X-ray scattering studies of a model complex of lipid and basic protein of myelin

Low-angle and wide-angle X-ray scattering data from phosphatidylglycerol complexed with myelin basic protein, poly(L-lysine) and calcium ions are analyzed. The results confirm our earlier report (Brady, G.W., Murthy, N.S., Fein, D.B., Wood, D.D. and Moscarello, M.A. (1981) Biophys. J. 34, 345-350) that the basic protein interacts primarily with the polar headgroups of the lipid; and that at high protein concentrations (greater than 35%) the bilayers aggregate to form multilayers with a repeat period of 68 A, the single bilayer to multilayer transition being a cooperative process. Polylysine and Ca2+ produce multilayers with a smaller repeat of approx. 55 A. Basic protein and polylysine do not change the fluid-like arrangement of the hydrocarbon chains (diffuse 4.6 A peak in the wide-angle pattern), whereas Ca2+ probably induces a two-dimensional order (4.3 A and 3.9 A peak in the wide-angle pattern). Electron density profiles of the lipid and lipid-basic protein vesicles indicate that the basic protein penetrates into the bilayer.     

X-ray scattering studies of heavy atom bound erythrocyte membrane suspensions

We have observed a periodic intensity variation of scattered x-rays from uranyl labeled erythrocyte membranes. Using unique x-ray scattering methods, we have made these measurements from membrane suspensions in which the vesicles appear, by phase contrast microscopy, to be normal in shape. The periodic intensity variation is not present for membranes labeled on one side only. The frequency of the variation permits calculation of membrane width, which we find to be 55Å.     

Characterization of lipid matrices for membrane protein crystallization by high-throughput small angle X-ray scattering

The lipidic cubic phase (LCP) has repeatedly proven to serve as a successful membrane-mimetic matrix for a variety of difficult-to-crystallize membrane proteins. While monoolein has been the predominant lipid of choice, there is a growing need for the characterization and use of other LCP host lipids, allowing exploration of a range of structural parameters such as bilayer thickness and curvature for optimal insertion, stability and crystallogenesis of membrane proteins. Here, we describe the development of a high-throughput (HT) pipeline to employ small angle X-ray scattering (SAXS) - the most direct technique to identify lipid mesophases and measure their structural parameters - to interrogate rapidly a large number of lipid samples under a variety of conditions, similar to those encountered during crystallization. Leveraging the identical setup format for LCP crystallization trials, this method allows the quickly assessment of lipid matrices for their utility in membrane protein crystallization, and could inform the tailoring of lipid and precipitant conditions to overcome specific crystallization challenges. As proof of concept, we present HT LCP-SAXS analysis of lipid samples made of monoolein with and without cholesterol, and of monovaccenin, equilibrated with solutions used for crystallization trials and LCP fluorescence recovery after photobleaching (FRAP) experiments.     

Comparative X-ray studies on the interaction of carotenoids with a model phosphatidylcholine membrane

The interaction of structurally different carotenoids with a membrane molecular model was examined by X-ray diffraction. The selected compounds were beta-carotene, lycopene, lutein, violaxanthin, zeaxanthin, and additionally carotane, a fully saturated derivative of beta-carotene. They present similarities and differences in their rigidity, the presence of terminal ionone rings and hydroxy and epoxy groups bound to the rings. The membrane models were multibilayers of dipalmitoylphosphatidylcholine (DPPC), chosen for this investigation because the 3 nm thickness of the hydrophobic core of its bilayer coincides with the thickness of the hydrophobic core of thylakoid membranes and the length of the carotenoid molecules. Results indicate that the six compounds induced different types and degrees of structural perturbations to DPPC bilayers in aqueous media. They were interpreted in terms of the molecular characteristics of DPPC and the carotenoids. Lycopene and violaxanthin induced the highest structural damage to the acyl chain and polar headgroup regions of DPPC bilayers, respectively.     

Experimental and theoretical studies of emodin interacting with a lipid bilayer of DMPC

Emodin is one of the most abundant anthraquinone derivatives found in nature. It is the active principle of some traditional herbal medicines with known biological activities. In this work, we combined experimental and theoretical studies to reveal information about location, orientation, interaction and perturbing effects of Emodin on lipid bilayers, where we have taken into account the neutral form of the Emodin (EMH) and its anionic/deprotonated form (EM^?). Using both UV/Visible spectrophotometric techniques and molecular dynamics (MD) simulations, we showed that both EMH and EM^? are located in a lipid membrane. Additionally, using MD simulations, we revealed that both forms of Emodin are very close to glycerol groups of the lipid molecules, with the EMH inserted more deeply into the bilayer and more disoriented relative to the normal of the membrane when compared with the EM^?, which is more exposed to interfacial water. Analysis of several structural properties of acyl chains of the lipids in a hydrated pure DMPC bilayer and in the presence of Emodin revealed that both EMH and EM^? affect the lipid bilayer, resulting in a remarkable disorder of the bilayer in the vicinity of the Emodin. However, the disorder caused by EMH is weaker than that caused by EM^?. Our results suggest that these disorders caused by Emodin might lead to distinct effects on lipid bilayers including its disruption which are reported in the literature.     

