Aquaporins: Phylogeny, Structure, and
Physiology of Water Channels
J. Bernard Heymann and Andreas Engel
How water permeates cellular membranes and what this means for cell functioning
and several diseases are now emerging from the study of the aquaporins (AQPs),
the water channel family. A combination of sequence analysis, three-dimensional
structure determination, and physiology of the AQP family proteins provides a
glimpse into the workings of water channels.
E
very living cell must deal with the osmotic and
hydrostatic pressure changes in its environment. However, the mechanisms cells employ to
transport water and maintain turgor were largely
unknown until the discovery of particular membrane proteins serving as channels specific for
water and other small nonionic molecules. The
first channel cloned and expressed in Xenopus
oocytes to show water permeation was aquaporin
(AQP)1 from human red blood cells (10).
The existence of protein channels for nonionic
compounds and, in particular, water has important implications for water management in living
organisms and presents interesting requirements
of their molecular design. The structure of such
proteins must enforce high specificity while
allowing a high flux through the channel. Some
variance in specificity among the different members of the water channel family appears to be
associated with subtle changes in the sequences.
How these features are encoded is the subject of
ongoing structural studies of various AQPs.
The need for such channels is clearly demonstrated in diseases such as nephrogenic diabetes
insipidus associated with defects in functional
AQP2 expression in the kidney collecting duct
and cataract formation as a consequence of
mutant AQP0 (= MIP, major integral protein) in
the eye lens. Although water may pass through
other channels such as those for sodium and calcium, the rates are insufficient to account for the
large fluxes observed (in the range of 109–1010
molecules·s-1·channel-1). The questions posed
vary from how the channel works to how this ties
in with water management and diseases.
The family of water channels
Long before anything was known of its function, the MIP (=AQP0) of the eye lens was
J. B. Heymann and A. Engel are in the M. E. Müller Institute
for Microscopic Structural Biology, Biozentrum, University
of Basel, CH-4056 Basel, Switzerland.
0886-1714/99 5.00 © 1999 Int. Union Physiol. Sci./Am.Physiol. Soc.
sequenced (for a review of the history, see Ref.
5). AQP1 was then cloned and classified with
some related sequences of suspected channel
proteins, followed by actual demonstration that it
is a water channel (10). With the subsequent dramatic increase in similar sequences found in
many organisms, these proteins became known
as the MIP family. However, using the MIP designation is problematic, because a search in any
of the popular sequence and structure databases
for the keyword “MIP” also yields proteins not
related to the aquaporins, such as the mitochondrial intermediate peptidase and the macrophage
infectivity potentiator. A renaming of the family
to the “aquaporin family” or “AQP family” is suggested and is used in this review.
The subsequent explosion in the number of
sequences obtained for organisms of most major
taxa suggests that the AQP family consists of old
proteins that are important for life. From the
scope and variety of AQP family sequences, the
impression is that homologs occur in most
organisms and most cell types. In some wellstudied organisms such as rats, humans, and Arabidopsis thaliana, several AQP isoforms with
somewhat different specificities and distributions
have been found. What is the significance of
these similarities and differences for structure
and function?
The rapid increase in the number of sequences
is not complemented by sufficient physiological
and functional studies, resulting in a confusion of
naming schemes and classifications. The names
given to the sequences are laboratory specific
and strongly influenced by historical issues.
Therefore, there exists a need to develop a consistent nomenclature based on function, cellular
location, and sequence similarity. Agre (1) initiated this effort by establishing a consistent naming scheme for mammalian AQPs. In this section,
the available sequences are analyzed to establish
relationships and to examine features possibly
associated with function, leading to classification
and nomenclature proposals.
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“. . . the AQP family
consists of old
proteins that are
important for life.”
187
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FIGURE 1. Phylogenetic analysis of the aquaporin (AQP) family suggests a classification into two clusters [AQP and glycerol
facilitator-like protein (GLP)], 16 subfamilies, and 46 types. The types are considered to be representative of the whole family of
160 sequences obtained from Genbank, SWISS-PROT, EMBL, and the genome databases.
“. . .some members of
the AQP family have
a very high specificity
for water. . . .”
188
Phylogenetic analysis showed subdivisions of
the aquaporin family agreeing mostly with those
given by Park and Saier (8) (Fig. 1, Table 1). Some
subfamilies and groupings within subfamilies are
overpopulated with highly similar members
[such as the tonoplast intrinsic protein (TIP) and
plasma membrane intrinsic protein (PIP) subfamilies], whereas others feature only single
sequences (such as the single sequence for the
archaea, AQParc). The complete absence of
sequences from many other taxonomic groups
further supports the anticipation of even more
complexity in the family.
