Structural basis of water-specific transport through the AQP1 water channel.

Water channels facilitate the rapid transport of water across cell membranes in response to osmotic gradients. These channels are believed to be involved in many physiological processes that include renal water conservation, neuro-homeostasis, digestion, regulation of body temperature and reproduction. Members of the water channel superfamily have been found in a range of cell types from bacteria to human. In mammals, there are currently 10 families of water channels, referred to as aquaporins (AQP): AQP0-AQP9. Here we report the structure of the aquaporin 1 (AQP1) water channel to 2.2 A resolution. The channel consists of three topological elements, an extracellular and a cytoplasmic vestibule connected by an extended narrow pore or selectivity filter. Within the selectivity filter, four bound waters are localized along three hydrophilic nodes, which punctuate an otherwise extremely hydrophobic pore segment. This unusual combination of a long hydrophobic pore and a minimal number of solute binding sites facilitates rapid water transport. Residues of the constriction region, in particular histidine 182, which is conserved among all known water-specific channels, are critical in establishing water specificity. Our analysis of the AQP1 pore also indicates that the transport of protons through this channel is highly energetically unfavourable.

Protein 4.1R core domain structure and insights into regulation of cytoskeletal organization.

The crystal structure of the core domain (N-terminal 30 kDa domain) of cytoskeletal protein 4.1R has been determined and shows a cloverleaf-like architecture. Each lobe of the cloverleaf contains a specific binding site for either band 3, glycophorin C/D or p55. At a central region of the molecule near where the three lobes are joined are two separate calmodulin (CaM) binding regions. One of these is composed primarily of an alpha-helix and is Ca 2+ insensitive; the other takes the form of an extended structure and its binding with CaM is dramatically enhanced by the presence of Ca 2+, resulting in the weakening of protein 4.1R binding to its target proteins. This novel architecture, in which the three lobes bind with three membrane associated proteins, and the location of calmodulin binding sites provide insight into how the protein 4.1R core domain interacts with membrane proteins and dynamically regulates cell shape in response to changes in intracellular Ca2+ levels.

Crystallization and preliminary X-ray crystallographic analysis of water channel AQP1.

Aquaporin-1 (AQP1), a water channel from bovine red blood cells has been deglycosylated, purified to homogeneity and crystallized in a form suitable for X-ray crystallographic study. Crystals are grown using polyethylene glycol as precipitant and belong to the tetragonal space group I422, with unit-cell parameters a = b = 93.4, c = 180.4 A. The crystals diffract beyond 2.2 A resolution.

Crystallization and preliminary X-ray crystallographic analysis of the 30 kDa membrane-binding domain of protein 4.1 from human erythrocytes.

The 30 kDa membrane-binding domain of protein 4.1 from human erythrocytes has been expressed in Escherichia coli and crystallized in a form suitable for X-ray crystallographic study. Crystals were grown using a salting-in technique. Crystals have a tetragonal plate shape and belong to the C2 space group, with unit-cell parameters a = 163.9, b = 106.5, c = 93.5 A, beta = 95.5 degrees. The crystals diffract to 2.8 A resolution.

Direct phase determination in protein electron crystallography: aquaporin channel-forming integral membrane protein.

The location of helix sites in the projected structure of the aquaporin channel-forming integral membrane protein from bovine red blood cells was determined by multisolution direct methods to a mean accuracy of +/-1.9 A, based on hk0 electron diffraction data extending to 6 A. The structure was assumed to be composed of pseudo-atoms, corresponding to the helix cross sections, and after re-scaling, normalized structure factors were used to order summation operatorn triples according to the A values. Initial phases were found by symbolic addition with algebraic unknowns. Probable solutions could be isolated by an overall Luzzati test for density flatness and restrictions on local density extremes. The best solution was identified by matching Patterson functions, generated from the trial map density sites, to the one calculated from observed intensities.

Two-dimensional crystallization and projection structure of KcsA potassium channel.

Potassium channels are integral membrane proteins that play a crucial role in regulating diverse cell functions in both electrically excitable and non-excitable cells. Molecular cloning has revealed a diverse family of genes that encode these proteins, and a variety of experimental strategies have defined functional domains. We have cloned, over-expressed and purified the KcsA potassium channel to homogeneity and reconstituted this channel protein with phospholipids to form two-dimensional crystals. The crystals belong to plane group p4 and have unit cell dimensions of a=b=48 A. A projection map at 6 A resolution has been obtained by electron crystallography. The map shows that the protein is a homotetramer, having a low-density region on the 4-fold axis that is the site of the ion conduction pathway. Each monomer contains density features that are consistent with the molecular model of a truncated form of KcsA recently determined by X-ray crystallography.

Recombinant expression, purification and characterization of Kch, a putative Escherichia coli potassium channel protein.