Monte Carlo studies of lipid chains and gramicidin A in a model membrane

The Monte Carlo method has been used to simulate the equilibrium properties of a planar array of 94 saturated lipid chains and one monomer of Gramicidin A. Chains are free to move laterally in the layer plane and to change conformation via gauche rotations and long axis rotations in a continuum. All non-hydrogen atoms on chains and on the Gramicidin A monomer interact via 6-12 potentials, and periodic boundary conditions are imposed. Calculated results consist of order parameter profiles for C-14 and C-16 chains. Profiles are calculated for chains which are neighbors to the Gramicidin A molecule and for chains which are not neighbors to the peptide. The main conclusion is that the average conformations of the chains neighboring the Gramicidin A monomer are very similar to those of the bulk chains.     

Small angle X-ray scattering as a complementary tool for high-throughput structural studies

Structural crystallography and nuclear magnetic resonance (NMR) spectroscopy are the predominant techniques for understanding the biological world on a molecular level. Crystallography is constrained by the ability to form a crystal that diffracts well and NMR is constrained to smaller proteins. Although powerful techniques, they leave many soluble, purified structurally uncharacterized protein samples. Small angle X-ray scattering (SAXS) is a solution technique that provides data on the size and multiple conformations of a sample, and can be used to reconstruct a low-resolution molecular envelope of a macromolecule. In this study, SAXS has been used in a high-throughput manner on a subset of 28 proteins, where structural information is available from crystallographic and/or NMR techniques. These crystallographic and NMR structures were used to validate the accuracy of molecular envelopes reconstructed from SAXS data on a statistical level, to compare and highlight complementary structural information that SAXS provides, and to leverage biological information derived by crystallographers and spectroscopists from their structures. All the ab initio molecular envelopes calculated from the SAXS data agree well with the available structural information. SAXS is a powerful albeit low-resolution technique that can provide additional structural information in a high-throughput and complementary manner to improve the functional interpretation of high-resolution structures.     

Neutron and X-ray scattering studies on the human complement protein properdin provide an analysis of the thrombospondin repeat

Properdin is a regulatory glycoprotein of the alternative pathway of the complement system of immune defense. It is responsible for the stabilization of the C3 convertase complex formed between C3b and the Bb fragment of factor B. Neutron and X-ray solution scattering experiments were performed on the dimeric and trimeric forms of properdin. These have RG values of 9.1 and 10.7 nm, respectively. The scattering curves were compared with Debye sphere modeling simulations for properdin. Good agreements were obtained for models similar to published electron micrographs showing that the properdin trimer has a triangular structure with sides of 26 nm. Such a structure also accounted for sedimentation coefficient data on properdin. Primary structure analyses for mouse and human properdin have shown that this contains six homologous motifs known as the thrombospondin repeat (TSR), which is the second most abundant domain type found in the complement proteins. Sequences for these 12 TSRs were aligned with 19 others found in thrombospondin and the late complement components. Three distinct groups of TSRs were identified, namely, the TSRs found in thrombospondin and properdin, the TSRs mostly found at the N-terminus of the late complement components, and the TSRs found at the C-terminus of the late components. Averaged secondary structure predictions suggested that all three groups contain similar backbone structures with two amphipathic turn regions and one hydrophilic beta-strand region. The mean dimensions of the TSRs of properdin in solution were determined to be approximately 4 nm X 1.7 nm X 1.7 nm, showing that these are elongated in structure.     

Semisynthetic latrunculin B analogs: Studies of actin docking support a proposed mechanism for latrunculin bioactivity

Latrunculins are unique macrolides containing a thiazolidinone moiety. Latrunculins A, B and T and 16-epi-latrunculin B were isolated from the Red Sea sponge Negombata magnifica. N-Alkylated, O-methylated analogs of latrunculin B were synthesized and biological evaluation was performed for antifungal and antiprotozoal activity. The natural latrunculins showed significant bioactivity, while the semisynthetic analogs did not. Docking studies of these analogs into the X-ray crystal structure of G-actin showed that, in comparison with latrunculins A and B, N-alkylated latrunculins did not dock satisfactorily. This suggests that the analogs do not fit well into the active site of G-actin due to steric clashes and provides an explanation for the absence of bioactivity.     

