Predictive evidence for a porin-type beta-barrel fold in CHIP28 and other members of the MIP family. A restricted-pore model common to water channels and facilitators

Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures

The amino acid composition and architecture of all beta-barrel membrane proteins of known three-dimensional structure have been examined to generate information that will be useful in identifying beta-barrels in genome databases. The database consists of 15 nonredundant structures, including several novel, recent structures. Known structures include monomeric, dimeric, and trimeric beta-barrels with between 8 and 22 membrane-spanning beta-strands each. For this analysis the membrane-interacting surfaces of the beta-barrels were identified with an experimentally derived, whole-residue hydrophobicity scale, and then the barrels were aligned normal to the bilayer and the position of the bilayer midplane was determined for each protein from the hydrophobicity profile. The abundance of each amino acid, relative to the genomic abundance, was calculated for the barrel exterior and interior. The architecture and diversity of known beta-barrels was also examined. For example, the distribution of rise-per-residue values perpendicular to the bilayer plane was found to be 2.7 +/- 0.25 A per residue, or about 10 +/- 1 residues across the membrane. Also, as noted by other authors, nearly every known membrane-spanning beta-barrel strand was found to have a short loop of seven residues or less connecting it to at least one adjacent strand. Using this information we have begun to generate rapid screening algorithms for the identification of beta-barrel membrane proteins in genomic databases. Application of one algorithm to the genomes of Escherichia coli and Pseudomonas aeruginosa confirms its ability to identify beta-barrels, and reveals dozens of unidentified open reading frames that potentially code for beta-barrel outer membrane proteins.

Cellular and molecular biology of the aquaporin water channels

The high water permeability characteristic of mammalian red cell membranes is now known to be caused by the protein AQP1. This channel freely permits movement of water across the cell membrane, but it is not permeated by other small, uncharged molecules or charged solutes. AQP1 is a tetramer with each subunit containing an aqueous pore likened to an hourglass formed by obversely arranged tandem repeats. Cryoelectron microscopy of reconstituted AQP1 membrane crystals has revealed the three-dimensional structure at 3-6 A. AQP1 is distributed in apical and basolateral membranes of renal proximal tubules and descending thin limbs as well as capillary endothelia. Ten mammalian aquaporins have been identified in water-permeable tissues and fall into two groupings. Orthodox aquaporins are water-selective and include AQP2, a vasopressin-regulated water channel in renal collecting duct, in addition to AQP0, AQP4, and AQP5. Multifunctional aquaglyceroporins AQP3, AQP7, and AQP9 are permeated by water, glycerol, and some other solutes. Aquaporins are being defined in numerous other species including amphibia, insects, plants, and microbials. Members of the aquaporin family are implicated in numerous physiological processes as well as the pathophysiology of a wide range of clinical disorders.

Progress on the structure and function of aquaporin 1

Life exists in water as universal solvent, and cells need to deal with its influx and efflux. Nature has accomplished the almost impossible, creating membrane channels with both a high flux and a high specificity for water. The first water channel was discovered in red blood cell membranes. Today known as aquaporin-1, this channel was found to be closely related to the major integral protein (MIP)1 of the eye lens. Cloning and sequencing of numerous related proteins of the MIP family revealed the widespread occurrence of such channels, suggesting an essential physiological function. Their structures hold the clues to the remarkable water channel activity, as well as to the arrangement of transmembrane segments in general. Recent medium-resolution three-dimensional electron microscopic studies determined a tetrameric complex with six tilted transmembrane helices per monomer. The helices within each monomer surround a central density formed by two interhelical loops implicated by mutagenesis in the water channel function. A combination of sequence analysis and assignment of the observed densities to predicted helices provides a basis for speculation on the nature of the water course through the protein. In particular, four highly conserved polar residues, E142-N192-N76-E17, are proposed to form a chain of key groups involved in the pathway of water flow through the channel.

Secondary structures comparison of aquaporin-1 and bacteriorhodopsin: a Fourier transform infrared spectroscopy study of two-dimensional membrane crystals

