Selectivity of lipid-protein interactions

The spin label ESR and intrinsic fluorescence quenching methods of determining the selectivity of interactions of lipids with integral membrane proteins are summarized. The selectivity patterns of phospholipids, fatty acids, and steroids are reviewed for a variety of integral proteins. Where appropriate, correlations are established with biochemical assays of the effects of specific lipids on enzymatic activity and transport function.     

Stoichiometry of lipid-protein interaction assessed by hydrophobic photolabeling

Here we undertook a comparative study of the composition of the lipid annulus of three ATPases pertaining to the P-type family: plasma membrane calcium pump (PMCA), sarcoplasmic reticulum calcium pump (SERCA) and Na,K-ATPase. The photoactivatable phosphatidylcholine analogue [(125)I]TID-PC/16 was incorporated into mixtures of dimyristoyl phosphatidylcholine (DMPC) and each enzyme with the aid of the nonionic detergent C(12)E(10). After photolysis, the extent of the labeling reaction was assessed to determine the lipid:protein stoichiometry: 17 for PMCA, 18 for SERCA, 24 for the Na,K-ATPase (alpha-subunit) and 5.6 mol PC/mol protein for the Na,K-ATPase (beta-subunit).     

ESR spin-label studies of lipid-protein interactions in membranes

Lipid spin labels have been used to study lipid-protein interactions in bovine and frog rod outer segment disc membranes, in (Na+, K+)-ATPase membranes from shark rectal gland, and in yeast cytochrome oxidase-dimyristoyl phosphatidylcholine complexes. These systems all display a two component ESR spectrum from 14-doxyl lipid spin-labels. One component corresponds to the normal fluid bilayer lipids. The second component has a greater degree of motional restriction and arises from lipids interacting with the protein. For the phosphatidylcholine spin label there are effectively 55 +/- 5 lipids/200,000-dalton cytochrome oxidase, 58 +/- 4 mol lipid/265,000 dalton (Na+, K+)-ATPase, and 24 +/- 3 and 22 +/- 2 mol lipid/37,000 dalton rhodopsin for the bovine and frog preparations, respectively. These values correlate roughly with the intramembrane protein perimeter and scale with the square root of the molecular weight of the protein. For cytochrome oxidase the motionally restricted component bears a fixed stoichiometry to the protein at high lipid:protein ratios, and is reduced at low lipid:protein ratios to an extent which can be quantitatively accounted for by random protein-protein contacts. Experiments with spin labels of different headgroups indicate a marked selectivity of cytochrome oxidase and the (Na+, K+)-ATPase for stearic acid and for cardiolipin, relative to phosphatidylcholine. The motionally restricted component from the cardiolipin spin label is 80% greater than from the phosphatidylcholine spin label for cytochrome oxidase (at lipid:protein = 90.1), and 160% greater for the (Na+, K+)-ATPase. The corresponding increases for the stearic acid label are 20% for cytochrome oxidase and 40% for (Na+, K+)-ATPase. The effective association constant for cardiolipin is approximately 4.5 times greater than for phosphatidylcholine, and that for stearic acid is 1.5 times greater, in both systems. Almost no specificity is found in the interaction of spin-labeled lipids (including cardiolipin) with rhodopsin in the rod outer segment disc membrane. The linewidths of the fluid spin-label component in bovine rod outer segment membranes are consistently higher than those in bilayers of the extracted membrane lipids and provide valuable information on the rate of exchange between the two lipid components, which is suggested to be in the range of 10(6)-10(7) s-1.     

