Neutron and X-ray diffraction structural analysis of phosphatidylinositol bilayers

Phosphatidylinositol (PI) bilayers, squeezed together by applied osmotic pressures, were studied by both neutron diffraction and X-ray diffraction. The lamellar repeat period for PI bilayers decreased from 9.5 nm at an applied pressure of 1.1.10(6) dyn/cm2 (1.1 atm) to 5.4 nm at an applied pressure of 1.6.10(7) dyn/cm2 (16 atm). Further increases in applied pressure, up to 2.7.10(9) dyn/cm2 (2700 atm) reduced the repeat period by only about 0.3 nm, to 5.1 nm. Thus, a plot of applied pressure versus repeat period shows a sharp upward break for repeat periods less than about 5.4 nm. For repeat periods of less than 5.4 nm, analysis of neutron-scattering density profiles and electron-density profiles indicates that the structure of the PI bilayers changes as the bilayers are dehydrated, even though there are only small changes in the repeat period. These structural changes are most likely due to removal of water from the headgroup regions of the bilayer. D2O/H2O exchange experiments show that, at an applied pressure of 2.8.10(7) dyn/cm2, water is located between adjacent PI headgroups in the plane of the bilayer. We conclude that, although electrostatics provide the dominant long-range repulsive interaction, hydration repulsion and steric hindrance between PI headgroups from apposing bilayers provide the major barriers for the close approach of adjacent PI bilayers for repeat periods less than 5.4 nm. This structural analysis also indicates that the phosphoinositol group extends from the plane of the bilayer into the fluid space between adjacent bilayers. This extended orientation for the headgroup is consistent with electrophoretic measurements on PI vesicles.     

Neutron diffraction studies of digalactosyldiacylglycerol

The structure of the digalactosyldiacylglycerol bilayer is calculated using neutron diffraction data. The polar head group of this lipid is oriented parallel to the plane of the bilayer such that the galactose moieties are tightly packed at the bilayer surface into a 0.8 nm thick polar layer. The thickness of this layer is independent of water activity over a wide range (15-100% relative humidity). The constant thickness of both the galactose layer and the hydrocarbon layer constrain the structure factor amplitudes to lie on a single continuous transform for repeat periods between 4 and 5 nm.     

Choosing membrane mimetics for NMR structural studies of transmembrane proteins

The native environment of membrane proteins is complex and scientists have felt the need to simplify it to reduce the number of varying parameters. However, experimental problems can also arise from oversimplification which contributes to why membrane proteins are under-represented in the protein structure databank and why they were difficult to study by nuclear magnetic resonance (NMR) spectroscopy. Technological progress now allows dealing with more complex models and, in the context of NMR studies, an incredibly large number of membrane mimetics options are available. This review provides a guide to the selection of the appropriate model membrane system for membrane protein study by NMR, depending on the protein and on the type of information that is looked for. Beside bilayers (of various shapes, sizes and lamellarity), bicelles (aligned or isotropic) and detergent micelles, this review will also describe the most recent membrane mimetics such as amphipols, nanodiscs and reverse micelles. Solution and solid-state NMR will be covered as well as more exotic techniques such as DNP and MAOSS.     

Neutron diffraction studies of the corneal stroma

Low-angle neutron diffraction patterns have been obtained from demembranated beef corneal stroma using the D11 camera available at the Institut Laue-Langevin, Grenoble. These diffraction patterns show three peaks: the first peak corresponds to the interfibrillar distance in the stroma and the others are the third and fifth orders of the collagen spacing. The position of the interfibrillar peak as a function of the hydration of the tissue and the swelling properties of the stroma have been studied at different pH values. The results suggest that in swollen cornea there may be a system of mutually repelling cylinders that expands uniformly to fill the space made available by the water present, and there seems little possibility for fibril cross-linking.     

