Atomic structure of a glycerol channel and implications for substrate permeation in aqua(glycero)porins.

The structure of a glycerol channel from Escherichia coli at 2.2 A resolution serves as a basis for the understanding of selective transmembrane substrate permeation. In the course of permeation, glycerol molecules diffuse through a tripathic channel with their alkyl backbone wedged against a hydrophobic corner, such that OH groups become acceptors and donors of hydrogen bonds at the same time. The structure of the channel explains the preferential permeability for linear carbohydrates and absolute exclusion of ions and charged solutes. Its gene-duplicated sequence has a structural counterpart in a pseudo two-fold symmetry within the monomeric channel protein.

Molecular mechanism for the crystallization of bacteriorhodopsin in lipidic cubic phases.

Crystals of transmembrane proteins may be grown from detergent solutions or in a matrix of membranous lipid bilayers existing in a liquid crystalline state and forming a cubic phase (in cubo). While crystallization in micellar solutions appears analogous to that for soluble proteins, crystallization in lipidic matrices is poorly understood. As this method was shown to be applicable to several membrane proteins, understanding its mechanism will facilitate a rational design of crystallization, minimizing the laborious screening of a large number of parameters. Using polarization microscopy and low-angle X-ray diffraction, experimental evidence is provided to support a mechanistic model for the in cubo crystallization of bacteriorhodopsin in a lipid matrix. Membrane proteins are thought to reside in curved lipid bilayers, to diffuse into patches of lower curvature and to incorporate into lattices which associate to form highly ordered three-dimensional crystals. Critical testing of this model is necessary to generalize it to other membrane proteins.

X-ray structure of sensory rhodopsin II at 2.1-A resolution.

Sensory rhodopsins (SRs) belong to a subfamily of heptahelical transmembrane proteins containing a retinal chromophore. These photoreceptors mediate the cascade of vision in animal eyes and phototaxis in archaebacteria and unicellular flagellated algae. Signal transduction by these photoreceptors occurs by means of transducer proteins. The two archaebacterial sensory rhodopsins SRI and SRII are coupled to the membrane-bound HtrI and HtrII transducer proteins. Activation of these proteins initiates phosphorylation cascades that modulate the flagellar motors, resulting in either attractant (SRI) or repellent (SRII) phototaxis. In addition, transducer-free SRI and SRII were shown to operate as proton pumps, analogous to bacteriorhodopsin. Here, we present the x-ray structure of SRII from Natronobacterium pharaonis (pSRII) at 2.1-A resolution, revealing a unique molecular architecture of the retinal-binding pocket. In particular, the structure of pSRII exhibits a largely unbent conformation of the retinal (as compared with bacteriorhodopsin and halorhodopsin), a hydroxyl group of Thr-204 in the vicinity of the Schiff base, and an outward orientation of the guanidinium group of Arg-72. Furthermore, the structure reveals a putative chloride ion that is coupled to the Schiff base by means of a hydrogen-bond network and a unique, positively charged surface patch for a probable interaction with HtrII. The high-resolution structure of pSRII provides a structural basis to elucidate the mechanisms of phototransduction and color tuning.

Structure of a glycerol-conducting channel and the basis for its selectivity.

Membrane channel proteins of the aquaporin family are highly selective for permeation of specific small molecules, with absolute exclusion of ions and charged solutes and without dissipation of the electrochemical potential across the cell membrane. We report the crystal structure of the Escherichia coli glycerol facilitator (GlpF) with its primary permeant substrate glycerol at 2.2 angstrom resolution. Glycerol molecules line up in an amphipathic channel in single file. In the narrow selectivity filter of the channel the glycerol alkyl backbone is wedged against a hydrophobic corner, and successive hydroxyl groups form hydrogen bonds with a pair of acceptor, and donor atoms. Two conserved aspartic acid-proline-alanine motifs form a key interface between two gene-duplicated segments that each encode three-and-one-half membrane-spanning helices around the channel. This structure elucidates the mechanism of selective permeability for linear carbohydrates and suggests how ions and water are excluded.

