Strong interactions between a spin-labeled cholesterol analog and erythrocyte proteins in the human erythrocyte membrane

Molecular dynamics simulations of lipid-protein interactions in SLC4 proteins

The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO3-, CO32-, Cl-, Na+, K+, NH3, and H+, which are necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl-/HCO3- exchanger) and NBCe1 (Na+-CO32-cotransporter). Previous computational studies of the outward-facing state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed coarse-grained and atomistic molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1, and NDCBE (an Na+-CO32-/Cl- exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin. The recently resolved inward-facing state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, phosphatidylcholine, and sphingomyelin in the three studied proteins, and their potential roles in the SLC4 transport function, conformational transition, and protein dimerization are discussed.

Coarse-grained molecular dynamics simulations of lipid-protein interactions in SLC4 proteins

The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO 3 -, CO 3 2- , Cl - , Na + , K + , NH 3 and H + necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl - /HCO 3 - exchanger) and NBCe1 (Na + -CO 3 2- cotransporter). Previous computational studies of the outward facing (OF) state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed multiple 50 µs coarse-grained molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1 and NDCBE (a Na + -CO 3 2- /Cl - exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine (POPC), phosphatidylethanolamine (POPE), phosphatidylserine (POPS), and sphingomyelin (POSM). The recently resolved inward-facing (IF) state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, POPC, and POSM in the three studied proteins and their potential roles in the SLC4 transport function, conformational transition and protein dimerization were discussed.

Statement of significance

The SLC4 protein family is involved in critical physiological processes like pH and blood pressure regulation and maintenance of ion homeostasis. Its members can be found in various tissues. A number of studies suggest possible lipid regulation of the SLC4 function. However, the protein-lipid interactions in the SLC4 family are still poorly understood. Here we make use of long coarse-grained molecular dynamics simulations to assess the protein-lipid interactions in three SLC4 proteins with different transport modes, AE1, NBCe1, and NDCBE. We identify putative lipid binding sites for several lipid types of potential mechanistic importance, discuss them in the framework of the known experimental data and provide a necessary basis for further studies on lipid regulation of SLC4 function.

Cholesterol Chip for the Study of Cholesterol-Protein Interactions Using SPR

Cholesterol, an important lipid in animal membranes, binds to hydrophobic pockets within many soluble proteins, transport proteins and membrane bound proteins. The study of cholesterol-protein interactions in aqueous solutions is complicated by cholesterol's low solubility and often requires organic co-solvents or surfactant additives. We report the synthesis of a biotinylated cholesterol and immobilization of this derivative on a streptavidin chip. Surface plasmon resonance (SPR) was then used to measure the kinetics of cholesterol interaction with cholesterol-binding proteins, hedgehog protein and tyrosine phosphatase 1B.

Interaction of the human erythrocyte Band 3 anion exchanger 1 (AE1, SLC4A1) with lipids and glycophorin A: Molecular organization of the Wright (Wr) blood group antigen

The Band 3 (AE1, SLC4A1) membrane protein is found in red blood cells and in kidney where it functions as an electro-neutral chloride/bicarbonate exchanger. In this study, we have used molecular dynamics simulations to provide the first realistic model of the dimeric membrane domain of human Band 3 in an asymmetric lipid bilayer containing a full complement of phospholipids, including phosphatidylinositol 4,5–bisphosphate (PIP₂) and cholesterol, and its partner membrane protein Glycophorin A (GPA). The simulations show that the annular layer in the inner leaflet surrounding Band 3 was enriched in phosphatidylserine and PIP₂ molecules. Cholesterol was also enriched around Band 3 but also at the dimer interface. The interaction of these lipids with specific sites on Band 3 may play a role in the folding and function of this anion transport membrane protein. GPA associates with Band 3 to form the Wright (Wr) blood group antigen, an interaction that involves an ionic bond between Glu658 in Band 3 and Arg61 in GPA. We were able to recreate this complex by performing simulations to allow the dimeric transmembrane portion of GPA to interact with Band 3 in a model membrane. Large-scale simulations showed that the GPA dimer can bridge Band 3 dimers resulting in the dynamic formation of long strands of alternating Band 3 and GPA dimers.

