Lummis, S. C. R. et al. Cis-trans isomerization at a proline opens the pore of a neurotransmitter-gated ion channel. Nature 438, 248-252

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
Nature (Impact Factor: 41.46). 12/2005; 438(7065):248-52. DOI: 10.1038/nature04130
Source: PubMed


5-hydroxytryptamine type 3 (5-HT3) receptors are members of the Cys-loop receptor superfamily. Neurotransmitter binding in these proteins triggers the opening (gating) of an ion channel by means of an as-yet-uncharacterized conformational change. Here we show that a specific proline (Pro 8*), located at the apex of the loop between the second and third transmembrane helices (M2-M3), can link binding to gating through a cis-trans isomerization of the protein backbone. Using unnatural amino acid mutagenesis, a series of proline analogues with varying preference for the cis conformer was incorporated at the 8* position. Proline analogues that strongly favour the trans conformer produced non-functional channels. Among the functional mutants there was a strong correlation between the intrinsic cis-trans energy gap of the proline analogue and the activation of the channel, suggesting that cis-trans isomerization of this single proline provides the switch that interconverts the open and closed states of the channel. Consistent with this proposal, nuclear magnetic resonance studies on an M2-M3 loop peptide reveal two distinct, structured forms. Our results thus confirm the structure of the M2-M3 loop and the critical role of Pro 8* in the 5-HT3 receptor. In addition, they suggest that a molecular rearrangement at Pro 8* is the structural mechanism that opens the receptor pore.

© 2005 Nature Publishing Group
Cistrans isomerization at a proline opens the pore
of a neurotransmitter-gated ion channel
Sarah C. R. Lummis
*, Darren L. Beene
*, Lori W. Lee
, Henry A. Lester
, R. William Broadhurst
& Dennis A. Dougherty
5-Hydroxytryptamine type 3 (5-HT
) receptors are members of
the Cys-loop receptor superfamily
. Neurotransmitter binding in
these proteins triggers the opening (gating) of an ion channel by
means of an as-yet-uncharacterized conformational change. Here
we show that a specific proline (Pro 8*), located at the apex of
the loop between the second and third transmembrane helices
, can link binding to g ating through a cistrans iso-
merization of the protein backbone. Using unnatural amino acid
mutagenesis, a series of proline analogues with varying preference
for the cis conformer was incorporated at the 8* position. Proline
analogues that strongly favour the trans conformer produced non-
functional channels. Among the functional mutants there was a
strong correlation between the intr insic cistrans energy gap of
the proline analogue and the activation of the channel, suggesting
that cistrans isomerization of this single proline provides the
switch that interconverts the open and closed states of the channel.
Consistent with this proposal, nuclear magnetic resonance studies
on an M2–M3 loop peptide reveal two distinct, structured forms.
Our results thus confirm the structure of the M2–M3 loop and the
critical role of Pro 8* in the 5-HT
receptor. In addition, they
suggest that a molecular rearrangement at Pro 8* is the structural
mechanism that opens the receptor pore.
The neurotransmitter binding site in the Cys-loop superfamily of
ion channels is located about 60 A
from the channel pore, presenting
a conundrum as to the molecular events that link binding and
. Evidence implicates the M2–M3 loop, and in low-
resolution structural studies this region interacts with loops 2 and
7 of the extracellular domain (Fig. 1)
. In the cation-selective
nicotinic acetylcholine (nACh) and 5-HT
receptors, the apex of
the M2–M3 loop contains a conserved proline (Pro 8*) that is ideally
placed to provide a hinge for movement of the channel-lining M2
helix. This proline is essential for receptor function in the 5-HT
receptor. We found that replacement of Pro 8* with Gly, Ala, Cys, Val,
Lys or Asn gave receptors that were trafficked to the membrane
properly and displayed wild-type binding properties for a radio-
labelled antagonist (Supplementar y Information); however, all
receptors were non-functional
. This indicates that mutations at
Pro 8* affect receptor function by altering gating, not ligand binding
or folding/assembly, and that a unique characteristic of proline is
absolutely required for the gating of the receptor.