Probing lipid-protein interactions using lipid microarrays

Lipids are central to the regulation and control of several cellular functions. They form many of the important structural features of cells, and are critical members of cellular signal transduction pathways. Cellular dysfunction is often caused by errors in lipid signaling; therefore, the proteins that interact with, synthesize or metabolize the lipids are potential therapeutic targets. Characterizing the contingent of cellular lipids and their abundance and how this is associated with disease will facilitate understanding how to intervene to correct diseases caused by dysfunctional lipid signaling. Since lipid-signaling networks involve several classes of proteins it is essential to determine the identity and role of these proteins in order to understand the networks. These proteins may be receptors, effectors, transporters or enzymes. We present tools, specifically, a lipid microarray platform, to uncover lipid-binding effector proteins that function in lipid signaling pathways. Lipid microarrays will allow researchers to obtain a comparable fingerprint of the proteins from a cell or tissue that bind to lipids, and also enable the identification of functionally important lipid-binding proteins. By applying a systematic approach to the quantification of lipid-protein interactions, lipid microarrays will provide an integrated knowledge base for the human lipidome. These tools have the potential to identify and validate targets to improve personalized medicine and health.     

Theoretical analysis of hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin.

We present a quantitative analysis of the effects of hydrophobic matching and membrane-mediated protein-protein interactions exhibited by gramicidin embedded in dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) bilayers (Harroun et al., 1999. Biophys. J. 76:937-945). Incorporating gramicidin, at 1:10 peptide/lipid molar ratio, decreases the phosphate-to-phosphate (PtP) peak separation in the DMPC bilayer from 35.3 A without gramicidin to 32.7 A. In contrast, the same molar ratio of gramicidin in DLPC increases the PtP from 30.8 A to 32.1 A. Concurrently, x-ray in-plane scattering showed that the most probable nearest-neighbor separation between gramicidin channels was 26.8 A in DLPC, but reduced to 23.3 A in DMPC. In this paper we review the idea of hydrophobic matching in which the lipid bilayer deforms to match the hydrophobic surface of the embedded proteins. We use a simple elasticity theory, including thickness compression, tension, and splay terms to describe the membrane deformation. The energy of membrane deformation is compared with the energy cost of hydrophobic mismatch. We discuss the boundary conditions between a gramicidin channel and the lipid bilayer. We used a numerical method to solve the problem of membrane deformation profile in the presence of a high density of gramicidin channels and ran computer simulations of 81 gramicidin channels to find the equilibrium distributions of the channels in the plane of the bilayer. The simulations contain four parameters: bilayer thickness compressibility 1/B, bilayer bending rigidity Kc, the channel-bilayer mismatch Do, and the slope of the interface at the lipid-protein boundary s. B, Kc, and Do were experimentally measured; the only free parameter is s. The value of s is determined by the requirement that the theory produces the experimental values of bilayer thinning by gramicidin and the shift in the peak position of the in-plane scattering due to membrane-mediated channel-channel interactions. We show that both hydrophobic matching and membrane-mediated interactions can be understood by the simple elasticity theory.     

Energetics of charge-charge interactions in proteins

Electrostatic interactions between pairs of atoms in proteins are calculated with a model based on the linearized Poisson-Boltzmann equation. The equation is solved accurately by a method that takes into account the detailed shape of the protein. This paper presents applications to several systems. Experimental data for the interaction of ionized residues with an active site histidine in subtilisin BPN' allow the model to be tested, using various assumptions for the electrical properties of the protein and solvent. The electrostatic stabilization of the active site thiolate of rhodanese is analyzed, with attention to the influence of alpha-helices. Finally, relationships between electrostatic potential and charge-charge distance are reported for large and small globular proteins. The above results are compared with those of simpler electrostatic models, including Coulomb's law with both a distance-dependent dielectric constant (epsilon = R) and a fixed dielectric constant (epsilon = 2), and Tanford-Kirkwood theory. The primary conclusions are as follows: 1) The Poisson-Boltzmann model agrees with the subtilisin data over a range of ionic strengths; 2) two alpha-helices generate a large potential in the active site of rhodanese; 3) epsilon = R overestimates weak electrostatic interactions but yields relatively good results for strong ones; 4) Tanford-Kirkwood theory is a useful approximation to detailed solutions of the linearized Poisson-Boltzmann equation in globular proteins; and 5) the modified Tanford-Kirkwood theory over-screens the measured electrostatic interactions in subtilisin.     

Mattress model of lipid-protein interactions in membranes.