Immunological templates: a new model and proposed mechanism of immunogenicity

Immunogenicity of an antigen is dependent both on possession of antigenic determinants, including the haptenic portion(s) of the antigen, and binding groups. The binding groups are necessary for processing of the antigen to occur whereas the antigenic determinants specify the antibody structure. Some arrangements of these antigenic determinants in relation to the binding groups are proposed, as well as the relationships of these ligands during processing on a cellular processing template to form an antibody RNA. The antibody RNA is manufactured by a unique mode of inverse translation.     

Collagen type I together with fibronectin provide a better support for endothelialization

Endothelialization of vascular implants is limited by the inability of cells to retain adhesion when exposed to flow. Extracellular matrix proteins, including fibronectin and collagen, enhance cell adherence on materials. This study investigated the behaviour of Human Umbilical Vein Endothelial Cells (HUVEC) on extracellular matrix coated polystyrene. Collagen and fibronectin were coated as single and double layers to analyse differences in cell proliferation, morphology, and cell-protein interactions. Significantly higher endothelial cell proliferation and migration rates were observed on the collagen and collagen+fibronectin coating compared to the uncoated or fibronectin-coated sample. Immmunofluorescent microscopy showed evidence of extracellular matrix remodelling in the double, collagen+fibronectin coating. These results strongly suggest that a double coating of collagen+fibronectin provides a better support structure for endothelial cell growth and contributes to improve the ability of vascular implants to become and remain endothelialized.     

Site-directed alkylation studies with LacY provide evidence for the alternating access model of transport

In total, 59 single Cys-replacement mutants in helix VII and helix X of the lactose permease of Escherichia coli were subjected to site-directed fluorescence labeling in right-side-out membrane vesicles to complete the testing of Cys accessibility or reactivity. For both helices, accessibility/reactivity is relatively low at the level of the sugar-binding site where the helices are tightly packed. However, labeling of Cys substitutions in helix VII with tetramethylrhodamine-5-maleimide decreases from the middle toward the cytoplasmic end and increases toward the periplasmic end. Helix X is labeled mainly on the side facing the central hydrophilic cavity with relatively small or no changes in the presence of ligand. In contrast, sugar binding causes a significant increase in accessibility/reactivity at the periplasmic end of helix VII. When considered with similar findings from N-ethylmaleimide alkylation studies, the results confirm and extend support for the alternating access model.     

In situ characterization of lipid A interaction with antimicrobial peptides using surface X-ray scattering

Lipid A structure at the air-aqueous interface has been studied using pressure-area isotherm methods coupled with the surface X-ray scattering techniques of X-ray reflectivity (XR) and grazing incidence X-ray diffraction (GIXD). Lipid A monolayers were formed at the air-aqueous interface to represent the lipid moiety of the outer membrane of Gram-negative bacteria. Lipid A structure was characterized at surface pressures between 10 and 35 mN/m. Interactions of α-helical antimicrobial peptides LL-37, SMAP-29 and D2A22 with lipid A monolayers were subsequently studied. Although insertion into the lipid A monolayers was observed with the α-helical peptides, little change was seen from the X-ray data, suggesting that the lipid A hydrocarbon chains are involved in reorientation during insertion and that the hydrocarbon chains have a relatively rigid structure.     

Liposomes as membrane model for study of lipid peroxidation

This article describes the properties, production and characterization of liposomes with special reference to their use as membrane model for the study of lipid peroxidation. It presents briefly the methods that can be used for the assay of liposomal lipid peroxidation and brings out the special advantages these liposomes provide in elucidating the mechanism of lipid peroxidation by different physical and chemical agents. Studies involving liposomal lipid peroxidation by different agents and the consequent changes in the structure and function of liposomal membrane have been reviewed briefly.     

Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design

UMP synthase (UMPS) catalyzes the last two steps of de novo pyrimidine nucleotide synthesis and is a potential cancer drug target. The C-terminal domain of UMPS is orotidine-5'-monophosphate decarboxylase (OMPD), a cofactor-less yet extremely efficient enzyme. Studies of OMPDs from micro-organisms led to the proposal of several noncovalent decarboxylation mechanisms via high-energy intermediates. We describe nine crystal structures of human OMPD in complex with substrate, product, and nucleotide inhibitors. Unexpectedly, simple compounds can replace the natural nucleotides and induce a closed conformation of OMPD, defining a tripartite catalytic site. The structures outline the requirements drugs must meet to maximize therapeutic effects and minimize cross-species activity. Chemical mimicry by iodide identified a CO(2) product binding site. Plasticity of catalytic residues and a covalent OMPD-UMP complex prompt a reevaluation of the prevailing decarboxylation mechanism in favor of covalent intermediates. This mechanism can also explain the observed catalytic promiscuity of OMPD.