Human Band 3 (AE1, SLC4A1), an abundant 911 amino acid glycoprotein, catalyzes the exchange of bicarbonate and chloride across the red blood cell membrane, a process necessary for efficient respiration. Malfunction of Band 3 leads to inherited diseases such as Southeast Asian Ovalocytosis, hereditary spherocytosis and distal renal tubular acidosis. Despite much available structural and functional data about Band 3, key questions about the conformational changes associated with transport and the molecular details of its interaction with lipids and other proteins remain unanswered. In this study, we have used computer simulations to investigate the dynamics of Band 3 in lipid bilayers that resemble the red blood cell plasma membrane. Our results suggest that negatively charged phospholipids and cholesterol interact strongly with Band 3 forming an annulus around the protein. Glycophorin A (GPA) interacts with Band 3 to form the Wright (Wr) blood group antigen. We were able to recreate this complex and show that GPA promotes the clustering of Band 3 in red blood cell membranes. Understanding the molecular details of the interaction of Band 3 with GPA has provided new insights into the nature of the Wright blood group antigen.

Interaction between glycophorin and a spin-labeled cholesterol analogue in reconstituted dimyristoylphosphatidylcholine bilayer vesicles

The interaction between glycophorin and a spin-labeled cholesterol analogue has been investigated by EPR spectroscopy. In vesicles which were reconstituted by the freeze and thaw technique, direct evidence was obtained for a reorganisation of the membrane at low protein content (protein/lipid ratio less than 1:300). From the spin exchange interaction we were able to show a protein-induced clustering of the steroid in fluid and in gel state membranes. Tryptic cleavage of the complete N-terminus of glycophorin vanishes the effect. Whereas the removal of the sialic acid residues by neuraminidase digest had no influence on the EPR spectra. The interaction seems to be cholestane spin label specific since it was not observed with an androstane spin-label.

Interactions between a paramagnetic analogue of cholesterol and filipin

A paramagnetic analogue of cholesterol (called 25-doxyl-27-norcholesterol (CNO)), labeled near the w-end of the hydrophobic tail, was used to study interactions of cholesterol with filipin. We observed by electron microscopy that CNO- and cholesterol-filipin complexes are structurally equivalent. Two kinds of complexes were seen by ESR spectroscopy and electron microscopy, depending on the stoichiometric R ratio between the antibiotic and sterol. When R was high, an immobilized ESR spectrum appeared, showing strong imbrication between CNO and filipin. When R was nearer to unity, an exchange-broadened spectrum emerged, corresponding to a new phase that was very rich in CNO (a fast exchange between spins could occur by nearest contacts). CNO was easily displaced from its complex (i) by gradual addition of genuine cholesterol; and (ii) by an excess of phospholipids, owing to the very poor affinity of CNO (and cholesterol, by extension) for filipin in the lipidic phase. Almost no difference appeared between the ESR spectra of oriented samples, i.e. the probe showed no long-range order in any complex of CNO with filipin.

A new paramagnetic analogue of cholesterol as a tool for studying molecular interactions of genuine cholesterol

The synthesis of a new paramagnetic (nitroxide) analogue of cholesterol is described. This compound (called CNO) contains a doxyl group in the lateral chain at position 25. Our results show that CNO retains three molecular interactions which characterize authentic cholesterol: It assumes an orientation perpendicular to the phospholipid bilayer with the doxyl group buried in the membrane core, as seen by ESR spectroscopy. It widens the transition temperature of dimyristoylphosphatidylcholine, to the same extent as cholesterol, as measured by Raman and ESR spectroscopies. It interacts with polyene antibiotics, such as amphotericin B and filipin, in the same manner as its model. This was proved on the one hand by the change in fluorescence of self quenched vesicle-entrapped calcein, after dilution in the external medium, provoked by filipin, and on the other hand by fluorescence quenching provoked by cobalt ions entering the vesicles under the influence of amphotericin B. We concluded that CNO, although it has a side chain different from genuine cholesterol, can help to solve many physiologically meaningful questions related to the distribution and movement rate of cholesterol itself.