To explore the possible role of Pro 8* in channel gating, we used
nonsense suppression in Xenopus oocytes to incorporate a series of
proline analogues (Fig. 2a) at position 8* of the 5-HT
. This
technique involves inserting a nonsense codon (TAG) in place of
the proline codon into the DNA encoding the receptor subunit,
synthesizing messenger RNA, and injecting this into Xenopus oocytes
along with a transfer RNA that both recognizes the TAG codon and
has the appropriate proline analogue attached at the 3
end. The
resulting mutant receptors were examined using voltage-
clamp analysis of 5-HT-induced whole-cell responses and
When incorporated into a protein, proline disrupts main-chain
hydrogen bonding, because it lacks a backbone NH moiety
Figure 1 | Overall layout of the 5-HT
receptor showing the extracellular
-sheet) and transmembrane (
-helical) regions. Shown
are two adjacent subunits from a homology model of the 5-HT
built from AChBP (extracellular domain)
and the nACh receptor
transmembrane domain (transmembrane domain)
. The binding site Trp is
purple; loop 7 is red; loop 2 is green; the conserved Leu thought to
contribute to the gate is yellow (space filling); and strand
7 is dark grey. The
region corresponding to the peptide studied by NMR (Fig. 4), comprising
the M2–M3 loop and parts of M2 and M3, is shown in blue, with Pro 8* in
space-filling model.
Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
Division of Chemistry and Chemical Engineering, and
Division of Biology,
California Institute of Technology, Pasadena, California 91125, USA.
*These authors contributed equally to this work.
Vol 438|10 November 2005|doi:10.1038/nature04130
Page 1
© 2005 Nature Publishing Group
Previously, we probed a highly conserved Pro in the middle of the
first transmembrane helix (M1) by substitution with an
acid such as Vah (
-hydroxyvaline; Fig. 2a), which similarly lacks an
. In M1 Vah substitutes effectively for Pro; however, at position
8* Vah produces non-functional receptors. Similarly, the N-methyl
amino acids Sar (sarcosine) and N-Me-Leu give non-functional
Proline is the only natural cyclic amino acid. Incorporation of nine
cyclic proline analogues at position 8* yielded mixed results: some
produced functional receptors and others did not (Fig. 2a). Thus,
neither the cyclic structure nor the lack of a hydrogen bond donor are
key to the proper functioning of Pro at 8*.
Proline is also unusual in forming cis peptide bonds at a frequency
(,5%) much higher than any other naturally occurring amino acid
, reflecting an intrinsic diminution of the energy gap
between cis and trans forms in proline
. The analogues 2,4-CH
and 2-Me-Pro show a reduced preference for a cis conformation
relative to Pro
, and these produced non-functional receptors (that
is, no current was seen in response to normally saturating concen-
trations of serotonin). Immunocytochemical experiments revealed
that these receptors did reach the cell surface (Supplementary
Of the proline analogues that give functional receptors, t-4F-Pro
and c-4F-Pro give near-wild-ty pe EC
(effector concentration for
half-maximum response) values (1.38 ^ 0.06 and 1.15 ^ 0.12
respectively), and also show intrinsic cistrans preferences similar
to native proline. Other analogues, however, show much greater
propensities to adopt the cis conformer. Most extreme is Dmp
(5,5-dimethylproline), which strongly favours the cis form
(Table 1). Incorporation of this amino acid at position 8* resulted
in a 60-fold decrease in EC
. Furthermore, in oocytes that expressed
Dmp-containing receptors, agonist exposure led to partially irrever-
sible inactivation, as evidenced by a continual increase in standing
current after initial receptor activation; this current could be sub-
stantially reversed by the addition of the channel blocker TMB-8
(ref. 11) (Fig. 3). Dmp and other analogues with high cis preference
showed low and variable expression levels in Xenopus oocytes. This
could reflect difficulties in folding the protein when a key proline is
present in an unconventional conformation. Overall, we found three
types of behaviours for incorporation of proline analogues. Pro
derivatives strongly favouring trans produced no responses to agonist
but did express and were inserted into the membrane. Intermediate
derivatives produced responses with a range of EC
values. The
most cis-producing residue produced highly sensitive receptors that
displayed partially irreversible activation.