Aquaporins are integral membrane proteins found in diverse animal and plant tissues that mediate the permeability of plasma membranes to water molecules. Projection maps of two-dimensional crystals of aquaporin-1 (AQP1) reconstituted in lipid membranes suggested the presence of six to eight transmembrane helices in the protein. However, data from other sequence and spectroscopic analyses indicate that this protein may adopt a porin-like beta-barrel fold. In this paper, we use Fourier transform infrared spectroscopy to characterize the secondary structure of highly purified native and proteolyzed AQP1 reconstituted in membrane crystalline arrays and compare it to bacteriorhodopsin. For this analysis the fractional secondary structure contents have been determined by using several different algorithms. In addition, a neural network-based evaluation of the Fourier transform infrared spectra in terms of numbers of secondary structure segments and their interconnections [sij] has been performed. The following conclusions were reached: 1) AQP1 is a highly helical protein (42-48% alpha-helix) with little or no beta-sheet content. 2) The alpha-helices have a transmembrane orientation, but are more tilted (21 degrees or 27 degrees, depending on the considered refractive index) than the bacteriorhodopsin helices. 3) The helices in AQP1 undergo limited hydrogen/deuterium exchange and thus are not readily accessible to solvent. Our data support the AQP1 structural model derived from sequence prediction and epitope insertion experiments: AQP1 is a protein with at least six closely associated alpha-helices that span the lipid membrane.

Surface topographies at subnanometer-resolution reveal asymmetry and sidedness of aquaporin-1

Aquaporin-1 (AQP1) is an abundant protein in human erythrocyte membranes which functions as a specific and constitutively active water conducting pore. Solubilized and isolated as tetramer, it forms well-ordered two-dimensional (2D) crystals when reconstituted in the presence of lipids. Several high resolution projection maps of AQP1 have been determined, but information on its three-dimensional (3D) mass distribution is sparse. Here, we present surface reliefs at 0.9 nm resolution that were calculated from freeze-dried unidirectionally metal-shadowed AQP1 crystals as well as surface topographs recorded with the atomic force microscope of native crystals in buffer solution. Our results confirm the 3D map of negatively stained AQP1 crystals, which exhibited tetramers with four major protrusions on one side and a large central cavity on the other side of the membrane. Digestion of AQP1 crystals with carboxypeptidase Y, which cleaves off a 5 kDa intracellular C-terminal fragment, led to a reduction of the major protrusions, suggesting that the central cavity of the tetramer faces the outside of the cell. To interpret the results, sequence based structure predictions served as a guide.

Characterization of the transmembrane orientation of aquaporin-1 using antibodies to recombinant fusion proteins

Aquaporin-1 (AQP1) is a member of a family of integral membrane proteins, the aquaporins, which function as molecular channels for the movement of water across the plasma membrane. While the primary structure of AQP1 has been obtained from the cloning of its cDNA, its secondary structure is less certain. In this study, antibodies have been generated to defined regions of AQP1 in order to characterize its secondary structure. The antibodies were produced in chickens against glutathione S-transferase fusion proteins which represented loops C and E, and the carboxyl terminus of AQP1 as defined in the six-transmembrane model of Preston and Agre [(1991) Proc. Natl. Acad. Sci. U.S.A. 88, 11110]. Characterization of the antibodies showed that they recognized their corresponding fusion proteins as well as native AQP1 in erythrocytes and recombinant AQP1 expressed in COS7 cells. They differed, however, with respect to the specific conditions required for recognition. Thus, the anti-C-terminal antibodies recognized COS7 cells transfected with AQP1 that were fixed and permeabilized but did not recognize live cells (unpermeabilized). Conversely, antibodies to loop C labeled both live and fixed cells, while antibodies to loop E labeled live cells but not fixed. The data indicate that the carboxyl terminus of aquaporin-1 is intracellular and that loops C and E are extracellular. Furthermore, antibody recognition of loop E is very sensitive to the labeling conditions which may reflect an active role in the functional protein.

Structure of aquaporin-2 vasopressin water channel

Aquaporin-2 (AQP-2) is a vasopressin-regulated water channel in the kidney collecting duct. AQP-2 is selectively permeable to water molecule and is translocated between the apical membrane and subapical endosomes in response to vasopressin. To investigate the localization and structure of the aqueous pathway of the AQP-2 water channel, a series of site-directed mutants was constructed and functionally analyzed. Insertion of N-glycosylation reporter sequence into each hydrophilic loop (HL) indicated that AQP-2 has a six-membrane spanning topology and that insertional mutations in HL-2 or HL-5 do not alter water channel function. Mercury-sensitive site of AQP-2 is located near the second asparagine-proline-alanine (NPA) domain at cysteine 181, but not near the first NPA domain. Replacement of HL-3 or HL-4 with the corresponding part of Escherichia coli glycerol facilitator abolished water channel function without changing plasma membrane expression of the channel protein. Introduction of cysteine residues in His-122, Asn-123, Gly-154, Asp-155, or Asn-156 induced partial mercury sensitivity, and point mutations in asparagine 123 significantly altered water permeability. Our results implicate that the structure of AQP-2 is different from models previously proposed for AQP-1 and that HL-3 and HL-4 are closely located to the aqueous pathway.

