MIPModDB: a central resource for the superfamily of major intrinsic proteins (original) (raw)
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Members of the superfamily of major intrinsic proteins (MIPs) facilitate water and solute permeability across cell membranes and are found in sources ranging from bacteria to humans. Aquaporin and aquaglyceroporin channels are the prominent members of the MIP superfamily. Experimental studies show that MIPs are involved in important phys- iological processes in mammals and plants. They are implicated in several human diseases and are considered to be attractive drug targets for a wide range of diseases such as cancer, brain edema, epilepsy, glaucoma, and congestive heart failure. Three-dimensional structures of MIP channels from diverse sources reveal that MIPs adopt a unique conserved hourglass helical fold consisting of six transmembrane heli- ces (TM1–TM6) and two half-helices (LB and LE). Conserved NPA motifs near the center and the aromatic/arginine selectivity filter (Ar/R SF) toward the extracellular side consti- tute two narrow constriction regions within the channel. Structural knowledge com- bined with simulation studies have helped to investigate the role of these two constriction regions in the transport and selectivity of the solutes. With the availability of many genome sequences from diverse species, a large number of MIP genes have been identified. Homology models of 1500 MIP channels have been used to derive structure-based sequence alignment of TM1–TM6 helices and the two half-helices LB and LE. Thirteen residues are highly conserved in different transmembrane helices and half-helices. High group conservation of small and weakly polar residues is observed in 27 positions at the interface of two interacting helices. Thus, although the MIP sequences are diverse, the hourglass helical fold is maintained during evolution with the conservation of these 40 positions within the transmembrane region. We have pro- posed a generic structure-based numbering scheme for the MIP channels that will facil- itate easier comparison of the MIP sequences. Analysis of Ar/R SF in all 1500 MIPs indicates the extent of diversity in the four residues that form this narrow region. Certain residues are completely avoided in the SF, even if they have the same chemical nature as that of the most frequently observed residues. For example, arginine is the most pre- ferred residue in a specific position of Ar/R SF, whereas lysine is almost always avoided in any of the four positions. MIP channels with highly hydrophobic or hydrophilic Ar/R SF have been identified. Similarly, there are examples of MIP channels in which all four res- idues of Ar/R SF are bulky, thus almost occluding the pore. Many plant MIPs possess small residues at all SF positions, resulting in a larger pore diameter. A majority of MIP channels are yet to be functionally characterized, and their in vivo substrates are not yet identified. A complete understanding of the relationship between the nature of Ar/R SF and the solutes that are transported is required to exploit MIP channels as potential drug targets.
Oligomerization of water and solute channels of the major intrinsic protein (MIP) family
Kidney International, 2001
(250 to 290 amino acids), and the high conservation intrinsic protein (MIP) family. Water and small solute fluxes throughout the MIP family may indicate a common fold: through cell membranes are ensured in many tissues by seleca NH 2 cytosolic portion followed by a hydrophobic stretch tive pores that belong to the major intrinsic protein family of six transmembrane helices ). Among highly (MIP). This family includes the water channels or aquaporins conserved amino acids in the family, two repetitions of (AQP) and the neutral solute facilitators such as the glycerol facilitator (GlpF). We have compared the characteristics of Asp, Pro, Ala residues (NPA box) localized in the B and representatives of each subfamily. Following solubilization in E loops draw the sequence signature of the family (Fig. the nondenaturing detergents n-octyl-glucoside (OG) and Tri-1B). The folding of these two loops in the membrane ton X-100 (T-X100), AQPs remain in their native homotetrabilayer is proposed to be responsible of the pore formameric state, while GlpF always behaves as a monomer. Solute facilitators are fully solubilized by the detergent N-lauroyl sartion and solute movement across the membrane [2, 3]. cosine (NLS), while AQPs are not. Analyses of mutants and Interestingly, AQPs are widely distributed in bacteria, chimeras demonstrate a close correlation between the water plants, and animals, while GlpFs have been characterized transport function and the resistance to NLS solubilization. only within microorganisms such as bacteria or yeast. In Thus, AQPs and solute facilitators exhibit different behaviors mammals, ten MIPs have been cloned and functionally in mild detergents; this could reflect differences in quaternary organization within the membranes. We propose that the oligocharacterized. Some of them, such as AQP1, AQP3, and merization state or the strength of self-association is part of the AQP4, are widely distributed in the body [4]. In contrast, mechanisms used by MIP proteins to ensure solute selectivity.