Mechanisms and consequences of cellular cholesterol exchange and transfer

It is apparent from consideration of the reactions involved in cellular cholesterol homeostasis that passive transfer of unesterified cholesterol molecules plays a role in cholesterol transport in vivo. Studies in model systems have established that free cholesterol molecules can transfer between membranes by diffusion through the intervening aqueous layer. Desorption of free cholesterol molecules from the donor lipid-water interface is rate-limiting for the overall transfer process and the rate of this step is influenced by interactions of free cholesterol molecules with neighboring phospholipid molecules. The influence of phospholipid unsaturation and sphingomyelin content on the rate of free cholesterol exchange are known in pure phospholipid bilayers and similar effects probably occur in cell membranes. The rate of free cholesterol clearance from cells is determined by the structure of the plasma membrane. It follows that the physical state of free cholesterol in the plasma membrane is important for the kinetics of cholesterol clearance and cell cholesterol homeostasis, as well as the structure of the plasma membrane. Bidirectional flux of free cholesterol between cells and lipoproteins occurs and rate constants characteristic of influx and efflux can be measured. The direction of any net transfer of free cholesterol is determined by the relative free cholesterol/phospholipid molar ratios of the donor and acceptor particles. Cholesterol diffuses down its gradient of chemical potential generally partitioning to the phospholipid-rich particle. Such a surface transfer process can lead to delivery of cholesterol to cells. This mechanism operates independently of any lipoprotein internalization by receptor-mediated endocytosis. The influence of enzymes such as lecithin-cholesterol acyltransferase and hepatic lipase on the direction of net transfer of free cholesterol between lipoproteins and cells can be understood in terms of their effects on the pool sizes and the rate constants for influx and efflux. Excess accumulation of free cholesterol in cells stimulates the rate of cholesteryl ester formation and induces deposition of cholesteryl ester inclusions in the cytoplasm similar to the situation in the 'foam' cells of atherosclerotic plaque. Clearance of cellular cholesteryl ester requires initial hydrolysis to free cholesterol followed by efflux of this free cholesterol. The rate of clearance of cholesteryl ester from cytoplasmic droplets is influenced by the physical state of the cholesteryl ester; liquid-crystalline cholesteryl ester is removed more slowly than cholesteryl ester in a liquid state.(ABSTRACT TRUNCATED AT 400 WORDS)

Ionic strength-dependent alterations of membrane structure of red blood cells

Electron paramagnetic resonance (EPR) measurements using various fatty acid spin labels were performed on membranes of intact human erythrocytes at physiological, and at low ionic strength. In the case of spin probes bearing the nitroxide near the polar head group, a less restricted motion at low ionic strength was seen than with those labels with a nitroxide deeper within the hydrophobic tail of the membrane. Although these data clearly show an influence of ionic strength on membrane structure, and possibly a modified protein-lipid interaction, they cannot be simply discussed in terms of an altered membrane fluidity.

A model for the asymmetric lipid distribution in the human erythrocyte membrane

The asymmetric transverse distribution of phospholipids in the human erythrocyte membrane can be explained by differences between the rate constants of flip and flop motion of the lipids. A selective interaction between aminophospholipids and spectrin does not need to be assumed for creating and maintaining the asymmetric localization of these lipids. Shape transformation of red cells could be caused by alterations of the flip-flop rate constants leading to a change of the lipid distribution and, consequently, to a differential area expansion of the outer and inner membrane leaflet.