Study Of Lipid-protein Interactions Research Articles

Nanodiscs as a New Tool to Examine Lipid-Protein Interactions.

The interactions between lipids and proteins are one of the most fundamental processes in living organisms, responsible for critical cellular events ranging from replication, cell division, signaling, and movement. Enabling the central coupling responsible for maintaining the functionality of the breadth of proteins, receptors, and enzymes that find their natural home in biological membranes, the fundamental mechanisms of recognition of protein for lipid, and vice versa, have been a focal point of biochemical and biophysical investigations for many decades. Complexes of lipids and proteins, such as the various lipoprotein factions, play central roles in the trafficking of important proteins, small molecules and metabolites and are often implicated in disease states. Recently an engineered lipoprotein particle, termed the nanodisc, a modified form of the human high density lipoprotein fraction, has served as a membrane mimetic for the investigation of membrane proteins and studies of lipid-protein interactions. In this review, we summarize the current knowledge regarding this self-assembling lipid-protein complex and provide examples for its utility in the investigation of a large number of biological systems.

Refining amino acid hydrophobicity for dynamics simulation of membrane proteins.

Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlates with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These experimental values serve as important anchor points in choosing between alternate CG models based on their observed permeation profiles, particularly for Arg, Lys and Gln residues where the all-atom OPLS solvation energy does not agree well with experiment. Available partitioning data was also used to reparameterize the representation of the peptide backbone, which needed to be made less attractive for the bilayer hydrophobic core region. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in studies of lipid-protein interactions and the conformational properties of diverse membrane protein systems.

Sphingolipids and their metabolism in physiology and disease.

Studies of bioactive lipids in general and sphingolipids in particular have intensified over the past several years, revealing an unprecedented and unanticipated complexity of the lipidome and its many functions, which rivals, if not exceeds, that of the genome or proteome. These results highlight critical roles for bioactive sphingolipids in most, if not all, major cell biological responses, including all major cell signalling pathways, and they link sphingolipid metabolism to key human diseases. Nevertheless, the fairly nascent field of bioactive sphingolipids still faces challenges in its biochemical and molecular underpinnings, including defining the molecular mechanisms of pathway and enzyme regulation, the study of lipid-protein interactions and the development of cellular probes, suitable biomarkers and therapeutic approaches.

Understanding phospholipid function: Why are there so many lipids?

In the 1970s, phospholipids were still considered mere building blocks of the membrane lipid bilayer, but the subsequent realization that phospholipids could also serve as second messengers brought new interest to the field. My own passion for the unique amphipathic properties of lipids led me to seek other, non-signaling functions for phospholipids, particularly in their interactions with membrane proteins. This seemed to be the last frontier in protein chemistry and enzymology to be conquered. I was fortunate to find my way to Eugene Kennedy's laboratory, where both membrane proteins and phospholipids were the foci of study, thus providing a jumping-off point for advancing our fundamental understanding of lipid synthesis, membrane protein biosynthesis, phospholipid and membrane protein trafficking, and the cellular roles of phospholipids. After purifying and characterizing enzymes of phospholipid biosynthesis in Escherichia coli and cloning of several of the genes encoding these enzymes in E. coli and Saccharomyces cerevisiae, I was in a position to alter phospholipid composition in a systematic manner during the cell cycle in these microorganisms. My group was able to establish, contrary to common assumption (derived from the fact that membrane proteins retain activity in detergent extracts) that phospholipid environment is a strong determining factor in the function of membrane proteins. We showed that molecular genetic alterations in membrane lipid composition result in many phenotypes, and uncovered direct lipid-protein interactions that govern dynamic structural and functional properties of membrane proteins. Here I present my personal "reflections" on how our understanding of phospholipid functions has evolved.

Proteoliposomes in nanobiotechnology.

Proteoliposomes are systems that mimic lipid membranes (liposomes) to which a protein has been incorporated or inserted. During the last decade, these systems have gained prominence as tools for biophysical studies on lipid-protein interactions as well as for their biotechnological applications. Proteoliposomes have a major advantage when compared with natural membrane systems, since they can be obtained with a smaller number of lipidic (and protein) components, facilitating the design and interpretation of certain experiments. However, they have the disadvantage of requiring methodological standardization for incorporation of each specific protein, and the need to verify that the reconstitution procedure has yielded the correct orientation of the protein in the proteoliposome system with recovery of its functional activity. In this review, we chose two proteins under study in our laboratory to exemplify the steps necessary for the standardization of the reconstitution of membrane proteins in liposome systems: (1) alkaline phosphatase, a protein with a glycosylphosphatidylinositol anchor, and (2) Na,K-ATPase, an integral membrane protein. In these examples, we focus on the production of the specific proteoliposomes, as well as on their biochemical and biophysical characterization, with emphasis on studies of lipid-protein interactions. We conclude the chapter by highlighting current prospects of this technology for biotechnological applications, including the construction of nanosensors and of a multi-protein nanovesicular biomimetic to study the processes of initiation of skeletal mineralization.

