An Introduction to Modelling G Protein-Coupled Receptors
This page describes the current research in our lab to better understand the
molecular mechanisms involved in receptor-ligand interactions.
For this purpose we use
This particular page is an excerpt from a publication:
- van Rhee, A.M.; Fischer, B.; Jacobson, K.A.
Modelling the P2Y purinoceptor using rhodopsin as template.
Drug Design Discovery, 1995, 13: 133-154.
which describes how we approached the problem of visualizing the molecular
architecture of the G protein-coupled
It is the intention to add more features (both classical medicinal chemistry
and computational chemistry) as we go along, but time is the limiting factor.
You could make a bookmark now, and check in every now and then.
A very characteristic feature of
G protein-coupled receptors
(GPCRs) is their overall topology:
They all have similar
with seven stretches of increased hydrophobicity, most probably corresponding
to alpha-helical regions spanning the cell membrane.
Unfortunately, isolation, purification and crystallization of
as for other GPCRs, remains to be demonstrated.
Not only is a crystallographic structure as yet unobtainable, but the very
limited quantities of receptor protein present in the membrane, and isolation
problems, prohibit the use of modern techniques, such as nuclear magnetic
resonance spectroscopy, towards structure elucidation.
of the ligand binding site and
have been shown to be useful techniques in understanding receptor-ligand
interactions, but is particularly in the case of
restricted by the lack of suitable radioligands.
A possible further approach is to construct models of the receptors and their
ligand complexes using molecular modelling, as was first proposed by
Hibert et al.
On these pages we present models of the chick
and the human
based on the electron density map of rhodopsin
, rather than on the bacteriorhodopsin template
Hibert et al.
The models are verified by incorporation of site-directed
and ligand affinity data.
Software and Hardware.
Calculations and manipulations were performed using the
Kyte-Doolittle hydrophobicity and
Emini surface probability
parameters were calculated using a 7 amino acid window. With these parameters,
(TMs) were identified.
Sequences of the putative transmembrane domains were aligned manually using
the alignment procedure described on our
Helices were built from the full length of the TM, using the Biopolymer module
in the Insight II program. The N terminus was capped with an acetamido group,
and the C terminus was capped with a carboxamido group. The secondary structure
was assumed to be a right-handed alpha helix (default phi and psi angles from
the Biopolymer module). After generation of the Amber atom type parameters and
template charges, the helices were energy minimized as described in the
Energy Minimization section.
The energy minimized helices were converted to
Protein Data Bank
(PDB) format files and imported in the Quanta program. Coils (an alpha
carbon backbone representation of the helix) of the minimized helices were
drawn, that resemble the helical wheel representation to aid in orienting
the individual helices towards each other.
The following constraints were used constructing the helical bundle:
- 1. The helical axes of the first, third, fifth and seventh helices were
quasi-antiparallel to those of the second, fourth and sixth helices.
- 2. The hydrophobic side of each helix was facing the lipid phase and the
hydrophilic side of each helix was facing either another helix or the pore
formed by the helical bundle.
- 3. Conserved residues, either identical throughout a subset or highly
homologous, determined the orientation of each helix relative to the other
- 4. Distances in the electron density map of
correlated to atomic coordinates in the model. This was obtained through
triangulation of the electron density map and conversion of the coordinates to
a grid on the screen.
- 5. The assembly of helices maintained a clockwise order, when seen from
the intracellular side, as argued by
- 6. None of the helices were intersecting.