An evaluation of a series of Pro analogues that exhibit a range of
intrinsic cistrans energy gaps revealed a remarkable trend. As shown
in Fig. 2b, a linear relationship was observed between the cistrans
energy gap of the proline analogue (DDG(ct)) and activation of the
, the functional output we measure, reflects a composite of
binding and gating events. However, as noted above, substitution at
Pro 8* by natural amino acids does not change antagonist binding
affinity. In addition, the apparent affinity of the 5-HT
competitive antagonist MDL72222 is not significantly altered when
Pro 8* is mutated to Pip (pipecolic acid) or Dmp (see Supplementary
Information). These data show that for amino acids with a wide
range of cis preferences (,0.1–71%) at Pro8*, the binding site is
unperturbed. We therefore consider the variations in EC
to reflect
changes in receptor gating, not binding
, justifying the free energy
treatment of Fig. 2b.
The slope of the line in Fig. 2b is 1, within experimental error. This
indicates that the full energetic perturbation of the proline cistrans
equilibrium induced by the mutation is felt in the gating equilibrium.
Together, these observations provide a compelling link between
the conformational isomerization at residue 8* and the gating of
the 5-HT
To provide further support that a proline in the M2–M3 loop can
serve as a structural switch, we used nuclear magnetic resonance
Figure 2 | Unnatural amino acid mutagenesis. a, Residues used in this
study. As noted in the text, the conventional amino acids Gly, Ala, Cys, Val,
Lys and Asn also give non-functional channels. b, Linear energy correlation
between cistrans isomerization and receptor activation. Data are from
Table 1. Error bars (s.e.m.) are plotted for all data points, but for Pro, Pip and
Aze they are partially obscured by the marker.
Table 1 | Influence of proline isomerism on receptor function
Residue Per cent cis*EC
(kcal mol
(kcal mol
Pro 5 1.29 ^ 0.07 0 0
Pip 12 0.75 ^ 0.06 20.54 20.32
Aze 18 0.42 ^ 0.03 20.85 20.66
Tbp 55 0.030 ^ 0.024 21.86 21.73
Dmp 71 0.021 ^ 0.009 22.28 22.47
*Determined from studies of model peptide systems reported previously
. Because
variations are seen depending on methodology and exact model system, all values are
referenced to the cistrans ratio seen for Pro in the same study, and Pro is set to 5%, the
value obtained from statistical surveys of protein structures.
Values are ^s.e.m.
Values are relative to proline.
§Equals 2RTln(EC
NATURE|Vol 438|10 November 2005 LETTERS
Page 2
© 2005 Nature Publishing Group
(NMR) spectroscopy to evaluate the structure of a 20-amino-acid
peptide spanning the M2–M3 loop (SDTLPATAIGTPLIGVYFVV;
Pro 8* is italic). When solubilized in a micellar solution of SDS,
this relatively short sequence is structured, with two segments
flanking Pro 8* displaying a significant amount of
-helical character
(residues 6–10 and 13–20 of the peptide; see Supplementary Infor-
mation). Thus, key features of the M2–M3 loop, as reported in the
low-resolution nACh receptor structure
(see also Fig. 1), are
recapitulated in the model peptide. Interestingly, two conformers
are clearly evident in the peptide structure, with the major form
about five times more prevalent than the minor form (Fig. 4). In the
major conformer Pro 8* was assigned the trans conformation based
on observed nuclear Overhauser effect connections. Some features of
the minor form cannot be resolved due to overlapping resonances,
but the TOCSY (total correlated spectroscopy) spectrum clearly
shows that the two glycines that flank Pro 8* (positions 10 and 15
in the peptide; 6* and 11* in the protein) are in different environ-
ments in the two conformers, with both pairs of diastereotopic H
nuclei giving separate resonances in the minor conformer (Fig. 4).