Crystallization in cubo: general applicability to membrane proteins.

Obtaining well ordered crystals of membrane proteins is the single most serious stumbling block in the pursuit of their high-resolution structures. The applicability of lipidic cubic phase-mediated crystallization is demonstrated on a diverse set of bacterial membrane proteins: two photosynthetic reaction centres, a light-harvesting complex and two retinal proteins, halorhodopsin and bacteriorhodopsin. Despite marked differences in molecular dimensions, subunit composition and membrane origin, one single lipid, monoolein, is sufficient to form a crystallization matrix for all the aforementioned systems. Therefore, the lipidic cubic phase approach is proposed as a general method for crystallizing membrane proteins.

High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle.

Bacteriorhodopsin is the simplest known photon-driven proton pump and as such provides a model for the study of a basic function in bioenergetics. Its seven transmembrane helices encompass a proton translocation pathway containing the chromophore, a retinal molecule covalently bound to lysine 216 through a protonated Schiff base, and a series of proton donors and acceptors. Photoisomerization of the all-trans retinal to the 13-cis configuration initiates the vectorial translocation of a proton from the Schiff base, the primary proton donor, to the extracellular side, followed by reprotonation of the Schiff base from the cytoplasm. Here we describe the high-resolution X-ray structure of an early intermediate in the photocycle of bacteriorhodopsin, which is formed directly after photoexcitation. A key water molecule is dislocated, allowing the primary proton acceptor, Asp 85, to move. Movement of the main-chain Lys 216 locally disrupts the hydrogen-bonding network of helix G, facilitating structural changes later in the photocycle.

Effects of ligand binding on the internal dynamics of maltose-binding protein.

Ligand binding to proteins often causes large conformational changes. A typical example is maltose-binding protein (MBP), a member of the family of periplasmic binding proteins of Gram-negative bacteria. Upon binding of maltose, MBP undergoes a large structural change that closes the binding cleft, i.e. the distance between its two domains decreases. In contrast, binding of the larger, nonphysiological ligand beta-cyclodextrin does not result in closure of the binding cleft. We have investigated the dynamic properties of MBP in its different states using time-resolved tryptophan fluorescence anisotropy. We found that the 'empty' protein exhibits strong internal fluctuations that almost vanish upon ligand binding. The measured relaxation times corresponding to internal fluctuations can be interpreted as originating from two types of motion: wobbling of tryptophan side-chains relative to the protein backbone, and orientational fluctuations of entire domains. After binding of a ligand, domain motions are no longer detectable and the fluctuations of some of the tryptophan side-chains become rather restricted. This transformation into a more rigid state is observed upon binding of both ligands, maltose and the larger beta-cyclodextrin. The fluctuations of tryptophan side-chains in direct contact with the ligand, however, are affected in a slightly different way by the two ligands.

Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 A resolution.

BACKGROUND: Bacteriorhodopsin (bR) from Halobacterium salinarum is a proton pump that converts the energy of light into a proton gradient that drives ATP synthesis. The protein comprises seven transmembrane helices and in vivo is organized into purple patches, in which bR and lipids form a crystalline two-dimensional array. Upon absorption of a photon, retinal, which is covalently bound to Lys216 via a Schiff base, is isomerized to a 13-cis,15-anti configuration. This initiates a sequence of events - the photocycle - during which a proton is transferred from the Schiff base to Asp85, followed by proton release into the extracellular medium and reprotonation from the cytoplasmic side. RESULTS: The structure of bR in the ground state was solved to 1.9 A resolution from non-twinned crystals grown in a lipidic cubic phase. The structure reveals eight well-ordered water molecules in the extracellular half of the putative proton translocation pathway. The water molecules form a continuous hydrogen-bond network from the Schiff-base nitrogen (Lys216) to Glu194 and Glu204 and includes residues Asp85, Asp212 and Arg82. This network is involved both in proton translocation occurring during the photocycle, as well as in stabilizing the structure of the ground state. Nine lipid phytanyl moieties could be modeled into the electron-density maps. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of single crystals demonstrated the presence of four different charged lipid species. CONCLUSIONS: The structure of protein, lipid and water molecules in the crystals represents the functional entity of bR in the purple membrane of the bacteria at atomic resolution. Proton translocation from the Schiff base to the extracellular medium is mediated by a hydrogen-bond network that involves charged residues and water molecules.