Zooming in on disordered systems: Neutron reflection studies of proteins associated with fluid membranes

Neutron reflectometry (NR) is an emerging experimental technique for the structural characterization of proteins interacting with fluid bilayer membranes under conditions that mimic closely the cellular environment. Thus, cellular processes can be emulated in artificial systems and their molecular basis studied by adding cellular components one at a time in a well-controlled environment while the resulting structures, or structural changes in response to external cues, are monitored with neutron reflection. In recent years, sample environments, data collection strategies and data analysis were continuously refined. The combination of these improvements increases the information which can be obtained from NR to an extent that enables structural characterization of protein–membrane complexes at a length scale that exceeds the resolution of the measurement by far. Ultimately, the combination of NR with molecular dynamics (MD) simulations can be used to cross-validate the results of the two techniques and provide atomic-scale structural models. This review discusses these developments in detail and demonstrates how they provide new windows into relevant biomedical problems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.     

Interaction of long-chain n-alcohols with fluid DOPC bilayers: a neutron diffraction study

Lamellar phases composed of fluid dioleoylphosphatidylcholine (DOPC) bilayers containing alkan-1-ols (CnOH, n = 8, 10, 14, 16, 18 is the number of carbon atoms) at CnOH : DOPC = 0.3 molar ratio and hydrated with heavy water at 20.2 ≥ D2O : DOPC ≥ 14.4 molar ratio were studied by neutron diffraction. The bilayer thickness d(L) and the bilayer surface area A(L) per DOPC at the bilayer-water interface were obtained from the lamellar repeat period d using molecular volumes of DOPC, CnOH and D2O, and the Luzatti's method. Both the d(L) and A(L) increase with the CnOH chain length n at CnOH : DOPC = 0.3 molar ratio: d(L) = (3.888 ± 0.066) + (0.016 ± 0.005)·n (in nm), A(L) = (0.6711 ± 0.0107) + (0.0012 ± 0.0008)·n (in nm2).     

X-ray diffraction studies of lecithin bilayers.

Counting the individuals in a population before and after an annual period of environmental stress allows the proportion s of the initial population surviving the period to be computed. A series of such observations over n annual periods gives a sequence s₁, s₂, …, s_n. A statistical model is formulated from axioms describing the survival process, and it is concluded that these observed values may usefully be regarded as realizations of a random variable that arises from the normal generated distribution (n.g.d.). Equations for estimating the n.g.d. parameters ζ and τ² from observed survival proportions by the method of moments and maximum likelihood are given. The distributions of parameter estimates ζ and τ² are obtained and discussed in the context of testing hypotheses comparing survival among different populations. Finally, the dependence of the n.g.d. upon parameters ζ and τ² is examined in terms of altering survival, either by population self-regulation mechanisms or man-induced controls. The intent is to provide insight into the relationship between the n.g.d. and its supporting axioms and, more generally, basic knowledge of population processes.     

Utility of surface-supported bilayers in studies of transmembrane helix dimerization

This review focuses on the methods that are available to study transmembrane (TM) helix dimerization in membrane-like environments (either bacterial membranes or lipid bilayers, as mimics of the eukaryotic cellular membrane), with an emphasis on the utility of surface-supported bilayers in such studies.     

Preparation and structural studies of cholesterol bilayers

Bilayers consisting, in their hydrophobic core, entirely of cholesterol can be constructed if a hydrophilic molecular anchor is supplied. $\text{O-}\text{Methoxyethoxyethoxyethylcholesterol}$ and cholesterol sulfate form multilayered liposomes in water. With equimolar cholesterol added, cholesterol sulfate, cholesterolphosphocholine, and $\text{O-}\text{methoxyethoxyethoxyethylcholesterol}$ form small unilamellar liposomes on prolonged sonication. The dimensions of cholesterol-cholesterolphosphocholine vesicles are comparable to those of phospholipid vesicles. ¹³C-NMR spectra suggest that the centers of the bilayers are liquid. The permeability of the cholesterol-cholesterolphosphocholine bilayer against glycerol is lower than that of dipalmitoylphosphatidylcholine-cholesterol bilayer; the activation energy of permeation is two times larger, an indication of a higher degree of structural organization in the ‘hydrogen belts’ of the cholesterol-cholesterolphosphocholine bilayer.     