The individual helices generated with Insight II's Biopolymer module were
energy minimized in Discover using a stepwise process. Initially, 200 steps of
Steepest Descent were performed, followed by minimization using the Conjugate
Gradient (CG) method until the gradient reached a value below 0.1
kcal/mol/Å. Use of the Amber forcefield in Discover required
all calculations the 1-4 nonbonded interactions were scaled by a factor 0.5,
and the dielectric constant was assumed to be distance independent with a
magnitude of 4. The bond, theta, phi, out-of-plane, nonbonded and Coulombic
interactions were all used to obtain the final energy, but were not expressly
The helical bundles generated with Quanta were energy minimized in Discover in
a stepwise process. Initially, 500 steps CG were performed with the backbone
of the helices tethered with a force constant of 100 kcal/Å.
consecutive runs (500 steps CG each), the force constant was reduced to 50
kcal/Å, then 25 kcal/Å and, finally, to 0
Selective and/or specific ligands for the receptors were fully minimized using
the MNDO hamiltonian of MOPAC. All ligands were rigidly docked into the helical
bundle using graphical manipulation coupled to continuous energy monitoring,
i.e. the ligand was manually docked into the binding site without
relaxing the atomic coordinates of either ligand or protein while continuously
calculating the energy of the whole. When a final position was reached,
consistent with a low local energy and known pharmacological data, the complex
of receptor and ligand was subjected to a minimization run of 4000 steps CG
(or until the gradient was < 0.1 kcal/mol/Å). Charges for the ligands
were imported from the MOPAC output files.
We will now briefly discuss the results obtained through this approach,
but the information specific to either the
receptor is kept on separate pages.
Alignment of G protein-coupled receptors
In TM1, the motif GXXXN (P2Y) or GXXGN
(P2U) occurs in P2 purinoceptors, rather than the
GN motif present in biogenic amine or adenosine receptors. The
however, are not exclusively used by P2 receptors, but are shared
with, e.g., the PGE3-II
(GXXGN) and the PAF (GXXXN) receptors. In
all sequences the last 5 C-terminal residues of this helix are frequently
occupied by lysine or arginine residues, indicating the end of the
transmembrane domain. Such basic residues may serve as 'membrane
and are useful in determining the position of the helix in the lipid
In TM2, the residue preceding the conserved leucine in the LXXXD
motif is a conserved serine for the biogenic amine receptors, but is either
an asparagine or a histidine in the P2Y and P2U
receptors, respectively. The asparagine is conserved among the P2Y,
AT1A, CKR1, IL-8A, PAF, NK2 receptors, the opsins and rhodopsin.
The histidine is shared between P2U and thrombin receptors.
Another difference between biogenic amine receptors and P2 receptors
is the position of the conserved proline relative to the conserved aspartate.
Although absent in the muscarinic receptor, the proline is consistently spaced
by 8 residues from the aspartate in the other biogenic amine receptors, whereas
in many other receptors, the P2 receptors included, only 7 residues
separate these two residues.
This last difference is possibly significant since the proline is located near
the luminal side of the receptor protein, which is thought to be important for
The only exceptions, observed so far, to the conservation of the aspartate
occur in the substance P receptor where it is substituted with a glutamate,
and in the gonadotropin-releasing hormone receptor where an asparagine replaces
The conserved aspartate in TM2 was shown by
Horstman et al
to be a sodium-dependent allosteric regulatory site in the
The DRY motif, characteristic of the third transmembrane domain in
biogenic amine receptors, is replaced by a HRY motif in the
P2Y1 receptor (HRC in the P2U receptor).
This motif has not been found in other receptors.
The only other substitution for the conserved aspartate, seems to be the D to
E in, e.g., the TXA2, PGE3-II, opsin and rhodopsin
sequences. The significance of this deviation is not clear, but is supposedly
important for coupling of the P2 receptors to G proteins and not
for ligand binding, the subject of this study.
One or more of the first 6 positions in the N-terminal sequence of TM4 are
generally (37 out of 40
aligned sequences of family A GPCRs
) occupied by lysine or arginine residues. Again these residues could
well serve as 'membrane anchors'. They seem to be occurring more frequently
towards the cytosolic side of helices than on the luminal side, thus reflecting
the polarity of the membrane. These 'membrane anchors' also occur much less
frequently in the C-terminal sequences of helices, than in the N-terminal
sequences, as is demonstrated by the alignment for TM5. The reason for this
disparity is believed to be the direction in which the side-chains are
pointing, i.e. opposite to the propagation direction of the helix,
allowing more rotational freedom for lysine and arginine residues near the
cytosolic N-terminus than for the cytosolic C-terminus.
