy.
(Top) Molecular model of cytochrome b
5 in a lipid bilayer. (Middle) One-dimensional 15N NMR
spectra and (bottom) two-dimensional HIMSELF spectrum of uniformly 15N-labeled cytochrome
b
5 embedded
in DMPC/DHPC q = 3.5 bicelles.
In order to understand how the spectral properties
observed in
1D 15N NMR experiments relate to the domains of cytochrome b
5, we conducted two-dimensional NMR experiments
that correlate 15N chemical shift with 1H–15N dipolar coupling.
280
Heteronuclear
isotropic mixing by HIMSELF experiments
229
that are advantageous compared to the more common PISEMA-type experiments
222,224
were used. HIMSELF experiments correlate the 15N chemical
shift of amide nitrogens with the 1H–15N dipolar coupling they exhibit with the directly
bonded amide proton.
Since the 15N-CSA-tensor and the 1H–15N dipolar interaction do not line up perfectly,
their correlation
gives distinctive spectral shapes that are characteristic for certain
types of a secondary structure. Figure 7C shows
the HIMSELF spectrum of a uniformly 15N-labeled cytochrome b
5 in DMPC/DHPC q = 3.5 bicelles.
A circular spectral pattern is observed in the region around 85 ppm
of 15N chemical shift, which was found to represent rigid
molecular regions. Such a circular spectral pattern is associated
with transmembrane α-helices and is referred to as a PISA-wheel.
We conclude that the spectral region around 85 ppm represents the
membrane anchor of cytochrome b
5 which
transverses the lipid bilayer as a transmembrane α-helix. This
is especially remarkable since in our preparation protocol, cytochrome b
5 was added to preformed bicelles. Hence, the
transmembrane α-helix of cytochrome b
5 is actually able to insert spontaneously into lipid bilayers. It
has to be noted that the observed PISA-wheel of Figure 7C is far from perfect. This
may be related to the fact that
a proline residue is found in the center of the α-helical domain,
since proline residues are known to induce kinks in α-helices.
281
A best-fit analysis of the observed PISA-wheel
revealed a tilt angle of 15° for the transmembrane domain of
cytochrome b
5 with respect to the lipid
bilayer normal.
In conclusion, we found that magnetically aligned
bicelles are
a suitable environment to study the structure of cytochrome b
5 in the membrane.
280
Figure 7A shows a molecular model that summarizes
the results. The membrane anchor was found to span the lipid bilayer
as a rigid α-helix. It may be kinked due to a proline residue
that is shown in green in the model. The globular domain is highly
mobile and is tethered only very loosely to the membrane anchor by
the linker region. The linker region is an example of an “entropic
chain” or intrinsically disordered region.
282
Opening ways for further investigations, it was possible
to extend
the studies to other types of lipid bicelles. These modified bicelles
have tunable bilayer thickness and charge, and they subtly influenced
cytochrome b
5’s structure.
278
Moreover, and most remarkably, it was found
that cytochrome b
5 can be studied in complex
with its most important interaction partner, cytochrome P450, an integral
membrane protein of approximately 56 kDa molecular weight.
278
Figure 6E shows the 31P NMR spectra of DMPC/DHPC bicelles harboring the cytochrome
b
5/cytochrome P450 complex. The quality of alignment
was very high and gave HIMSELF spectra of comparable quality as the
one shown in Figure 7C. Our bicelle samples
also gave interesting spectra under magic-angle spinning;
283
see section 10.
Recently, new methods have been developed for the study of proteins
incorporated into aligned bicelles containing cytochrome b
5. By using two-dimensional proton-evolved local-field
(PELF) in combination with WIM and COMPOZER-CP pulse sequences,
284
we were able to clearly resolve peaks for both
the transmembrane and soluble domains of bicelle-bound cytochrome b
5.
285
Furthermore,
the helical tilt angle of cytochrome b
5’s transmembrane helix was determined to be 13° with
respect to the bilayer normal, with 8° of fluctuation.
285
Dipolar enhanced polarization transfer (DREPT)
is based on INEPT-type magnetization transfer; it eliminates 1H–1H dipolar interactions,
making it highly
sensitive and especially useful for the detection of side-chain dynamics
in proteins embedded in aligned bicelles.