Lipid—Protein Interactions Revealed by Two‐Photon Microscopy and Fluorescence Correlation Spectroscopy

AbstractFor Abstract see ChemInform Abstract in Full Text.

A New Method for Studying in vitro Lipid Transport: The 45-kDa Protein from Rat Olfactory Epithelium Is a Specific Carrier of Phosphatidylinositol 3,4,5-Triphosphate

A new method for studying lipid-protein interactions in vitro is developed. It enables the study of the transporting activity of a protein toward a lipid ligand, including the case of an unknown lipid type. The method can be considered as a variant of partition three-phase chromatography with two stationary (donor and acceptor) phases and one mobile phase. The protein under study is dissolved in an aqueous mobile phase and induces a specific delivery of a lipid to the acceptor lipid layer. The transported lipid is identified in Folch lipid extracts from the acceptor layer and aqueous phase. The secretory protein with M 45 kDa from the rat olfactory epithelium is shown to be a carrier of phosphatidylinositol 3,4,5-triphosphate. Our approach opens up new possibilities in the study of lipid-protein interactions in vitro and has a number of advantages over the methods now used for these purposes.

Lipid−Protein Interactions Revealed by Two-Photon Microscopy and Fluorescence Correlation Spectroscopy

Cellular processes involve a multitude of chemical reactions that must be kept in delicate equilibrium to maintain cellular homeostasis. Powerful biophysical techniques are needed to measure the localization and concentration of target molecules as well as to quantify complex molecular processes in model and in vivo systems. Two-photon microscopy and fluorescence correlation spectroscopy (FCS) can measure association and dynamics of appropriate molecules under equilibrium conditions. FCS provides information on motility (diffusion coefficients), concentration (number of particles), association (molecular brightness), and localization (image) of the target molecules. All of this information, in conjunction with computational modeling techniques, can help us to better understand the network of complex molecular interactions, which are at the basis of cellular processes. Fluorescence imaging techniques add the beauty of visualization to the scientific information. Photons emitted by a fluorescent dye are digitized, and the associated spatial information and intensity can be translated into different colors and shades providing the researcher not only with quantitative intensity information but also with spatial resolution and visual comprehension of two- or three-dimensional images. In this Account, we review the use of two-photon excitation microscopy and FCS in the study of lipid-protein interactions. We discuss these new methodologies and techniques, and we present examples of different complexity from qualitative to quantitative, from simple model systems to studies in living cells.

Interaction of membrane-spanning proteins with peripheral and lipid-anchored membrane proteins: perspectives from protein-lipid interactions (Review).

Studies of lipid-protein interactions in double-reconstituted systems involving both integral and peripheral or lipid-anchored proteins are reviewed. Membranes of dimyristoyl phosphatidylglycerol containing either myelin proteolipid protein or cytochrome c oxidase were studied. The partner peripheral proteins bound to these membranes were myelin basic protein or cytochrome c, respectively. In addition, the interactions between the myelin proteolipid protein and avidin that was membrane-anchored by binding to N-biotinyl phosphatidylethanolamine were studied in dimyristoyl phosphatidylcholine membranes. Steric exclusion plays a significant role when sizes of the peripheral protein and transmembrane domain of the integral protein are comparable. Even so, the effects on avidin-linked lipids are different from those induced by myelin basic protein on freely diffusible lipids, both interacting with the myelin proteolipid protein. Both the former and the cytochrome c/cytochrome oxidase couple evidence a propagation of lipid perturbation out from the intramembrane protein interface that could be a basis for formation of microdomains.