Journal of Biological Chemistry, 2002
We previously observed that aquaporins and glycerol facilitators exhibit different oligomeric states when studied by sedimentation on density gradients following nondenaturing detergent solubilization. To determine the domains of major intrinsic protein (MIP) family proteins involved in oligomerization, we constructed protein chimeras corresponding to the aquaporin AQPcic substituted in the loop E (including the proximal part of transmembrane domain (TM) 5) and/or the C-terminal part (including the distal part of TM 6) by the equivalent domain of the glycerol channel aquaglyceroporin (GlpF) (chimeras called AGA, AAG, and AGG). The analogous chimeras of GlpF were also constructed (chimeras GAG, GGA, and GAA). cRNA corresponding to all constructs were injected into Xenopus oocytes. AQPcic, GlpF, AAG, AGG, and GAG were targeted to plasma membranes. Water or glycerol membrane permeability measurements demonstrated that only the AAG chimera exhibited a channel function corresponding to water transport. Analysis of all proteins expressed either in oocytes or in yeast by velocity sedimentation on sucrose gradients following solubilization by 2% n-octyl glucoside indicated that only AQPcic and AAG exist in tetrameric forms. GlpF, GAG, and GAA sediment in a monomeric form, whereas GGA and AGG were found mono/dimeric. These data bring new evidence that, within the MIP family, aquaporins and GlpFs behave differently toward nondenaturing detergents. We demonstrate that the Cterminal part of AQPcic, including the distal half of TM 6, can be substituted by the equivalent domain of GlpF (AAG chimera) without modifying the transport specificity. Our results also suggest that interactions of TM 5 of one monomer with TM 1 of the adjacent monomer are crucial for aquaporin tetramer stability.
Biochemistry, 2005
Major intrinsic proteins (MIPs) are a diverse class of integral membrane proteins that facilitate the transport of water and some small solutes across cellular membranes. X-ray structures of MIPs indicate that a tetrad of residues (the ar/R region) form a narrow pore constriction that constitutes the selectivity filter. In comparison with mammalian and microbial species, plants have a greater number and diversity of MIPs with greater than 30 genes encoding four phylogenetic subfamilies with eight different classes of ar/R sequences. The nodulin 26-like intrinsic protein (NIP) subfamily in Arabidopsis can be subdivided into two ar/R subgroups: the NIP subgroup I, which resembles the archetype of the family, soybean nodulin 26, and the NIP subgroup II, which is represented by the Arabidopsis protein AtNIP6;1. These two NIPs differ principally by the substitution of a conserved alanine (NIP subgroup II) for a conserved tryptophan (NIP subgroup I) in the helix 2 position (H2) of the ar/R filter. A comparison of the water and solute tranport properties of the two proteins was performed by expression in Xenopus laeVis oocytes. Nodulin 26 is an aquaglyceroporin with a modest osmotic water permeability (P f) and the ability to transport uncharged solutes such as glycerol and formamide. In constrast, AtNIP6;1 showed no measurable water permeability but transported glycerol, formamide, as well as larger solutes that were impermeable to nodulin 26. By site-directed mutagenesis, we show that the H2 position is the crucial determinant that confers these transport behaviors. A comparison of the NIPs and tonoplast-intrinsic proteins (TIP) shows that the H2 residue can predict the transport profile for water and glycerol with histidine found in TIPlike aquaporins, tryptophan found in aquaglyceroporins (NIP I), and alanine found in water-impermeable glyceroporins (AtNIP6;1).