There are no other marked differences between the
various receptor subfamilies for either TM4 or TM5.
The CXXP motif used for the alignment of TM6 could be substituted
by WXP for most receptors, but the P2 receptors
deviate at this position. The P2Y receptor has a tyrosine at the
position of the conserved tryptophan, and this seems to be rather unique. The
phenylalanine in the P2U receptor at the same position occurs more
frequently, such as in the thrombin, and various orphan receptors.
Characteristic of the P2 receptors is the presence of a lysine
(P2Y: K269) or an arginine (P2U: R265) at an otherwise
non-conserved position. It shares this feature only with the endothelin
receptors (both ET-A and ET-B subtypes) and the orphan receptor RSC338. The
proposed 'membrane anchors' occur quite frequently at the first position in
the alignment of this transmembrane domain.
TM7 is best aligned by means of the NPXXY motif. However, the
P2 receptors, the gonadotropin-releasing hormone receptor, the
TXA2, PGE3-II, and several orphan receptors constitute
an exception to this rule. The conserved asparagine is replaced by an
aspartate residue in the latter cases. A non-conserved aspartate (D352) in
the 5HT1B receptor aligns perfectly with aspartates in the IL-8A
receptor (D288), and in the D1B receptor (D342), a glutamine in
the P2Y receptor (Q296) and a lysine in the P2U receptor
(K289). Arginines 299 (P2Y) and 292 (P2U) align with
Y530 in the m3, E291 in the IL-8A and E287 in the CKR1 receptor, respectively.
Both positions are near the luminal side of the receptor and are likely
involved in ligand binding. The K and R residues occurring near the C-terminus
are probably better characterized as 'membrane anchors'.
If you are interested in the
alignment of over 150 GPCRs,
mutagenesis studies of GPCRs,
just follow these links. You might want to read our
Bacteriorhodopsin, included in this study to facilitate comparison with other
modelling studies, [e.g.,
is clearly not related to any of the GPCR subfamilies. The degree of
relatedness between bacteriorhodopsin and GPCRs shown in the
is probably an overestimate of the actual distance, caused by the residue
alignment procedure of the GCG program.
and Emini surface probability analysis.
At the portion of the sequence where proteins are supposed to
cross the lipid bilayer membrane, the hydrophobicity of that segment is usually
increased relative to the cytosolic and luminal portions. The procedure
Kyte and Doolittle
uses this phenomenon to identify transmembrane domains in protein sequences
with unknown structure. In the case of GPCRs, these transmembrane domains
are thought to be alpha helical, and more importantly amphiphilic. The
amphiphilicity of the TMs supposedly reflects the way a GPCR is built out of
seven of these helical transmembrane domains. Consequentially, the
hydrophobicity profile of these GPCRs is not as clear as one would wish.
An example of this effect is the poor separation of the sixth (VI) and
seventh (VII) TM in both the P2Y1 receptor profile (below) and
the bacteriorhodopsin profile (not shown).
To facilitate identification of TMs, the Kyte-Doolittle hydrophobicity method
is often supplemented with methods describing other sequence dependent vectorial
parameters, such as the 'conservation moment' and
for each helix or other computational methods
. Use of the 'conservation moment' method requires a particularly well
defined alignment of highly homologous sequences, and can not be applied to the
P2 GPCRs because of the low sequence similarity of these receptors
with any other GPCR subfamily. The 'hydrophilic moment' method relies on a
database of partial hydrophilic factors for any given amino acid and is
dependent on the method with which these factors were measured. Furthermore,
the high incidence of basic residues in the P2Y receptor sequence
greatly influences the results obtained with this method.