Interaction of benzene with bilayers. Thermal and structural studies

The thermal and structural properties of saturated phosphatidylcholine liposomes are significantly altered by benzene. Upon the addition of benzene, the liposomes first swell and then disperse into small multilamellar vesicles. At 20 degrees C these vesicles contain striations or ripples in the plane of the bilayer. Major changes in the thermal behavior of DSPC-benzene liposomes occur near mole ratios of 2:1 and 1:1. At a 2:1 mole ratio, the area under the main endothermic peak, delta Hm, essentially disappears; however, the total heat absorbed, delta Hf, remains approximately equal to that of the control. This occurs because for benzene mole fractions 0.12 less than x less than 0.50, benzene increases the apparent molar heat capacity, Cp, of the gel phase to about 1.2 kcal/(mol . deg). We interpret this increase in heat capacity to be due to an increase in the concentration of defects (or disorder) in the gel phase. At mole fractions of benzene between 0.5 and 0.9, the transition temperature decreases by 20-30 degrees C, and broad, multiple transitions are observed. From 0.5 less than or equal to x less than or equal to 0.9, the apparent molar heat capacity of the liquid-crystal phase increases to that of the defected rippled gel phase. The value of delta Hf approaches the heat of fusion for 2 mol of n-octadecane, suggesting that benzene uncouples the liquid-crystalline acyl chains. The lipids affected by benzene or "boundary lipids" have higher heat capacity than nonperturbed lipids. The apparent molar specific heat, Cp, of 1,2-distearoyl-sn-glycero-3-phosphorylcholine (and 1,2-dipalmitoyl-sn-glycero-3-phosphorylcholine) multilamellar vesicles is 0.20 +/- 0.05 kcal/(mol. deg) in the L beta', P beta, and L alpha phases. Cp fluctuates about this value in all three phases upon repeated phase transitions in the same sample. However, the value of Cp in the P beta (rippled) phase exhibits much greater fluctuations in Cp than that in the L alpha phase. We attribute these fluctuations to crystal packing defects.     

Lipid conformation in crystalline bilayers and in crystals of transmembrane proteins

Dihedral torsion angles evaluated for the phospholipid molecules resolved in the X-ray structures of transmembrane proteins in crystals are compared with those of phospholipids in bilayer crystals, and with the phospholipid conformations in fluid membranes. Conformations of the lipid glycerol backbone in protein crystals are not restricted to the gauche C1-C2 rotamers found invariably in phospholipid bilayer crystals. Lipid headgroup conformations in protein crystals also do not conform solely to the bent-down conformation, with gauche-gauche configuration of the phospho-diester, that is characteristic of phospholipid bilayer membranes. This suggests that the lipids that are resolved in crystals of membrane proteins are not representative of the entire lipid-protein interface. Much of the chain configurational disorder of the membrane-bound lipids in crystals arises from energetically disallowed skew conformations. This indicates a configurational heterogeneity in the lipids at a single binding site: eclipsed conformations occur also in some glycerol backbone torsion angles and C-C torsion angles in the lipid headgroups. Stereochemical violations in the protein-bound lipids are evidenced by one-third of the ester carboxyl groups in non-planar configurations, and certain of the carboxyls in the cis configuration. Some of the lipid structures in protein crystals have the incorrect enantiomeric configuration of the glycerol backbone, and many of the branched methyl groups in structures of the phytanyl chains associated with bacteriorhodopsin crystals are in the incorrect S-configuration.     