286
When applied to cytochrome b
5, it was
found that the immobile transmembrane domain and the mobile soluble
domain can be selectively observed by changing the length of the refocusing
period, as seen in Figure 8. In addition, by
utilizing 2D DREPT it was possible to measure 15N–1H dipolar couplings in histidine,
tryptophan, and arginine
side chains in cytochrome b
5.
286
Further studies using DREPT may provide important
insights into the exact orientation of these side chains and the mechanism
of cytochrome b
5’s function.
Figure 8
15N Chemical shift spectra of oriented bicelles containing
cytochrome b
5 in RampCP and RINEPT (A)
and DREPT (B) experiments.
Refocusing delay times vary as indicated in (B). Short refocusing
periods are sufficient for the production of peaks from cytochrome b
5’s rigid domain while longer delay times
are necessary for the detection of soluble domain resonances. (C,
D) 2D spectra obtained using the RINEPT sequence with refocusing delays
of 1 ms and 80 μs, respectively. Reprinted with permission from
ref (286). Copyright
2010 American Chemical Society.
10
MAS Studies on Bicelles
The broad
nuclear resonances observed in solid samples are dealt
with by two different major strategies. In the preceding section,
the use of macroscopically aligned samples was described. The alternative
approach of magic-angle spinning (MAS) is more common but has found
less application to bicellar samples. This section presents the application
of MAS to proteins in bicelles.
10.1
Bicelles under MAS
By running a
solid-state NMR experiment while spinning the sample at the “magic
angle” of 54.7° relative to the external magnetic field,
the dominant anisotropic interactions dipolar coupling, chemical shift
anisotropy, and quadrupolar coupling can be suppressed. In particular,
very narrow lines can be observed since homogeneous line broadening
caused by strong dipolar coupling is absent under magic angle spinning
(MAS). Thus, high-resolution spectra (comparable to those of solution
NMR) full of dynamic and structural information about bilayer-associated
membrane proteins can be obtained. The effect of sample spinning on
aligned bicelles has been studied in detail.
287−289
When aligned bicelles are spun at an angle smaller than the magic
angle, their bilayer normal aligns perpendicular with respect to the
spinning axis. This alignment was used to determine signed values
of residual dipolar coupling for a myristoic acid derivative in the
bicelles.
287
At angles larger than the
magic angle, the bilayer normal aligns parallel with the spinning
axis. When the spinning axis approaches the magic angle, mosaic spread
increases.
289
Finally, at the magic angle,
bicelle alignment vanishes; that is, there is no more preferred orientation
for the bilayer normals and they distribute isotropically.
MAS
experiments conducted on spinning bicelles have proven useful in the
study of peptides and proteins. It has been found that the width of
lines observed in spinning bicelles can be reduced by a factor of
3
290
compared to what is typically observed
in lipid vesicles.
291
A direct comparison
of line width in bicelles and proteoliposomes under MAS was performed
and interpreted with respect to theoretical expectations.
292
This study used the pentapeptide methionine-enkephalin
and NeuTM35 for demonstration, a 35-residue transmembrane
fragment of a tyrosine kinase receptor. Switched-angle spinning was
applied to the study of Leu-enkephalin in bicelles.
293
The study of residual dipolar couplings (RDC) of
soluble proteins
in the presence of oriented bicelles can also benefit from sample
spinning. Because bicelle alignment is suppressed by MAS, the same
sample can be used with and without MAS to record isotropic and weakly
aligned spectra, respectively. Recording both spectra in the presence
of bicelles keeps the influence of protein–bicelle interaction
identical for both spectra. This has been demonstrated for ubiquitin,
where precise site-specific 15N CSA tensors could be determined.
294
Similarly, the use of variable-angle spinning
has improved the observation of scaled RDC in ubiquitin.
295
This was later expanded to include very strong
RDC and chemical shift variations of ubiquitin’s 15N resonances.
296
For the second and third
transmembrane segment of GlyR, the human glycine receptor, incorporation
into low-q bicelles resulted in weak alignment; MAS
and static spectra yielded J-couplings and RDC values
with high accuracy.
100
For the fourth transmembrane
domain of the γ-subunit of the nicotinic acetylcholine receptor
in high-q bicelles, a similar comparison of static
and spinning spectra yielded precise values for 13C- and 15N-CSA and isotropic chemical
shift. The measured values indicate
a tilt of 15° for the transmembrane domain with respect to the
bilayer normal.