Osmotic permeability in a molecular dynamics simulation of water transport through a single-occupancy pore

The aim of this work is to determine plausible values for the rate constants of kinetic models representing water transport through narrow pores. We present here the results of molecular dynamics simulations of the movement of water molecules through a single-site hydrophilic pore. The system consists of a rectangular box of water molecules, some of which are positionally restrained so as to act as a membrane. This membrane separates two compartments where water molecules move freely; one of the positions in the membrane is initially vacant (the 'single-site pore'), but can be occupied by mobile molecules. To analyze the results, we represented the pore by a two-state kinetic diagram in which the vacant and occupied states are linked by transitions corresponding to the binding and release of water molecules. The mean occupancy and vacancy times directly yield the rate constants of binding and release, which in turn yield the osmotic water permeability coefficient per pore pf. We also compute the apparent activation energies delta E* for the rate constants and for pf. The pf value was (1.56 +/- 0.04).10(-11) cm3/s (at 307 K), which is much larger than those determined for CHIP28 and for gramicidin A (of about 10(-13) and 10(-14) cm3/s, respectively). These values were compared with those arising from a model of a symmetric single-file pore through which one-vacancy-mediated water transport takes place. The model yields an expression for pf as a function of the rate constants and of the number of molecular positions (n) in the file. When n = 1, this expression becomes the one corresponding to the single-site pore studied in our current simulation. Using the rate constants of binding and release derived from our simulation, the pf values are consistent with an occupancy value of 5-6 found for gramicidin A, and with occupancies of 4-7 that can be estimated for the single-file pore of a recently proposed model for CHIP28. delta E* for pf is 3.0 kcal/mol, a value similar to that determined for CHIP28. Hence, the system simulated here appears plausible and can be used to mimic some physical properties of water transport through biological pores.

Transbilayer pores formed by beta-barrels: molecular modeling of pore structures and properties

Transmembrane beta-barrels, first observed in bacterial porins, are possible models for a number of membrane channels. Restrained molecular dynamics simulations based on idealized C alpha beta templates have been used to generate models of such beta-barrels. Model beta-barrels have been analyzed in terms of their conformational, energetic, and pore properties. Model beta-barrels formed by N = 4, 8, 12 and 16 anti-parallel Ala10 strands have been developed. For each N, beta-barrels with shear numbers S = N to 2N have been modeled. In all beta-barrel models the constituent beta-strands adopt a pronounced right-handed twist. Interstrand interactions are of approximately equal stability for all models with N > or = 8, whereas such interactions are weaker for the N = 4 beta-barrels. In N = 4 beta-barrels the pore is too narrow (minimum radius approximately 0.6 A) to allow ion permeation. For N > or = 8, the pore radius depends on both N and S; for a given value of N an increase in S from N to 2N is predicted to result in an approximately threefold increase in pore conductance. Calculated maximal conductances for the beta-barrel models are compared with experimental values for porins and for K+ channels.

The CHIP28 water channel visualized in ice by electron crystallography

Electron crystallography of frozen-hydrated two-dimensional crystals of deglycosylated human erythrocyte CHIP28 reveals an aqueous vestibule in each monomer leading to the water-selective channel that is enclosed by multiple transmembrane alpha-helices.

Multifunctional transporter models: lessons from the transport of water, sugars, and ring compounds by GLUTs

Facilitative glucose transporters (GLUTs) have recently been shown to be multifunctional, transporting substrates other than sugars, such as water and ring compounds as large as nitrobenzene-diazol-aminoglucose. Other membrane proteins, including transporters and cystic fibrosis transmembrane conductance regulator, have also revealed a finite permeability to water. We compare the alpha-helical and beta-barrel models for the structure of GLUTs, discuss recent evidence, and argue that a beta-barrel fold explains it better. We show a model for GLUTs consisting of a relatively rigid beta-barrel translocation unit ("channel") of diameter ample enough to allow permeation of the above substrates (approximately 20 A) but gated shut by mobile loops at both ends. Such gates would open only after aromatic interactions would lead to binding of the ring substrates for GLUTs; water would, however, traverse crevices in the closed gates. Using the insights gained from GLUTs, we propose that other transporters may share with GLUTs the motif of a beta-barrel channel and would be permeable to water due to the presence of such channels together with similarly behaving gates.

Aquaporin water channels: unanswered questions and unresolved controversies

The long-standing biophysical question of how water crosses plasma membranes has been answered by the recent discovery of the aquaporins. Identification of this large family of membrane water-transport proteins has generated new questions about the physiological functions, tissue distributions, and regulatory mechanisms of individual aquaporins. The fast pace of developments in this field has also resulted in major discrepancies in published reports which warrant resolution.