Neutron diffraction studies of collagen in fully mineralized bone

Neutron diffraction measurements have been made of the equatorial and meridional spacings of collagen in fully mineralized mature bovine bone and demineralized bone collagen, in both wet and dry conditions. The collagen equatorial spacing in wet mineralized bovine bone is 1.24 nm, substantially lower than the 1.53 nm value observed in wet demineralized bovine bone collagen. Corresponding spacings for dry bone and demineralized bone collagen are 1.16 nm and 1.12 nm, respectively. The collagen meridional long spacing in mineralized bovine bone is 63.6 nm wet and 63.4 nm dry. These data indicate that collagen in fully mineralized bovine bone is considerably more closely packed than had been assumed previously, with a packing density similar to that of the relatively crystalline collagens such as wet rat tail tendon. The data also suggest that less space is available for mineral within the collagen fibrils in bovine bone than had previously been assumed, and that the major portion of the mineral in this bone must be located outside the fibrils.     

Using protein structural information in evolutionary inference: transmembrane proteins

We present a model of amino acid sequence evolution based on a hidden Markov model that extends to transmembrane proteins previous methods that incorporate protein structural information into phylogenetics. Our model aims to give a better understanding of processes of molecular evolution and to extract structural information from multiple alignments of transmembrane sequences and use such information to improve phylogenetic analyses. This should be of value in phylogenetic studies of transmembrane proteins: for example, mitochondrial proteins have acquired a special importance in phylogenetics and are mostly transmembrane proteins. The improvement in fit to example data sets of our new model relative to less complex models of amino acid sequence evolution is statistically tested. To further illustrate the potential utility of our method, phylogeny estimation is performed on primate CCR5 receptor sequences, sequences of l and m subunits of the light reaction center in purple bacteria, guinea pig sequences with respect to lagomorph and rodent sequences of calcitonin receptor and K-substance receptor, and cetacean sequences of cytochrome b.     

The achondroplasia mutation does not alter the dimerization energetics of the fibroblast growth factor receptor 3 transmembrane domain

The Gly380 --> Arg mutation in the TM domain of fibroblast growth factor receptor 3 (FGFR3) of the RTK family is linked to achondroplasia, the most common form of human dwarfism. The molecular mechanism of pathology induction is under debate, and two different mechanisms have been proposed to contribute to pathogenesis: (1) Arg380-mediated FGFR3 dimer stabilization and (2) slow downregulation of the activated mutant receptors. Here we show that the Gly380 --> Arg mutation does not alter the dimerization energetics of the FGFR3 transmembrane domain in detergent micelles or in lipid bilayers. This result indicates that pathogenesis in achondroplasia cannot be explained simply by a higher dimerization propensity of the mutant FGFR3 TM domain, thus highlighting the importance of the observed slow downregulation in phenotype induction.     

Constitutive activation of fibroblast growth factor receptor 3 by the transmembrane domain point mutation found in achondroplasia.

Achondroplasia, the most common genetic form of dwarfism, is an autosomal dominant disorder whose underlying mechanism is a defect in the maturation of the cartilage growth plate of long bones. Achondroplasia has recently been shown to result from a Gly to Arg substitution in the transmembrane domain of the fibroblast growth factor receptor 3 (FGFR3), although the molecular consequences of this mutation have not been investigated. By substituting the transmembrane domain of the Neu receptor tyrosine kinase with the transmembrane domains of wild-type and mutant FGFR3, the Arg380 mutation in FGFR3 is shown to activate both the kinase and transforming activities of this chimeric receptor. Residues with side chains capable of participating in hydrogen bond formation, including Glu, Asp, and to a lesser extent, Gln, His and Lys, were able to substitute for the activating Arg380 mutation. The Arg380 point mutation also causes ligand-independent stimulation of the tyrosine kinase activity of FGFR3 itself, and greatly increased constitutive levels of phosphotyrosine on the receptor. These results suggest that the molecular basis of achondroplasia is unregulated signal transduction through FGFR3, which may result in inappropriate cartilage growth plate differentiation and thus abnormal long bone development. Achondroplasia may be one of the number of cogenital disorders where constitutive activation of a member of the FGFR family leads to development abnormalities.     