These results are consistent wit h two conformations at Pro 8*
producing two conformers of the peptide.
We propose the following mechanism for gating in the 5-HT
receptor. In the closed state of the channel, Pro 8* is in the trans
Figure 4 |
H NMR of a model peptide. The H
fingerprint region of a
TOCSY spectrum for the 20-residue peptide discussed in the text resolves
signals for the major (blue) and minor (red) conformers in a micellar
solution of SDS at 298 K. Integration indicates that 13–20% of the minor
conformer is present. Signals arising from distinct H
or H
within a particular residue are connected with vertical lines.
Figure 3 | Current traces in voltage-clamp experiments (at approximately
and approximately I
) for receptors expressing unnatural amino
For Dmp at position 8* (residue 308 of 5-HT
), a full dose–response
range is given along with the TMB-8 block of standing cur rents seen after
receptor activation. Bars represent 5-HT application.
Figure 5 | A proposed gating mechanism. A single 5-HT
receptor subunit
is depicted, illustrating how transcis isomerization at Pro 8* (blue space-
filling model) could function as a hinge for movement of M2 (green) during
gating, moving the occluding Leu 9
residue (yellow) away from the channel
region. The open structure on the right was generated by manually
converting Pro 308 to the cis conformation and treating M2 as a rigid body.
Top: side view; bottom: top view, showing only M2, M3 and the M2–M3
LETTERS NATURE|Vol 438|10 November 2005
Page 3
© 2005 Nature Publishing Group
conformation. Binding of ligand initiates a structural change that
culminates in isomerization of Pro 8* to the cis form. This change at a
crucial pivot point reorients the M2 transmembrane helix, opening
the channel. We have crudely modelled the change that would occur
if Pro 8* isomerized from the trans to the cis conformation (Fig. 5),
treating the M2
-helix as a rigid body. Because of the hinge location
of Pro 8*, the structurally modest cistrans isomerization at this
single residue propagates to a substantial structural effect more than
adequate to gate the channel.
Our model also suggests a natural coupling between the agonist
binding site and the conformational change associated with gating.
Several workers have noted the proximity of loops 2 and 7 (the
eponymous Cys loop) to the M2–M3 loop
. Although the image
of Fig. 1 is not based on atomic-resolution data, Pro 8* in its position
at the apex of M2–M3 is in close proximity to both loops 2 and 7. It
has been proposed that loops 2 and 7 ‘lock’ the M2 helix in the closed
. Expanding upon this model, we propose that loops 2
and 7 act as a caliper to immobilize Pro 8* in a trans conformation.
Arrival of agonist causes a movement of the key binding site
tryptophan (Trp 183 in the 5-HT
receptor; Trp 149 in the nACh
. This Trp is directly linked to loop 7 by a six-amino-
acid stretch of sheet structure termed
7 (dark grey in Fig. 1). Thus,
the binding site Trp may be the actuator that, perhaps via
7, releases
the clamp on M2–M3. Pro 8* can then undergo a spontaneous (or
protein aided) cistrans isomerization, gating the channel.
The per cent cis values of Table 1 are based on model peptide
; in any particular context the equ ilibrium could be
perturbed. It may well be that structural features of the wild-type
receptor act to favour the cis conformer of the native proline at
position 8*, once the structural change as sociated with agonist
binding has occurred. There is also an issue of timescale. Estimates
of the opening rate for the 5-HT
receptor are in the 10–100 s
. Intrinsic prolyl cistrans isomerization rates in peptides are
within a factor of ten of this regime, and structural features of the
receptor could act to accelerate significantly the isomerization rate.