Among the 160 sequences available, many
appear to be minor variants from different
species (such as AQP2) or different tissues (such
as those in Arabidopsis thaliana), leading to overrepresentation of some sequence types. To compare the sequences without overrepresentation,
only one sequence of a type was further used in
alignment and analysis. A type is defined as a set
of sequences with a phylogenetic divergence of
<13%. This definition was designed to maintain
the various mammalian isoforms in the AQP0
subfamily as distinct types, as given in Agre (1).
These type sequences for the AQP family were
classified into clusters and subfamilies (following
Ref. 8). Subfamilies were assigned by visual
inspection of the most consistent phylogenetic
trees (the consensus shown in Fig. 1) and can be
defined based on major taxonomic groupings
(e.g., animal, plant, yeast, bacteria, archaea). The
subfamilies show sequence divergences between
13 and 35%.
The phylogenetic analysis revealed a suggestive dichotomy, with two clear clusters of subfamilies [Fig. 1; also evident in the work of Park
and Saier (8)]. In addition, the archaea aquaporin
(AQParc) is positioned as an intermediate
sequence between these clusters, suggesting a
very ancient divergence. The phylogenetic divergence for the two clusters is ∼43%, not much
higher than for the subfamilies. We suggest that
these clusters be called the AQP and glycerol
facilitator-like protein (GLP) clusters (Fig. 1).
It is well known from physiological data that
some members of the AQP family have a very
high specificity for water, whereas others also
allow the passage of larger nonionic compounds
such as glycerol and urea. It is therefore tempting
to associate this apparent functional distinction
with the phylogenetic clusters. That this picture is
too simple is emphasized by the absence of plant
sequences in the GLP cluster, whereas some proteins such as AQP0 also transport glycerol (7).
The two clusters are therefore unlikely to represent strict functional distinctions. Also, whereas
the fundamental design apparently remained
unaltered through evolution (6 helices around 2
central loops, see below), functional diversity
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Table 1. Classification of aquaporin family sequences based on phylogeny into 2 clusters, 16 subfamilies, and 46 types
Subfamily
AQP0
(Animal)
AQP8
(Animal)
TIP
(Plant tonoplast
intrinsic proteins)
PIP
(Plant plasma
membrane
intrinsic proteins)
NIP
(Plant nodulin
26-like
intrinsic proteins)
AQPD
(Slime mold)
AQPY
(Yeast)
AQPZ
(Bacteria)
AQPS
(Synechococcus sp.)
AQPA
(Archaeoglobus fulgidus)
GLPA
(Animal)
GLPY1
(Yeast)
GLPY2
(Yeast)
GLPB1
(Gram-negative bacteria)
GLPB2
(Gram-positive bacteria)
GLPB3 (Mycoplasma,
gram positive)
Synonyms†
Type
Type Sequence*
AQP0
AQP1
AQP2
AQP4
AQP5
AQP6
AQPcic
AQPbib
AQPhin
AQP8
AQPcel
aTIP
gTIP
dTIP
TIPpic
PIP1
AQP cluster
MIP_HUMAN
AQP1_HUMAN
AQP2_HUMAN
AQP4_HUMAN
AQP5_HUMAN
AQP6_HUMAN
g1279358
BIB_DROME
g1262285
AQP8_RAT
g1359543
TIPA_ARATH
TIPG_ARATH
g1145697
g3021538
WC1A_ARATH
PIP2
NIPgly
NIPnic
NIPara
NIPory
AQPdic
WC2A_ARATH
NO26_SOYBN
PMIP_NICAL
E1249637
Q40746
g1562532
C32C4.2,F40F9.9
bTIP,MP23,MP28
TIP1,RB7,VM23,TIPR,TIPS,NOD26§
DIP,RB7,TIP7,TIP18,RT-TIP
MIPr
WC1,TIPW,PIPB,PMIP,RAMP, WSI-TIP,
PTOM75, MIPA, MIPB, MIPD, PAMIP1,
EMIP, PM28B
WC2,AQUA,MIPC,MIPE,PM28A,PIP3
Nodulin-26
PMIP
MIP,NLM1
MIP
WacA
AQY
AQPL_YEAST
YPR192W,AQY1,AQY2
AQPZ
AQPscy
AQPsco
AQPZ_ECOLI
P73809
Q55998
AQParc
O28846
AQP3
AQP7
AQP9
GLPcel1
GLPcel2
GLPcel3
GLPcel4
GLPY1
GLP cluster
AQP3_HUMAN
AQP7_RAT
g2887407
g669031
g1065485
Q21473
g521003
YFF4_YEAST
F32A5.5
K02G10.7
M02F4.8
C01G6.1
YFF4,YFL054C
GLPY2
FPS1_YEAST
FPS1,YLL043W
GLPFeco
GLPFhae
GLPFpse
GLPFsal
GLPFbac
GLPFstr
GLPFlac
GLPFmga
GLPFmge
GLPFmpn
GLPF_ECOLI
GLPF_HAEIN
GLPF_PSEAE
PDUF_SALTY
GLPF_BACSU
GLPF_STRPN
YDP1_LACLC
GLPF_MYCGA
GLPF_MYCGE
GLPF_MYCPN
MIP26
CHIP28, DER2, AQP-CHIP,‡ FA-CHIP
WCH2, WCH-CD, AQP-CD‡
WCH4,MIWC‡
hKID,WCH3‡
Big brain protein
GLIP,BLIP‡
AQPAP,AQP7L
PDUF
*Names for type sequences from SWISS-PROT and accession numbers from Genbank (g) or TREMBL (O, P and Q);
synonyms include all sequences classified within the same type; ‡see Ref. 1; §three sequences can be obtained in the
databases for nodulin-26. Two of these are highly similar to gTIP (Q39882 and Q39883 in TREMBL), while the other
(NO26_SOYBN) is classified in the NIP subfamily.