Neutron diffraction studies of oral stratum corneum model lipid membranes

In this work we have investigated model lipid mixtures simulating a lipid component of oral stratum corneum (OSC). Neutron diffraction experiments on oriented samples have revealed that SM (bovine brain)/dipalmitoylphosphatidylethanolamine/dipalmitoylphosphatidylcholine (DPPE/DPPC) mixtures at molar ratios of 1/2/1 and 1/1/1 are one-phase membranes. The incorporation of low concentrations of ceramide 6 and cholesterol into SM/DPPC/DPPE bilayers does not result in a phase separation, affecting membrane hydration. The model OSC membrane composed of ceramide 6/cholesterol/fatty acids/cholesterol sulfate/SM (bovine brain)/DPPE/DPPC is characterized by coexistence of several lamellar phases, that behave differently during their hydration in water excess. The phase with lamellar repeat distance of about 45 Å is likely a ceramide-rich phase and shows a restricted swelling in water, while another phase with repeat distance of 50 Å swells very quickly on 15 Å and then disappears. Our results indicate that phospholipid-rich and ceramide-rich domains could possibly coexist in the intercellular space of oral epithelium.     

Thermal transitions of DMPG bilayers in aqueous solution: SAXS structural studies

Dimyristoylphosphatidylglycerol (DMPG) has been extensively studied as a model for biological membranes, since phosphatidylglycerol is the most abundant anionic phospholipid in prokaryotic cells. At low ionic strengths, this lipid presents a peculiar thermal behavior, with two sharp changes in the light scattering profile, at temperatures named here T(on)(m) and T(off)(m). Structural changes involved in the DMPG thermal transitions are here investigated by small angle X-ray scattering (SAXS), and compared to the results yielded by differential scanning calorimetry (DSC) and electron spin resonance (ESR). The SAXS results show a broad peak, indicating that DMPG is organized in single bilayers, for the range of temperature studied (10-45 degrees C). SAXS intensity shows an unusual effect, starting to decrease at T(on)(m), and presenting a sharp increase at T(off)(m). The bilayer electron density profiles, obtained from modeling the SAXS curves, show a gradual decrease in electron density contrast (attributed to separation between charged head groups) and in bilayer thickness between T(on)(m) and T(off)(m). Results yielded by SAXS, DSC and ESR indicate that a chain melting process starts at T(on)(m), but a complete fluid phase exists only for temperatures above T(off)(m), with structural changes occurring at the bilayer level in the intermediate region.     

Penetration of lipid chains into transmembrane surfaces of membrane proteins: studies with MscL

The transmembrane surface of a multi-helix membrane protein will be rough with cavities of various sizes between the transmembrane alpha-helices. Efficient solvation of the surface by the lipid molecules that surround the protein in a membrane requires that the lipid fatty acyl chains be able to enter the cavities. This possibility has been investigated using fluorescence quenching methods. Trp residues have been introduced into lipid-facing sites in the first transmembrane alpha-helix (M1) of the mechanosensitive channel of large-conductance MscL; lipid-facing residues at the N-terminal end of M1 are buried below the transmembrane surface of the protein. Fluorescence emission maxima for lipid-facing Trp residues in M1 vary with position in the bilayer comparably to those for Trp residues in the second transmembrane alpha-helix (M2) despite the fact that lipid-facing residues in M2 are on the surface of the protein. Fluorescence emission spectra for most Trp residues on the periplasmic sides of M1 and M2 fit well to a model proposing a trough-like variation of dielectric constant across the membrane, but the relationship between location and fluorescence emission maximum on the cytoplasmic side of the membrane is more complex. The fluorescence of Trp residues in M1 is quenched efficiently by phospholipids with bromine-containing fatty acyl chains, showing that the lipid chains must be able to enter the Trp-containing cavities on the surface of MscL, resulting in efficient solvation of the surface.