Protein prolyl isomerases are well known, and even a simple hydro-
gen bond to the proline amide nitrogen can accelerate isomerization
. It is possible that the receptor has incorporated struc-
tural features that facilitate cistrans isomerization. Therefore, prolyl
cistrans isomerization is a kinetically viable candidate for the gating
We have established a clear correlation between the conformation-
al preference of a single, specific proline residue and the gating
efficiency of a Cys-loop receptor. Proline has unique structural and
conformational properties, and it is found with anomalously high
frequency in the transmembrane regions of ion channels a nd
transporters, suggesting a key role in structural changes associated
with transmembrane signalling
. The unnatural amino acid muta-
genesis approach has allowed an exquisitely detailed probe of the
Pro 8* site, yielding an experimentally bas ed model of channel
opening involv ing a precise structural change at the amino acid
level that induces gating. The model is consistent with all available
structural data, and it suggests much future work. It will be inter-
esting to perform the same ‘proline scan’ on the nACh receptor,
which also contains a proline at position 8*, but which displays a
much faster opening rate. In contrast, other Cys-loop receptors do
not contain this proline, and the possibility of a cistrans isomeriza-
tion at a non-proline site or a completely different gating mechanism
should be explored.
Mutagenesis and preparation of cRNA and oocytes. Mutant 5-HT
subunits were developed using pcDNA3.1 (Invitrogen) containing the complete
coding sequence for the 5-HT
subunit from mouse neuroblastoma N1E-115
cells as previously described
. For nonsense suppression, the proline codon at
308 was replaced by TAG as previously described
. Wild type and mutant
receptor subunit coding sequences were then subcloned into pGEMHE. This
was linearized with Nhe1 (New England Biolabs) and cRNA synthesized using
the T7 mMESSAGE mMACHINE kit (Ambion). Oocytes from Xenopus laevis
were prepared and maintained as described previously
Synthesis of tRNA and dCA-amino acids. Unnatural amino acids were
chemically synthesized as nitroveratryloxycarbonyl (NVOC) protected cyano-
methyl esters and coupled to the dinucleotide dCA, which was then enzymati-
cally ligated to 74-mer THG73 tRNA
as detailed previously
. Immediately
before co-injection with mRNA, tRNA-aa was deprotec ted by photolysis.
Typically, 5 ng mRNA and 25 ng tRNA-aa were injected into stage V–VI oocytes
in a total volume of 50 nl. For control experiments, mRNA was injected in the
absence of tRNA, and with the THG73 74-mer tRNA. Experiments were
performed 18–36 h after injection.
Characterization of mutant receptors. 5-HT-induced currents were recorded
from individual oocytes using two-electrode voltage clamp with eithe r a
GeneClamp 500 amplifier or an OpusXpress system (Molecular Devices Axon
Instruments). All experiments were performed at 22–25 8C. Serotonin (creati-
nine sulphate complex, Sigma) was stored as 25 mM aliquots at 280 8C, diluted
in calcium-free ND96, and delivered to cells via computer-controlled perfusion
systems. The holding potential was 260 mV unless otherwise specified. EC
data were obtained from at least six independent experiments using oocytes from
at least three different batches. Further details are available in Supplementary
NMR. The NMR sample was prepared containing 1 mM peptide, 200 mM
sodium dodecyl-d25 sulphate, 150 mM sodium chloride, 20 mM sodium phos-
phate, 1 mM EDTA, 20
M 3,3,3-trimethylsilylpropionate and 10% D
pH 6.0 to a final volume of 550
l in a 5-mm Ultra-Imperial grade NMR tube
(Wilmad). All experiments were recorded at both 298 K and 303 K on a Bruker
DRX500 spectrometer equipped with a z-shielded gradient triple resonance
probe using standard procedures. Two dimensional nuclear Overhauser and
exchange spectroscopy (NOESY) and TOCSYexperiments, with mixing times of
200 and 72.5 ms, respectively, were collected with 256 and 1,024 pairs of complex
points and acquisition times of 26 and 102 ms in the indirectly and directly
acquired dimensions, respectively. Data processing and analysis were carried out
on a Silicon Graphics O2 workstation using the programs AZARA and CCPNmr
Received 24 March; accepted 8 August 2005.