Detergent-free membrane protein crystallization.

A comprehensive understanding of structure-function relationships of proteins requires their structures to be elucidated to high resolution. With most membrane proteins this has not been accomplished so far, mainly because of their notoriously poor crystallizability. Here we present a completely detergent-free procedure for the incorporation of a native purple membrane into a monoolein-based lipidic cubic phase, and subsequent crystallization of three-dimensional bacteriorhodopsin crystals therein. These crystals exhibit comparable X-ray diffraction quality and mosaicity, and identical crystal habit and space group to those of bacteriorhodopsin crystals that are grown from detergent-solubilized protein in cubic phase.

Lipidic Cubic Phases: New Matrices for the Three-Dimensional Crystallization of Membrane Proteins.

The major constraint in attaining high resolution structures of membrane proteins by X-ray crystallography is the growth of well-ordered three-dimensional crystals. To enable such crystallizations, we have used lipidic cubic phases consisting of monoglycerides and water. Bacteriorhodopsin and lysozyme, as paradigms of membrane and soluble proteins, nucleate and grow to well-ordered crystals that diffract X-rays isotropically in all three dimensions to 2.0 Å. We envisage bacteriorhodopsin to partition into, and diffuse within, the bilayer of a lipidic cubic matrix, while the polar lysozyme resides in the aqueous compartment thereof. The phenomenology of bicontinuous cubic phases, consisting of curved bilayers whose structures follow infinitely periodic minimal surfaces (IPMS), is presented. Detailed prescriptions of the preparation of lipidic cubic phase matrices are given and their potential for the crystallization of other biological macromolecules is discussed. Copyright 1998 Academic Press.

Manipulation and molecular resolution of a phosphatidylcholine-supported planar bilayer by atomic force microscopy.

The morphology of supported planar bilayers has been investigated below phase transition temperature by atomic force microscopy in contact and tapping mode. The bilayers were formed by the vesicle-spreading technique. In contact mode at low scanning forces of about 1 nN true molecular resolution could be achieved for supported phosphatidylcholine bilayers. The resolution was confirmed by experiments that captured the location, average area of individual lipid headgroups and the manipulation of the bilayer surface. Repeated scanning in contact mode shifted the random topology of the surface consecutively to a striped pattern. Height profiles of defect-containing bilayers were analyzed. The shape of the defects became smooth by repeated scanning. The height profiles allowed the estimation of the indentation of the tip into the surface-adsorbed membrane. In tapping mode a disordered pattern of headgroups became visible. Our morphological data at molecular resolution suggest that the native arrangement of the choline head-groups is disordered, free of large packing defects and becomes ordered in Schallamach waves by scanning in contact mode.

Lipid vesicle adsorption versus formation of planar bilayers on solid surfaces.

The absorption and spreading behavior of lipid vesicles composed of either palmitoyloleoylphosphatidylcholine (POPC) or Escherichia coli lipid upon contact with a glass surface was examined by fluorescence measurements. Fluorescently labeled lipids were used to determine 1) the amount of lipid adsorbed at the surface, 2) the extent of fusion of the vesicles upon contact with the surface, 3) the ability of the adsorbed lipids to undergo lateral diffusion, and 4) the accessibility of the adsorbed lipids by external water soluble molecules. The results of these measurements indicate that POPC vesicles spread on the surface and form a supported planar bilayer, whereas E. coli lipid vesicles adsorb to the surface and form a supported vesicle layer. Supported planar bilayers were found to be permeable for small molecules, whereas supported vesicles were impermeable and thus represented immobilized, topologically separate compartments.