Spin-label studies of lipid-protein interactions with reconstituted band 3, the human erythrocyte chloride-bicarbonate exchanger

Lipid-protein interactions in reconstituted band 3 preparations were investigated by using spin-labeled lipids in conjunction with electron paramagnetic resonance (EPR) spectroscopy. Purified erythrocyte band 3 was reconstituted into egg phosphatidylcholine liposomes at high protein density with preservation predominantly of the dimeric state. Lipid-protein associations were revealed by the presence of a component in the EPR spectra that, when compared to spectra obtained from protein-free bilayers, indicated that lipid chain motions are restricted by interactions with the protein. From the fraction of the motionally restricted component obtained from the phosphatidylcholine spin-label, a value of 64 ± 14 annular lipids per band 3 dimer was obtained. This agrees with a value of 62 for the number of lipids that may be accommodated around the electron density map of a band 3 dimer. Selectivity of various spin-labeled lipids for the protein revealed that androstanol had a lower affinity for the band 3 interface, whereas a distinct preference was observed for the negatively charged lipids phosphatidylglycerol and stearic acid over phosphatidylcholine. This preference for negatively charged lipids could not be screened by 1-M salt, indicating that electrostatic lipid-protein interactions are not dominant. Estimates of annular lipid exchange rates from measured acyl chain segmental motions suggested that the rate of exchange between bilayer and boundary lipids was ~106 s-1, at least an order of magnitude slower than the rate of lipid lateral diffusion in protein-free bilayers.Key words: band 3, reconstitution, electron paramagnetic resonance, lipid-protein interactions.

Spin-label studies of lipid-protein interactions with reconstituted band 3, the human erythrocyte chloride-bicarbonate exchanger.

Lipid-protein interactions in reconstituted band 3 preparations were investigated by using spin-labeled lipids in conjunction with electron paramagnetic resonance (EPR) spectroscopy. Purified erythrocyte band 3 was reconstituted into egg phosphatidylcholine liposomes at high protein density with preservation predominantly of the dimeric state. Lipid-protein associations were revealed by the presence of a component in the EPR spectra that, when compared to spectra obtained from protein-free bilayers, indicated that lipid chain motions are restricted by interactions with the protein. From the fraction of the motionally restricted component obtained from the phosphatidylcholine spin-label, a value of 64 +/- 14 annular lipids per band 3 dimer was obtained. This agrees with a value of 62 for the number of lipids that may be accommodated around the electron density map of a band 3 dimer. Selectivity of various spin-labeled lipids for the protein revealed that androstanol had a lower affinity for the band 3 interface, whereas a distinct preference was observed for the negatively charged lipids phosphatidylglycerol and stearic acid over phosphatidylcholine. This preference for negatively charged lipids could not be screened by 1-M salt, indicating that electrostatic lipid-protein interactions are not dominant. Estimates of annular lipid exchange rates from measured acyl chain segmental motions suggested that the rate of exchange between bilayer and boundary lipids was approximately 10(6) s(-1), at least an order of magnitude slower than the rate of lipid lateral diffusion in protein-free bilayers.

The Study of Lipid-Protein Interactions: Effect of Melittin on Phase Transition of Phosphatidylethanolamine and Sensitivity of Phospholipases to Phase State1

The effects of melittin on the bilayer-to-inverted hexagonal (HII) phase transition of egg phosphatidylethanolamine (EPE) and the influence of the phase state of membrane matrix on hydrolysis of EPE by phospholipases have been studied. The phase transitions were measured using the fluorescent probe N-(7-nitro-2,1,3-benzoxadiazol-4-yl)phosphatidylethanolamine (N-NBD-PE) and differential scanning calorimetry. In the presence of melittin at a lipid-to-melittin molar ratio (R1) of 200, 100, and 20, the phase transition of EPE disappeared, indicating that melittin stabilizes the bilayer structure. In the presence of 10 mol% of cholesterol, the phase transition temperature (TH) decreased and TH was observed even in the presence of melittin at R1 of 200 and 100. The fluorescence intensity of the tryptophan residue of melittin is sensitive to the phase transition and the wavelength of emission maxima shift from 352 to 337 nm upon addition of EPE and EPE-cholesterol (10 mol%) at R1 of 200. Kinetic parameters for phospholipase-catalyzed hydrolysis of EPE in bilayer and HII phases showed that HII phase of EPE is a poorer substrate for phospholipases and that cholesterol decreases the susceptibility of EPE to phospholipases.