1. Lester, H. A., Dibas, M. I., Dahan, D. S., Leite, J. F. & Dougherty, D. A. Cys-loop
receptors: new twists and turns. Trends Neurosci. 27, 329–-336 (2004).
2. Meeus, N. & Lummis, S. C. R. Proline 307 in the mouse 5–-HT
receptor links
binding and function. pa2online 1, 015P (2003).
3. Lummis, S. C. R. The transmembrane domain of the 5-HT
receptor: its role in
selectivity and gating. Biochem. Soc. Trans. 32, 535–-539 (2004).
4. Bera, A. K., Chatav, M. & Akabas, M. H. GABA
receptor M2–-M3 loop
secondary structure and changes in accessibility during channel gating. J. Biol.
Chem. 277, 43002–-43010 (2002).
5. Grosman, C., Salamone, F. N., Sine, S. M. & Auerbach, A. The extracellular
linker of muscle acetylcholine receptor channels is a gating control element.
J. Gen. Phys. 116, 327–-339 (2000).
6. Lynch, J. W., Han, N. L. R., Haddrill, J., Pierce, K. D. & Schofield, P. R. The
surface accessibility of the glycine receptor M2–-M3 loop is increased in the
channel open state. J. Neurosci. 21, 2589–-2599 (2001).
7. Kash, T. L., Jenkins, A., Kelley, J. C., Trudell, J. R. & Harrison, N. L. Coupling of
agonist binding to channel gating in the GABA
receptor. Nature 421, 272–-275
8. Unwin, N. Refined structure of the nicotinic acetylcholine receptor at 4 A
resolution. J. Mol. Biol. 346, 967–-989 (2005).
9. Nowak, M. W. et al. In vivo incorporation of unnatural amino acids into ion
channels in Xenopus oocyte expression system. Methods Enzymol. 293,
504–-529 (1998).
10. Macarthur, M. W. & Thornton, J. M. Influence of proline residues on protein
conformation. J. Mol. Biol. 218, 397–-412 (1991).
11. Dang, H., England, P. M., Farivar, S. S., Dougherty, D. A. & Lester, H. A. Probing
the role of a conserved M1 proline residue in 5-hydroxytryptamine(3) receptor
gating. Mol. Pharm. 57, 1114–-1122 (2000).
12. Jabs, A., Weiss, M. S. & Hilgenfeld, R. Non-proline cis peptide bonds in
proteins. J. Mol. Biol. 286, 291–-304 (1999).
13. Dugave, C. & Demange, L. Cis-trans isomerization of organic molecules and
biomolecules: Implications and applications. Chem. Rev. 103, 2475–-2532
14. Colquhoun, D. Binding, gating, affinity and efficacy: the interpretation of
structure-activity relationships for agonists and of the effects of mutating
receptors. Br. J. Pharmacol. 125, 924–-947 (1998).
15. Miyazawa, A., Fujiyoshi, Y. & Unwin, N. Structure and gating mechanism of the
acetylcholine receptor pore. Nature 423, 949–-955 (2003).
16. Taly, A. et al. Normal mode analysis suggests a quaternary twist model for the
nicotinic receptor gating mechanism. Biophys. J. 88, 3954–-3965 (2005).
NATURE|Vol 438|10 November 2005 LETTERS
Page 4
© 2005 Nature Publishing Group
17. Zhong, W. et al. From ab initio quantum mechanics to molecular neurobiology:
A cation-
binding site in the nicotinic receptor. Proc. Natl Acad. Sci. USA 95,
12088–-12093 (1998).
