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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.
| Abstract |
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| Introduction |
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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 1091010 moleculess-1channel-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 |
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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 well-studied 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.
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.
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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 based on subtle changes may have developed several times and in different taxonomic groups.
| The AQP1 three-dimensional structure |
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The three 3-D maps of AQP1 all clearly demarcate the monomers in the tetrameter as six-helix 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).
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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 |
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| Flux of water through AQPs |
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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 cm3s-1channel-1 = 1.8 x 109 water moleculess-1channel-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 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
913 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 = 116 x 10-14 cm3s-1channel-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 = 0.030.3 x 10-14 cm3s-1channel-1, such as that for AQP0, whereas AQP4 has been reported to have a pf = 1524 x 10-14 cm3s-1channel-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 (25 x 10-14 cm3s-1channel-1).
| Selectivity for and flux of nonionic compounds |
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The functional difference between the two clusters of the family shown in Fig. 1 is not clear-cut. 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.
| Selectivity against ions |
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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 moleculess-1channel-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 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 |
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| Acknowledgments |
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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.
| References |
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