Adsorption of cytochrome c to phospholipid monolayers studied by reflection spectroscopy

The uptake of cytochrome c by charged and neutral lipid monolayers was studied by using reflection spectroscopy. The method was shown to be a very sensitive and useful technique in studies of lipid-protein interactions. It was found that cytochrome c is preferentially bound to monolayers of negatively charged monolayers in the solid phase. Polarized light under oblique incidence was used to determine the average orientation of chromophores in cytochrome c bound to lipid monolayer. The transition moments of chromophore are oriented parallel to the monolayer plane.

Lipid-protein interactions in biomembranes studied through the phospholipid specificity of d-β-hydroxybutyrate dehydrogenase

Since the biological membranes are fundamental units in the living cells, the studies of lipid-protein interactions are crucial for the understanding of their structure, functions and properties. Beside hydrophobic interactions between fatty acids chain of phospholipids and intrinsic membrane proteins, the interactions between charged groups of the protein with the polar heads of phospholipids generally confer the specificity which may be absolute or preferential. This paper reports essential results obtained these last few years with D-beta-hydroxybutyrate dehydrogenase (BDH) from inner mitochondrial membrane, one of the most interesting and best documented examples of a lipid-requiring enzyme. This is a review of the molecular basis--knowledge and strategy of study--of the lipid specificity for membrane protein functions.

Estimation of lipid regions in a cytochrome oxidase-lipid complex using spin labeling electron spin resonance: distribution effects on the spin label.

The distribution of lipid in the cytochrome oxidase-lipid complex from beef heart mitochondria has been studied by the spin labeling electron spin resonance technique. The spectra of a phospholipid spin label incorporated in the complex reveals an immobilized (on the ESR time scale) component in addition to the fluid component which is found in aqueous dispersions of the extracted lipids. The first component corresponds to the domain of lipid influenced by the protein, and the second component to the remaining lipid. A theory taking into account not only the sizes of the lipid regions in which the spin label molecule distributes itself, but also the different affinities of the label for the two domains, has been developed. Taking advantage of the variation in spectra obtained with increasing amounts of spin label, computer calculations have been performed to estimate the distribution of lipid in the different regions of the cytochrome oxidase-lipid complex. An extrapolation of the amount of immobilized spin-labeled phospholipid to zero concentration of label allows a calculation of the number of fatty acid residues interacting with the protein to be made. It has been found that the number of aliphatic chains influenced by the protein is higher than that calculated for a single boundary layer around the protein. The approach used in this paper can be used for studies of protein-lipid interactions in other systems.

Synthesis of spin-labelled 2-(16'-(N-oxyl-4'',4''-dimethyloxazolidine)stearoyl)-phosphatidylcholine.

Chemical synthesis of spin-labelled lecithin 2-(16'-(N-oxyl-4'',4''-dimethyloxazolidine)stearoyl)-phosphatidylcholine was achieved by reaction of equimolar amounts of purified egg yolk lyso-lecithin with commercially available 16-(N-oxyl-4',4'-dimethyloxazolidine)stearic acid activated with N,N-carbonyldiimidazole. After purification by silicic acid column chromatography, spin-labelled lecithin was obtained in 52.2% yield and had an ester: phosphorus:spin molar ratio of 2.0:1.1:1.0. When dimyristoyl-phosphatidylcholine and dimyristoyl-phosphatidylcholine:cholesterol (10:1) liposomes, containing 2-(16'-(N-oxyl-4'',4''-dimethyloxazolidine)stearoyl)-phosphatidylcholine as a probe were examined for thermotropic changes monitored by electron spin resonance spectroscopy, transition temperatures of 24.0 and 24.2 degrees C, respectively, were obtained in a very good agreement with previously reported values obtained with different probes and by different techniques, and with our own differential scanning calorimetry measurements. The potential usefulness of synthetic 2-(16'-(N-oxyl-4'',4''-dimethyloxazolidine)stearoyl)-phosphatidylcholine as a spin-label probe in studies of lipid-protein interactions in biological membranes was discussed.

The study of lipid-protein interactions in membranes by fluorescent probes

1. 1. We report the fluorescence of 1-anilinonaphthalene-8-sulfonate from 220 mμ up in various solvents, in association with lecithin and lysolecithin and bound to membranes of human erythrocytes. 2. 2. The membrane spectra indicate that there is transfer of electronic excitation energy from some of the tryptophans of membrane-bound 1-anilinonaphthalene-8-sulfonate. 3. 3. Our findings raise the possibility that some or all of the membrane-bound 1-anilinonaphthalene-8-sulfonate is associated with membrane proteins; the dye can therefore not be assumed to act solely as a probe for possible lipid regions in membranes.