297
10.2
Cytochrome b
5 in Bicelles under MAS
The Ramamoorthy laboratory has utilized
MAS techniques to study cytochrome b
5 (cyt b
5) in bicelles.
283
Using full-length rabbit cyt b
5 with
uniform 15N-labeling and 5 kHz MAS, we found that cyt b
5 yielded higher resolution spectra when incorporated
into bicelles than into liposomes. By using ramped cross-polarization
(RampCP)
298
for polarization transfer to 15N-nuclei under MAS, it was possible to observe not
only backbone
amide-15N resonances, but also arginine and lysine side
chain-15N resonances of cyt b
5 in bicelles (Figure 9A). We also studied
uniformly 13C,15N-labeled cyt b
5 in bicelles under MAS. Experiments using nuclear Overhauser
effect (NOE) transfer, refocused INEPT (RINEPT) pulse sequence,
299
and RampCP for polarization transfer to 13C-nuclei were compared, finding that NOE
experiments produced
particularly strong resonances for the carbonyl carbons of cyt b
5, while RINEPT produced strong signals for
the acyl carbons of the bicelle lipids, DHPC and DMPC. In addition,
two-dimensional CTUC COSY and DARR experiments were conducted on cyt b
5 to record 13C–13C correlations. Because of the high resolution achieved in these
MAS experiments, it was possible to assign peaks to specific amino
acids. It was found that RINEPT and CTUC experiments are best suited
for the study of cyt b
5’s mobile
domain, while RampCP and DARR experiments showed resonances mainly
from the immobile, transmembrane domain of the protein (Figure 9B). We conclude that
MAS on bicelles is especially
useful in the study of membrane bound proteins with soluble domains,
such as cyt b
5, where both highly mobile
and immobile regions are present. MAS techniques may become invaluable
tools in the structure determination of such proteins.
Figure 9
Spectra showing the 15N isotropic chemical shift of 15N-labeled rabbit
cyt b
5 in q = 3.5 DMPC/DHPC
bicelles (A). Comparison of RampCP (a)
and RINEPT (b) polarization transfer schemes, where RampCP shows arginine
and lysine side chain resonances. 2D 13C chemical shift
correlation spectra of 13C,15N-labeled rabbit
cyt b
5 in bicelles (B). CTUC COSY (a)
and DARR (b) spectra are pictured, with amino acid cross peaks labeled
in (a). Collage of parts of two figures reprinted with permission
from ref (283). Copyright
2008 John Wiley & Sons, Inc.
11
Lipid–Protein Interactions by SLF-NMR
Spectroscopy of Bicelles
In addition to the study of protein
structure and dynamics, bicelles
can also be used to determine the effect that a protein has on the
surrounding lipid bilayer. Traditionally, the addition of deuterated
lipids to liposomes has been used to determine site-specific lipid
order parameters in 2H NMR experiments.
300,301
2H NMR investigation of deuterated lipid probes has been
applied to bicelles; but deuteration of lipids is costly and was found
to alter thermotropic behavior while site-specific assignment is ambiguous.
302
As an alternative approach, SLF experiments
were employed to study
the long-chain lipid molecules in a bicelle. SLF experiments, such
as the PISEMA experiment,
224
are described
in section 9.2. In the current context,
they correlate 1H–13C dipolar coupling
(which gives information on local order parameters) with 13C chemical shift (which
gives unambiguous identification of each 13C-site in the lipid molecule). Most notably,
these experiments
do not need isotopic labeling since natural-abundance 13C-nuclei in the lipid molecules
give sufficient intensity to carry
out two-dimensional experiments. By using the HIMSELF scheme,
229
SLF could be successfully applied to magnetically
aligned bicelles.
303,304
Advantages of using laboratory-frame
SLF experiments to measure small heteronuclear dipolar couplings from
mobile regions of bicelles and also from embedded ligands have also
been demonstrated.
305
By running
an SLF experiment on bicelles, 1H–13C
dipolar couplings can be measured for each resolved 13C-site,
yielding an order parameter profile as given in Figure 10. The open symbols in Figure
10 give
a 1H–13C dipolar coupling
value determined for each 13C-site in the DMPC molecule
as shown on top of Figure 10. As is known,
large dipolar couplings, that is, order parameters, are found in the
rigid bilayer region of the glycerol backbone, while order parameters
become small toward the mobile end of the choline headgroup and especially
toward the very mobile ends of the acyl chains. The SLF experiment
was used to characterize order parameter profiles for bicelles in
a wide range of temperatures, hydration levels, and q-ratios.