†
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based on subtle changes may have developed
several times and in different taxonomic groups.
The AQP1 three-dimensional structure
“A . . . path for water
flow . . . is difficult to
distinguish. . . .”
190
Hydropathy analysis of the majority of
sequences in the AQP family suggests six transmembrane segments. Although a few sequences
yield somewhat ambiguous hydropathy plots, the
average hydropathy of the whole family, based
on the same alignment used in the phylogeny
analysis, definitively indicates six transmembrane segments (Fig. 2A) consistent with topology and mutagenic analysis, leading to the hourglass model (Fig. 2B; Ref. 6).
Determination of the structure of AQP1 at 6Å resolution by electron crystallography combined
with
metal-shadowing
electron
microscopy and atomic force microscopy provided a clear picture of the architecture of the
water channel (3, 11). The hourglass model (6)
was confirmed, and examination of the threedimensional (3-D) map allowed an assignment
of the six predicted helices, with implications
for water permeation (5).
The three 3-D maps of AQP1 all clearly
demarcate the monomers in the tetrameter as sixhelix bundles surrounding density assigned to
the functional loops B and E (3, 11). Also in
agreement is the likely position of the water
channel through the protein (Fig. 3), adjacent to
the central density (loop E) and toward the fourfold axis of the tetramer (3, 5).
The putative water channel starts on the extracellular side with a cavity between the central
density and the helices around the fourfold axis
with a width of ∼10-12 Å. Below this opening,
within the cytoplasmic half of the monomer, the
presence of a large amount of density suggests
that this is the narrow part of the channel. A particular path for water flow through this region is
difficult to distinguish, and multiple paths may
be possible.
It is interesting to compare the conserved
residues within the helices and loops B and E
with residues known to line water pockets in
membrane proteins. Such an analysis on the
photosynthetic reaction center, cytochrome-c
oxidase, bacteriorhodopsin, and cytochrome f
led to a speculative model of the channel-lining
residues (5). The salient feature of this model is a
string of highly conserved polar residues that
can be placed adjacent to the functional loops
and along the center of the six-helix bundle. The
inherent sequence symmetry of the molecule is
also reflected in the symmetrical arrangement of
these residues with respect to the membrane
plane. This assignment imposes constraints on
the angular orientation of the helices and also
locates these conserved residues away from the
lipid environment. As this is in agreement with
available mutagenesis data, it may help in producing a reasonable atomic model of a water
channel protein.
The physiology of water permeation
Because the AQP family has only recently
been discovered, physiological and functional
analyses are quite limited. Of particular interest
is the high flux combined with high selectivity for
water found for the best-studied member, AQP1.
Water channels are a physiological necessity to
deal with osmotic pressure variations and cell
volume changes. However, it is unclear how the
passage of ions is prevented, especially protons,
which are able to tunnel through the matrix of
hydrogen bonds in water.
Flux of water through AQPs
Water channel proteins lower the activation
energy of a membrane for water permeation from
10-20 kcal/mol to <5 kcal/mol. This allows a
high flux of water through the channel when the
membrane is subjected to hydrostatic or osmotic
pressure. To measure the water flux through
membrane channels, AQPs are commonly
expressed in Xenopus oocytes, giving a typical
permeability coefficient Pf = 0.02 cm/s compared to Pf = 0.001 cm/s without channels (6).