In contrast, the Emini surface probability
can be calculated from a given
sequence, indicating the propensity of a stretch of amino acids (the window)
to be at the surface of a protein. The combination of an increase in the
Kyte-Doolittle hydrophobicity index
and a decrease in the Emini surface probability index was successfully applied
to predict the TMs in the P2Y1 receptor (see figure above) and in
the reference protein bacteriorhodopsin. The start and end residue of each
helix was usually predicted within 3 residues of the TMs used by
Henderson et al.
The only major deviation in the P2Y1 receptor prediction occurred
at the N-terminus of TM7 (VII). This particular sequence contains 3
hydrophilic residues (K, Q and R) that are possibly involved in ligand
binding, thus delaying the start of the predicted TM.
Building the receptor model.
G protein-coupled receptors
has become an important tool in understanding drug-receptor interactions
and in the development of new ligands for these receptors.
The first widely accepted method was the homology modeling method
Hibert et al.
This method involved the alignment of the receptor sequence with the sequence
of bacteriorhodopsin, and the subsequent mapping of the sequence onto the
structure of bacteriorhodopsin that was determined by
Henderson et al.
Bacteriorhodopsin is a proton pump in the outer membrane of Halobacterium
halobium, and lacks any functional or sequence homology with GPCRs.
Nevertheless, the procedure was based on the assumption that there would be
considerable structural homology. This structural homology was inferred by
the extraordinary similarity in the hydrophobicity plots, or
of the biogenic amine subfamily of GPCRs and bacteriorhodopsin.
Recently, a low resolution electron density map of rhodopsin, a true member
of the GPCR superfamily, was published.
The low sequence homology with bacteriorhodopsin, the structural
differences that must arise from the different placement of proline residues
(causing bends in helices) in bacteriorhodopsin- and GPCR-sequences, and the
availability of an electron density map of a true member of the GPCR
superfamily prompted us to adapt a new method to build models of
This novel method is based on a computational approach rather than strict
compliance with the atomic coordinates of a distantly related protein,
albeit with higher resolution.
To ascertain the viability of modelling transmembrane proteins (based on the
structure of rhodopsin
) by the methods described in the paper, we built models of
bacteriorhodopsin (data not shown) based on the electron density map of
and rhodopsin (data not shown) based on the electron density map of
bovine rhodopsin as published by
Schertler et al.
Root mean square (r.m.s.) distance calculations on superimposed structures
were performed to establish how well the models fitted the experimental data.
The bacteriorhodopsin model that was constructed, compared with the one
deposited in the PDB,
had an r.m.s. value of 2.15 Å when measured on all backbone atoms
and 2.06 Å on all Calpha atoms. Both values are lower than
the resolution of the model, i.e. 3.5 Å. When the rhodopsin model was
compared with the bacteriorhodopsin model by
Henderson et al,
however, the r.m.s. value increased to 16.96 Å when measured on all
backbone atoms and 16.86 Å on all Calpha atoms. These
rather high values indicate that there are more structural differences between
bacteriorhodopsin and rhodopsin than have been assumed thus
In our opinion, the position of the proline residues in the helices is a
major determinant in this matter. As can be seen from the
alignment for the helices,
proline residues occur less frequently and at different positions in the
sequence of bacteriorhodopsin than in the sequence of rhodopsin. The
influence of proline residues in alpha-helices was extensively studied by
Sankararamakrishnan and Vishveshwara and
We have found that applying the Amber forcefield to our calculations yields
results in agreement with
Sankararamakrishnan and Vishveshwara and
and that those results are consistent with data
obtained from a crystallographic study of the transmembrane protein
photosynthetic reaction center (PDB:1prc), and globular proteins such as
phosphoglycerate kinase (PDB:3pgk), lysozyme (PDB:1l27) and alcohol
dehydrogenase (PDB:5adh). The differences between the structures derived
from the electron density maps of bacteriorhodopsin and rhodopsin also
illustrate why helical wheel models, widely used by molecular biologists,
are highly imprecise when applied to GPCRs.
The general picture looks like this:
For a detailed view of either our
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