58
It was also used to characterize
the bilayer perturbation caused by an antimicrobial peptide MSI-78
303
and the ligands desipramine
305
and curcumin.
306
By use of the
SAMMY pulse sequence,
230
similar investigations
were carried out on bicelles containing the transmembrane segment
of phospholamban, an antimicrobial peptide (KIGAKI)3, and
cholesterol.
307
Recent studies have shown
that analogous experiments are also possible under magic angle spinning
conditions.
308−310
2D RPDLF experiments have been used to determine
the interaction of dendrimers with lipid bilayers.
311
Figure 10
Order parameter profiles of pure DMPC bilayers (open symbols)
and
DMPC bilayers in the presence of 10 wt % myelin basic protein (filled),
lines are meant to guide the eye. On top, a DMPC molecular scheme
gives the employed site naming scheme.
As a demonstration of the potential of this application
of SLF
experiments, we present our unpublished results on myelin basic protein
(MBP). MBP is a major component of the myelin sheath in the central
nervous system of higher vertebrates and is implicated in multiple
sclerosis. MBP is intrinsically unstructured in solution, but binds
to bilayers and may assume tertiary structure in membrane environment.
312−315
Previously, we had used 31P- and 2H NMR to
investigate the interaction of MBP with MLVs and mechanically aligned
bilayers.
316
For conducting SLF experiments,
we incorporated bovine MBP at 10 wt % into q = 3.5
DMPC/DHPC bicelles. The profile of 1H–13C dipolar couplings acquired on MBP-containing
bicelles is shown
as filled symbols in Figure 10. When compared
to results on identical bicelles without MBP, shown as open symbols,
several observations can be made. For the choline headgroup, almost
no change in local order is observable. In the glycerol backbone and
the acyl chains, the order parameter profile shows an overall decrease
in order parameter to about 90%. For the g1-carbon of the DMPC glycerol
backbone, three different 1H–13C splitting
values were observed. This may indicate a tight and specific interaction
of MBP with this particular site of the DMPC molecule in the lipid
bilayer.
12
Summary and Outlook
Lipid bicelles
have added yet another facet to the tremendous wealth
of lipid morphologies.
317
The structural
and thermodynamic properties of bicellar phases have been understood
in detail, and powerful techniques are available to quickly and reliably
establish phase diagrams and characterize morphological properties.
Properties of bicellar formulations are so well understood and so
many specific compositions have been established that today they are
routinely used in an ever increasing number of structural studies
of membrane proteins.
Some very specific and unique properties
of bicelles lie at the
core of their success, not only in NMR but in fields as diverse as
crystallography, chromatography, and drug formulations. Bicelles are
the most versatile model membrane system presently available. Dozens
of compositions have been tested and used, and there is most probably
potential for more. Bicelles with small q values
can be used for high-throughput solution NMR studies, while those
with large q values are ideal for solid-state NMR
studies. Since bicelles contain bulk water, they enable natural folding
of even those membrane-associated proteins that contain large soluble
domains and therefore render the feasibility of physiologically relevant
structural studies. This property of bicelles is therefore well suited
to investigate the structures of single-pass in addition to multipass
transmembrane proteins that are unusually difficult to study due to
their combination of hydrophobic and water-soluble domains. In fact,
very few structures of single pass TM proteins are reported in the
PDB. The most serious drawback of bicellar phases is the fact that
they are found in restricted regions of the phase diagram that are
bound by limiting temperatures and hydration levels that may be restrictive
for some application. Continuous effort is put into developing new
formulations where the region of bicellar phase is extended. New developments
include adding designed lipids with biphenyl-containing acyl chains
61,62
or stabilizing bicelles by sialylated lipids.
68
Today, bicelles have perfused most areas where structure
and dynamics
of membrane proteins are investigated. In fact, the current contribution
reads like a cross-section through the entire field of structural
biology of membrane proteins. As a result, the scope of this contribution—proteins
studied in bicelles—may feel too restricted in the very near
future, since the focus of the most interesting studies will be purely
on structural and functional aspects of membrane proteins. Bicelles
as the actual tool used to gain these insights—however powerful
they may be—will step into the background.