This allows semiquantitative measurements, but
the uncertainty in the level of expression of particular proteins makes interpretation difficult.
Two-dimensional crystallization of AQP1 in
the presence of lipids into closed vesicles offered
a system in which the protein density in the
membrane is known with high accuracy (12). In
these crystalline vesicles of ∼3-µm diameter, the
osmotic permeation coefficient for water flowing
through the AQP1 channel was found to be Pf =
0.472 cm/s (12). For a crystalline unit cell of 9.6
nm x 9.6 nm containing eight AQP1 monomers
(11.5 nm2/channel), this translates into a unit
osmotic permeability coefficient of pf = 5.43 x
10-14 cm3·s-1·channel-1 = 1.8 x 109 water molecules·s-1·channel-1.
An attractive and simple model for the selectivity of the aquaporins is a size-exclusion mechanism, originally proposed by Heller et al. (4) for
GlpF from Escherichia coli. It was concluded that
the AQP1 channel specificity is also based on size
exclusion, with the channel showing decreasing
permeability for formamide compared with water
(13). This indicated that the channel has a narrow
part with a diameter about the size of a water
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FIGURE 2. A: average hydrophobicity of the 46 AQP family
sequence types, showing only those residues represented in
AQP1 (smoothed over a 19-residue window). B: the hourglass
model: topology and functional loops in aquaporin [major
integral protein (MIP)] family proteins derived from sequence
analysis, mutagenesis, labeling, and functional analysis (6).
molecule, ∼4 Å [cross-sectional area (A) ≈ 13 Å2].
However, the existence of glycerol-specific channels with a lower water permeability than the
water channels (7) suggests a different selectivity
mechanism, with the width of the channel constriction being only one consideration.
The high selectivity of the AQP1 channel suggests that it functions according to the single-file
model, in which a single chain of water molecules has to pass through the narrowest part of
the pore. This allows the determination of the
length (L) of this narrow part of the channel from
the ratio of osmotic to diffusive flow of water (the
file number). Analysis of the low permeability of
formamide indicated that this constriction might
be quite short, L ≈ 9–13 Å (13).
The 6-Å 3-D structure of AQP1 shows a wide
funnel on the extracellular side of ∼10- to 12-Å
diameter, narrowing towards the middle of the
membrane plane. The narrow part of the channel
thus appears to lie on the cytoplasmic side and
may vary from 10 to 20 Å in length. Given these
measurements for the AQP1 channel, the apparent diffusion coefficient of water in the channel
can be calculated as Dw ≈ 0.4 x 10-5 to 0.8 x 10-5
cm2/s (Dw = (L/A)pf). Compared to bulk water diffusion, Dw = 2.1 x 10-5 cm2/s, diffusion in the
channel is therefore about three to five times
lower. Of course, the implicit assumption is that
there is only one course of water or solute flow.
If there are several paths for water passage, the
apparent diffusion coefficient within the channel
must be lower.
Other measurements have been done for
AQP1, giving the unit permeability coefficient pf
= 1–16 x 10-14 cm3·s-1·channel-1. The high variability in the determined permeabilities is likely
caused by uncertainty about the number of channels per unit membrane area. The determination
for the crystalline vesicles is taken as definitive,
with several other measurements yielding comparable permeabilities.
Some aquaporins have low water permeability, pf = 0.03–0.3 x 10-14 cm3·s-1·channel-1, such
as that for AQP0, whereas AQP4 has been reported
to have a pf = 15–24 x 10-14 cm3·s-1·channel-1 (14).
Because AQP4 remains selective for water (14),
the higher flux through AQP4 may be associated
with multiple paths for water permeation to yield
a diffusion coefficient significantly lower than in
bulk water. Other aquaporins have permeabilities comparable to that of AQP1 (2–5 x 10-14
cm3·s-1·channel-1).
“. . . it functions
according to the
single-file model. . . .”
Selectivity for and flux of nonionic
compounds
The weight of the literature data on the AQP
family is in favor of channels permeated by small
nonionic molecules in the size range of water to
glycerol. Although xylitol is the largest compound reported to pass through the E. coli GlpF,
it was impermeant to pentoses (4). The linear xylitol molecule has a width similar to that of glycerol, whereas the sugars are ring structures with
a larger cross section.
The functional difference between the two
clusters of the family shown in Fig. 1 is not clearcut. For instance, the AQP cluster proteins AQP0
and nodulin 26 (NIP)gly both transport glycerol,
whereas AQP9 of the GLP cluster is impermeant
to glycerol. The characterization of the AQP family physiology is therefore still shrouded in a
cloud of questions.