The Escherichia coli gene kch, similar in primary structure to eukaryotic voltage-gated potassium channels, was cloned and overexpressed in E. coli. The protein was solubilized from the plasma membrane with dodecylmaltopyranoside, lauryldimethylamine oxide or N-laurylsarcosine and was purified in milligram amounts by imidazole elution from a nickel-chelate column. The molecular mass of the purified protein in a number of detergents with 12 carbon atom chains suggests that rKch forms primarily tetramers of the 50 kDa monomers. CD spectroscopy of the purified protein indicates a significant alpha-helical content that is preserved upon addition of SDS.

Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex.

Mitochondrial cytochrome bc1 complex performs two functions: It is a respiratory multienzyme complex and it recognizes a mitochondrial targeting presequence. Refined crystal structures of the 11-subunit bc1 complex from bovine heart reveal full views of this bifunctional enzyme. The "Rieske" iron-sulfur protein subunit shows significant conformational changes in different crystal forms, suggesting a new electron transport mechanism of the enzyme. The mitochondrial targeting presequence of the "Rieske" protein (subunit 9) is lodged between the two "core" subunits at the matrix side of the complex. These "core" subunits are related to the matrix processing peptidase, and the structure unveils how mitochondrial targeting presequences are recognized.

Molecular design of aquaporin-1 water channel as revealed by electron crystallography.

The electron crystallographic structure of the aquaporin-1 water channel, determined at approximately 6A, reveals that the protein has six transmembrane alpha-helices forming a trapezoid-like cylinder. There is a branched rod-like structure within the cylinder that traverses the membrane and likely contains at least one alpha-helix.

Purification, visualization, and biophysical characterization of Kv1.3 tetramers.

The voltage-gated K+ channel of T-lymphocytes, Kv1.3, was heterologously expressed in African Green Monkey kidney cells (CV-1) using a vaccinia virus/T7 hybrid expression system; each infected cell exhibited 10(4) to 5 x 10(5) functional channels on the cell surface. The protein, solubilized with detergent (3-[cholamidopropyl)dimethylammonio]-1-propanesulfonic acid or cholate), was purified to near-homogeneity by a single nickel-chelate chromatography step. The Kv1.3 protein expressed in vaccinia virus-infected cells and its purified counterpart are both modified by a approximately 2-kDa core-sugar moiety, most likely at a conserved N-glycosylation site in the external S1-S2 loop; absence of the sugar does not alter the biophysical properties of the channel nor does it affect expression levels. Purified Kv1.3 has an estimated size of approximately 64 kDa in denaturing SDS-polyacrylamide electrophoresis gels, consistent with its predicted size based on the amino acid sequence. By sucrose gradient sedimentation, purified Kv1.3 is seen primarily as a single peak with an approximate mass of 270 kDa, compatible with its being a homotetrameric complex of the approximately 64-kDa subunits. When reconstituted in the presence of lipid and visualized by negative-staining electron microscopy, the purified Kv1.3 protein forms small crystalline domains consisting of tetramers with dimensions of approximately 65 x 65 A. The center of each tetramer contains a stained depression which may represent the ion conduction pathway. Functional reconstitution of the Kv1.3 protein into lipid bilayers produces voltage-dependent K+-selective currents that can be blocked by two high affinity peptide antagonists of Kv1.3, margatoxin and stichodactylatoxin.

Structure and functional mechanism of porins.

Cellular organisms such as gram-negative bacteria are enclosed by a dual lipid bilayer system. The outer membranes of the dual bilayer envelopes predominantly contain large numbers of water-filled transmembrane protein channels known as porins. The recent availability of the molecular structures of several bacterial porins has provided the opportunity for comparing the results of a wide range of functional studies with the atomic level structural details of these membrane channels. Taken together, the structure and function data present the most comprehensive set of boundary conditions available for the evaluation of theory and models predicting the characteristics of solute transport through membrane protein channels. In this paper, we review the high-resolution structure data from the bacterial porins, as well as recent theoretical studies, in the context of biophysical and biochemical observations and discuss the molecular mechanisms responsible for the transport of solutes through porin channels. Particular emphasis has been placed on the features and roles of common structural elements, channel sterics and electrostatics, and voltage-dependent gating. A model for water-coordinated transport, providing a qualitative view of the porin transport mechanism, is also described.

Preliminary cryocrystallographic study of the mitochondrial cytochrome bc1 complex: improved crystallization and flash-cooling of a large membrane protein.

Ubiquinol-cytochrome c reductase is a crucial integral membrane protein in the mitochondrial respiratory cycle. Eleven subunits containing three cytochrome heme groups and a 2Fe-2S Rieske center make up this 240 kDa enzyme complex. Previously, many different crystal forms of the bc1 complex have displayed diffraction to as far as 4.5 A. However, rapid degradation of the protein in the X-ray beam at room temperature has obstructed the collection of a full data set from a single crystal. As slight heterogeneities between crystals severely hampered merging of data from different crystals, we sought a method to stabilize the protein crystal in the X-ray beam in order to collect a full data set from one crystal sample. To this end, water soluble protein crystals are frequently flash-cooled to cryogenic temperatures; however, there is no report of cryocrystallography for membrane proteins. In this communication, we report on a successful experiment in which flash-cooled bc1 membrane protein crystals have given rise to sustained diffraction over a 60 hour data collection period at a synchrotron source. Furthermore, we present an improved purification and crystallization protocol yielding crystals readily diffracting out to 3.3 A. These results should greatly aid in the future realization of the molecular structure of the bc1 complex as well as other membrane proteins.