A new subfamily LIP of the major intrinsic proteins
BMC Genomics, 2014
Background: Proteins of the major intrinsic protein (MIP) family, or aquaporins, have been detected in almost all organisms. These proteins are important in cells and organisms because they allow for passive transmembrane transport of water and other small, uncharged polar molecules. Results: We compared the predicted amino acid sequences of 20 MIPs from several algae species of the phylum Heterokontophyta (Kingdom Chromista) with the sequences of MIPs from other organisms. Multiple sequence alignments revealed motifs that were homologous to functionally important NPA motifs and the so-called ar/R-selective filter of glyceroporins and aquaporins. The MIP sequences of the studied chromists fell into several clusters that belonged to different groups of MIPs from a wide variety of organisms from different Kingdoms. Two of these proteins belong to Plasma membrane intrinsic proteins (PIPs), four of them belong to GlpF-like intrinsic proteins (GIPs), and one of them belongs to a specific MIPE subfamily from green algae. Three proteins belong to the unclassified MIPs, two of which are of bacterial origin. Eight of the studied MIPs contain an NPM-motif in place of the second conserved NPA-motif typical of the majority of MIPs. The MIPs of heterokonts within all detected clusters can differ from other MIPs in the same cluster regarding the structure of the ar/R-selective filter and other generally conserved motifs. Conclusions: We proposed placing nine MIPs from heterokonts into a new group, which we have named the LIPs (large intrinsic proteins). The possible substrate specificities of the studied MIPs are discussed.
Membrane Water Transport Proteins - Aquaporins
The mechanism of water movement across cell membranes remained unclear until 1992, when the first water specific channel was identified in the human erythrocyte membrane.1 It belongs to an ancient protein family (MIP) found in most li ving organisms, from prokaryotes to mammalians and plants.2 This protein, as well as the others recently discovered were named "aquapori ns " (AQP's). Today, ten water channels have been identified
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 specu- late 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.
Structure and Function of Aquaporins: the Membrane Water Channel Proteins
Biointerface Research in Applied Chemistry, 2021
Aquaporins are integral membrane proteins which are also known as water channel proteins. They aid quick transportation of water across membranes and are important in controlling cell volume and transcellular water passage. Aquaporins are present in organisms, and they vary from archaea and bacteria to plants and animals. They are also found in insects and yeast. Presently, 13 mammalian aquaporins (AQP0 to AQP12) have been cloned and identified in every tissue in the body. These aquaporins are alike in basic structure with monomers containing six transmembrane and two short helical segments that enclose cytoplasmic and extracellular vestibules linked by aqueous pore. They have distinctive structures that define their functions, mode of action, and even their various control methods. Phylogenetic analysis of aquaporin consists of aquaporins, glycerol facilitators, plasma membrane integral proteins of plants, tonoplast integral proteins of plants, nodules of plants, and AQP8s. Aquapor...
Plant Physiology, 1997
Aquaporins, proteins that enhance the permeability of biological membranes to water, are widely distributed in living organisms. They are 26- to 29-kD proteins that belong to the major intrinsic protein (MIP) family of channels. By searching the Arabidopsis thaliana expressed sequence tag database and by using the polymerase chain reaction with oligonucleotides to conserved plant aquaporin domains, we identified 23 expressed Arabidopsis MIP genes. Eight of these had been previously identified as active aquaporins, and two additional ones are now reported to have water-transport activity in Xenopus laevis oocytes. One of these is highly expressed in suspension-cultured cells. On a dendrogram these 23 MIP sequences cluster into three groups: the first group has 11 members and contains the plasma membrane aquaporins, the second group also has 11 members and contains the tonoplast aquaporins, and the third group has only a single member. This MIP protein, provisionally called At-NLM1, i...