The permeability of glycerol and urea of GLP
cluster proteins is three to four orders of magnitude lower than the water permeability, as
shown, for example, for AQP0 (7). This suggests
that in these channels a large flux of water
accompanies solute permeation.
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FIGURE 3. A proposed course of the channel through AQP1. The 6-Å 3-D map of the AQP1 monomer (11) is shown cut through
the middle to expose the functional loops B and E (cytoplasmic side at bottom). The channel starts on the extracellular side as
a wide opening, narrowing down toward the cytoplasmic side (~4 Å wide). Also shown are the assigned helices 1–4, with helices
5 and 6 completely cut away.
Selectivity against ions
“. . . the AQP1
channel has no
intrinsic ion
conductance. . . .”
192
As demonstrated in several laboratories, the
AQP1 channel has no intrinsic ion conductance
ability (2, 15). If the flow of water through the
channel is accompanied by ions without selection, the conductivity in a 100 mM salt is
expected to be (0.1 M/55 M) 3.3 x 109 water
molecules·s-1·channel-1 = 6 x 106 ions·s-1·channel-1, which is comparable to the single-channel
current observed for ion channels.
AQP1 and many of the other AQP family
members show a strong concentration of positive
charge on the cytoplasmic side (especially loop
D) and negative charge on the extracellular side.
Perhaps these strongly charged entrances to the
channel form highly efficient electrostatic filters
preventing the passage of ions.
Alternatively, the inability of the AQP1 channel to conduct ions may be explained by the size
of hydrated ions. However, protons should be
easily conducted along a water chain, as is the
case for the gramicidin A channel (9). In addition, at a rate of water passage through AQP1 of
∼109 molecules·s-1·channel-1, only the protons
swept along with the water should lead to a fast
drop in the pH gradient across the membrane.
However, a pH shift experiment did not show
any proton conductance through AQP1, whereas
the control, gramicidin A, dissipated the proton
gradient efficiently (15).
An examination of the mechanisms of proton
conductance through the gramicidin A channel
suggested a fast forward reaction associated with
the propagation of an ionic defect and a slower
backward reaction associated with a reorientation of the water chain through propagation of a
bonding defect (9). The passage of protons is thus
similar to a tunneling effect, with proton propagation much faster than the movement of the
actual water molecules. This study also suggested
that clusters of water bound to the protein slow
down proton transfer, whereas a single-file
hydrogen-bonded chain of water molecules conducts a proton more efficiently (especially when
electrostatic interactions with the protein wall of
the channel are switched off; Ref. 9). Hence the
structure of the water at the charged channel
entrances may prevent proton flow. Furthermore,
the orientations of the water molecules required
for the transmission of the defect along the water
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chain may be restricted or disallowed within the
channel. Thus the specific interactions and
arrangement of the water in the pore may provide a barrier to proton conduction.
Another mechanism might rely on the requirement of the transmission of a defect along the
water chain to reorient the water molecules correctly for proton translocation. A gap in the water
chain too large to bridge by significant tunneling
of a proton might prevent proton conductance.
Conclusion
That the AQP family is an important group of
proteins is emphasized by its abundance and its
involvement in diseases. The emergence of a large
amount of sequence data on this family, together
with progress on the 3-D structure of some of its
members and physiological studies, provides a
fascinating picture of how such a channel is constructed and how it functions. The diversity of isoforms and functional variation in many organisms
indicates multiple roles in cellular and tissue functioning. Here an attempt is made to classify the
available sequences into a consistent scheme, taking into account the similarities on different levels,
namely, clusters, subfamilies, and types. Sequence
analysis and the available 3-D structures suggest
one architecture for the family, that of a tetramer
with each monomer a six-helix bundle surrounding two inward-pointing loops. The channel is
thought to be located within this bundle next to
the loops, with a narrow region towards the cytoplasmic side. The available evidence indicates that
all these channels allow permeation of the very
small water molecule. Some of the channels transport glycerol as well, but three to four orders of
magnitude more slowly than water. Although
some suggestions regarding the exclusion of ions
have been made, the real explanation for ion nonconductance must still be found. Determination of
an atomic model and further functional studies are
essential to understand how these channels work.
We wish to thank all the people in the aquaporin field
contributing valuable suggestions, in particular Peter Agre,
Christophe Maurel, Peter Deen, Frédérique Tacnet, and
Soren Nielsen.
This work was supported by the Swiss National Foundation for Scientific Research (grant 31-42435.94 to A. Engel)
and the Maurice E. Müller Foundation of Switzerland.
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“Some of the channels
transport glycerol as
well. . . .”
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