Structure of the osmo-regulated H2O-channel, AQP-CHIP, in projection at 3.5 A resolution.

An osmo-regulated H2O-channel, aquaporin-CHIP, from bovine red blood cell membranes was purified and reconstituted with lipids, forming two-dimensional crystalline patches that diffract to about 3.0 A resolution. Electron diffraction patterns and high-resolution images of the crystalline patches embedded in glucose were recorded and used to calculate the projection map at 3.5 A resolution. The map confirms that the osmo-regulated H2O-channel basic packing unit is a tetramer and begins to reveal it's structural design. The basic architecture of the H2O-channel protein consists of a trapezoid-like envelope and a substructure located within the trapezoid that could play a crucial role in the channel structure itself; near this substructure there is a region of very low density, which is the probable site of the channel. The trapezoid-like envelope is composed of high density regions many of which can be interpreted as projections of alpha-helices along their axes.

2D crystallization: from art to science.

The techniques as well as the principles of the 2D crystallization of membrane and water-soluble proteins for electron crystallography are reviewed. First, the biophysics of the interactions between proteins, lipids and detergents is surveyed. Second, crystallization of membrane proteins in situ and by reconstitution methods is discussed, and the various factors involved are addressed. Third, we elaborate on the 2D crystallization of water-soluble proteins, both in solution and at interfaces, such as lipid monolayers, mica, carbon film or mercury surfaces. Finally, techniques and instrumentations that are required for 2D crystallization are described.

X-ray diffraction by crystals of beef heart ubiquinol: cytochrome c oxidoreductase.

Beef heart mitochondrial ubiquinol:cytochrome c oxidoreductase has been crystallized in the shape of hexagonal bipyramids. At present the crystals diffract X-rays to 4.7 A. From preliminary analysis the diffraction pattern appears to be consistent with space group P6(1)22 or P6(5)22 and with unit cell parameters a = b = 212 A and c = 352 A.

What spectroscopy can still tell us about the secondary structure of bacteriorhodopsin.

The recently published model of the structure of bacteriorhodopsin (bR), developed by fitting the peptide chain to a high-resolution, three-dimensional density map, rules out the existence of transmembrane beta-sheet and provides an accurate estimate of the helix content. The precise geometry of the dihedral angles in the helical regions of the polypeptide cannot yet be specified from the diffraction data, however. Published data on the circular dichroism (CD) spectrum between 190 and 240 nm, and the infrared (IR) spectrum in the amide I band suggest that the helical conformation in bR may be, for the most part, a rather unusual one. The precise structural model, which specifies the number of residues in transmembrane helices, can now be used as an additional constraint in seeking models of the helical conformation that are in quantitative agreement with the CD and IR spectroscopic data. Further spectroscopic measurements can also be used to determine whether there are changes in the unusual dihedral-angle conformation within the helices during the photocycle.

Stoichiometry of maltodextrin-binding sites in LamB, an outer membrane protein from Escherichia coli.

We have directly measured the stoichiometry of maltodextrin-binding sites in LamB. Scatchard plots and computer fitting of flow dialysis (rate-of-dialysis) experiments clearly establish three independent binding sites per LamB trimer, with a dissociation constant of approximately 60 microM for maltoheptaose. The current model for LamB's function as a specific pore is discussed with respect to the symmetry in LamB's kinetic properties and the implications of our results.

Structural architecture of an outer membrane channel as determined by electron crystallography.

Porins are a family of membrane channels commonly found in the outer membranes of Gram-negative bacteria where they serve as diffusional pathways for waste products, nutrients and antibiotics, and can also be receptors for bacteriophages. Porin channels have been shown in vitro to be voltage-gated. They can exhibit slight selectivities for certain solutes; for example PhoE porin has some selectivity for anionic and phosphate-containing compounds. Unlike many known membrane proteins which often contain long stretches of hydrophobic segments that are believed to traverse the membrane in a helical conformation, porins are found to have charged residues distributed almost uniformly along their primary sequences and have most of their secondary structure in a beta-sheet conformation. We have made crystalline patches of PhoE porin embedded in a lipid bilayer and have used these to determine the structure of PhoE porin by electron crystallography to a resolution of 6A. The basic structure consists of a trimer of elliptically shaped, cylindrical walls of beta sheet. Each cylinder has an inner lining, formed by parts of the polypeptide, that defines the channel size. The structure provides a clue as to how deletions of segments of polypeptide, which are found in certain mutants, can result in an actual increase in the channel size.