18. Beene, D. L. et al. Cation-
interactions in ligand recognition by serotonergic
) and nicotinic acetylcholine receptors: The anomalous binding
properties of nicotine. Biochemistry 41, 10262–-10269 (2002).
19. Brejc, K. et al. Crystal structure of an ACh-binding protein reveals the
ligand-binding domain of nicotinic receptors. Nature 411, 269–-276 (2001).
20. Gao, F. et al. Agonist-mediated conformational changes in acetylcholine-
binding protein revealed by simulation and intrinsic tryptophan fluorescence.
J. Biol. Chem. 280, 8443–-8451 (2005).
21. An, S. S. A. et al. Retention of the cis proline conformation in tripeptide
fragments of bovine pancreatic ribonuclease A containing a non-natural
proline analogue, 5,5-dimethylproline. J. Am. Chem. Soc. 121, 11558–-11566
22. Kern, D., Schutkowski, M. & Drakenberg, T. Rotational barriers of cis/trans
isomerization of proline analogues and their catalysis by cyclophilin. J. Am.
Chem. Soc. 119, 8403–-8408 (1997).
23. Halab, L. & Lubell, W. D. Use of steric interactions to control peptide turn
geometry. Synthesis of type VI
-turn mimics with 5-tert-Butylproline. J. Org.
Chem. 64, 3312–-3321 (1999).
24. Breitinger, H. G., Geetha, N. & Hess, G. P. Inhibition of the serotonin 5-HT
receptor by nicotine, cocaine, and fluoxetine investigated by rapid chemical
kinetic techniques. Biochemistry 40, 8419–-8429 (2001).
25. Kelley, S. P., Dunlop, J. I., Kirkness, E. F., Lambert, J. J. & Peters, J. A. A
cytoplasmic region determines single-channel conductance in 5-HT
Nature 424, 321–-324 (2003).
26. Cox, C. & Lectka, T. Intramolecular catalysis of amide isomerization: Kinetic
consequences of the 5-NH- -N
hydrogen bond in prolyl peptides. J. Am. Chem.
Soc. 120, 10660–-10668 (1998).
27. Brandl, C. J. & Deber, C. M. Hypothesis about the function of membrane-
buried proline residues in transport proteins. Proc. Natl Acad. Sci. USA 83,
917–-921 (1986).
28. Sansom, M. S. P. & Weinstein, H. Hinges, swivels and switches: the role of
prolines in signalling via transmembrane
-helices. Trends Pharm. Sci. 21,
445–-451 (2000).
29. Beene, D. L., Price, K. L., Lester, H. A., Dougherty, D. A. & Lummis, S. C. R. L.
Tyrosine residues that control binding and gating in the 5-hydroxytryptamine
receptor revealed by unnatural amino acid mutagenesis. J. Neurosci. 24,
9097–-9104 (2004).
30. Reeves, D. C., Sayed, M. R. F., Chau, P. L., Price, K. L. & Lummis, S. C. R.
Prediction of 5-HT
receptor agonist-binding residues using homology
modeling. Biophys. J. 84, 2338–-2344 (2003).
Supplementary Information is linked to the online version of the paper at
Acknowledgements S.C.R.L. is a Wellcome Trust Senior Research Fellow in
Basic Biomedical Science. The work at Caltech was supported by the National
Institutes of Health. We thank K. L. Price and A. J. Thompson for assistance with
Author Information Reprints and permissions information is available at The authors declare no competing
financial interests. Correspondence and requests for materials should be
addressed to D.A.D. (
LETTERS NATURE|Vol 438|10 November 2005
Page 5
  • Source
    • "Agonist binding induces rigid body motions, which are translated into transient movements of the pore lining M2 a helices of the transmembrane domain (TMD) by a series of loops at the ECD/TMD interface (Althoff et al., 2014; Sauguet et al., 2014; Unwin and Fujiyoshi, 2012). Considerable attention has focused on elucidating the gating movements of these interfacial loops, which form the primary allosteric path leading from the agonist site to the channel gate (Grutter et al., 2005; Jha et al., 2007; Lee and Sine, 2005; Lummis et al., 2005). In contrast, structures not directly involved in the primary allosteric path have received less attention, even though a number of allosteric modulators influence gating via these auxiliary sites (Figure 1A). "
    [Show abstract] [Hide abstract] ABSTRACT: The gating of pentameric ligand-gated ion channels is sensitive to a variety of allosteric modulators that act on structures peripheral to those involved in the allosteric pathway leading from the agonist site to the channel gate. One such structure, the lipid-exposed transmembrane α helix, M4, is the target of lipids, neurosteroids, and disease-causing mutations. Here we show that M4 interactions with the adjacent transmembrane α helices, M1 and M3, modulate pLGIC function. Enhanced M4 interactions promote channel function while ineffective interactions reduce channel function. The interface chemistry governs the intrinsic strength of M4-M1/M3 inter-helical interactions, both influencing channel gating and imparting distinct susceptibilities to the potentiating effects of a lipid-facing M4 congenital myasthenic syndrome mutation. Through aromatic substitutions, functional studies, and molecular dynamics simulations, we elucidate a mechanism by which M4 modulates channel function. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Full-text · Article · Jul 2015 · Structure
  • Source
    • "Reorganization of transmembrane helices and rigid body rotation of an extracellular domain are the important changes observed in the open and closed state structures of pentameric ligand-gated ion channels [26]. Using a series of proline analogs, experiments have suggested that cis–trans isomerization of a single proline residue provides a molecular switch for inter-converting open and closed states in the channels formed by 5HT3 receptors which are members of Cys-loop receptor superfamily [27]. "
    [Show abstract] [Hide abstract] ABSTRACT: The superfamily of major intrinsic proteins (MIPs) includes aquaporin (AQP) and aquaglyceroporin (AQGP) and it is involved in the transport of water and neutral solutes across the membrane. Diverse MIP sequences adopt a unique hour-glass fold with six transmembrane helices (TM1 to TM6) and two half-helices (LB and LE). Loop E contains one of the two conserved NPA motifs and contributes two residues to the aromatic/arginine selectivity filter. Function and regulation of majority of MIP channels are not yet characterized. We have analyzed the loop E region of 1468 MIP sequences and their structural models from six different organism groups. They can be phylogenetically clustered into AQGPs, AQPs, plant MIPs and other MIPs. The LE half-helix in all AQGPs contains an intra-helical salt-bridge and helix-breaking residues Gly/Pro within the same helical turn. All non-AQGPs lack this salt-bridge but have the helix destabilizing Gly and/or Pro in the same positions. However, the segment connecting LE half-helix and TM6 is longer by 10-15 residues in AQGPs compared to all non-AQGPs. We speculate that this longer loop in AQGPs and the LE half-helix of non-AQGPs will be relatively more flexible and this could be functionally important. Molecular dynamics simulations on glycerol-specific GlpF, water-transporting AQP1, its mutant and a fungal AQP channel confirm these predictions. Thus two distinct regions of loop E, one in AQGPs and the other in non-AQGPs, seem to be capable of modulating the transport. These regions can also act in conjunction with other extracellular residues/segments to regulate MIP channel transport. Copyright © 2015. Published by Elsevier B.V.
    Full-text · Article · Mar 2015 · Biochimica et Biophysica Acta
  • Source
    • "In the process of amyloid fibril formation they are important, both, in the nucleation and in fibril elongation [26] [27]. The cis/trans isomerization of the peptide bond preceding proline is considered to form an intrinsic molecular switch controlling several physiologically relevant processes, such as opening of the pore of a neurotransmitter-gated ion channel [28] [29]. Peptidyl prolyl cis/trans isomerases (PPIases) are enzymes that catalyze the cis/ trans isomerization of prolyl bonds. "
    Full-text · Dataset · Mar 2014
Show more