A thermodynamic model is proposed for describing phase diagrams of mixtures of lipid bilayers and amphiphilic proteins or polypeptides in water solution. The basic geometrical variables of the model are the thickness of the hydrophobic region of the lipid bilayer and the length of the hydrophobic region of the proteins. The model incorporates the elastic properties of the lipid bilayer and the proteins, as well as indirect and direct lipid-protein interactions expressed in terms of the geometrical variables. The concept of mismatch of the hydrophobic regions of the lipids and proteins is an important ingredient of the model. The general phase behavior is calculated using simple real solution theory. The phase behavior turns out to be quite rich and is used to discuss previous experiments on planar aggregations of proteins in phospholipid bilayers and to propose a systematic study of synthetic amphiphilic polypeptides in bilayers of different thicknesses. The model is used to interpret the influence of the lipid-protein interaction on calorimetric measurements and on local orientational order as determined by deuterium nuclear magnetic resonance.     

Divalent cation and lipid-protein interactions of biomembranes

Divalent cations play an important role in the functions of biomembranes. This review deals with three topics: (1) Mg²⁺-mediated change in physical state of phospholipid induces conformation and activity change of reconstituted mitochondrial H⁺-ATPase, (2) a proper transmembrane Ca²⁺ gradient is essential for the higher enzymatic activity of adenylate cyclase, and (3) role of transmembrane Ca²⁺ gradient in the modulation of reconstituted sarcoplasmic reticulm Ca²⁺-ATPase activity.     

Experimental evidence for hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin.

Hydrophobic matching, in which transmembrane proteins cause the surrounding lipid bilayer to adjust its hydrocarbon thickness to match the length of the hydrophobic surface of the protein, is a commonly accepted idea in membrane biophysics. To test this idea, gramicidin (gD) was embedded in 1, 2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and 1, 2-myristoyl-sn-glycero-3-phosphocholine (DMPC) bilayers at the peptide/lipid molar ratio of 1:10. Circular dichroism (CD) was measured to ensure that the gramicidin was in the beta6.3 helix form. The bilayer thickness (the phosphate-to-phosphate distance, or PtP) was measured by x-ray lamellar diffraction. In the Lalpha phase near full hydration, PtP is 30.8 A for pure DLPC, 32.1 A for the DLPC/gD mixture, 35.3 A for pure DMPC, and 32.7 A for the DMPC/gD mixture. Gramicidin apparently stretches DLPC and thins DMPC toward a common thickness as expected by hydrophobic matching. Concurrently, gramicidin-gramicidin correlations were measured by x-ray in-plane scattering. In the fluid phase, the gramicidin-gramicidin nearest-neighbor separation is 26.8 A in DLPC, but shortens to 23.3 A in DMPC. These experiments confirm the conjecture that when proteins are embedded in a membrane, hydrophobic matching creates a strain field in the lipid bilayer that in turn gives rise to a membrane-mediated attractive potential between proteins.     

Insights into lipid-protein interactions from computer simulations

Lipid-protein interactions play an important direct role in the function of many membrane proteins. We argue they are key players in membrane structure, modulate membrane proteins in more subtle ways than direct binding, and are important for understanding the mechanism of classes of hydrophobic drugs. By directly comparing membrane proteins from different families in the same, complex lipid mixture, we found a unique lipid environment for every protein. Extending this work, we identified both differences and similarities in the lipid environment of GPCRs, dependent on which family they belong to and in some cases their conformational state, with particular emphasis on the distribution of cholesterol. More recently, we have been studying modes of coupling between protein conformation and local membrane properties using model proteins. In more applied approaches, we have used similar methods to investigate specific hypotheses on interactions of lipid and lipid-like molecules with ion channels. We conclude this perspective with some considerations for future work, including a new more sophisticated coarse-grained force field (Martini 3), an interactive visual exploration framework, and opportunities to improve sampling.     

A theoretical study of lipid-protein interactions in bilayers.

We present a theoretical study of the effect of different types of lipid-protein interactions on the thermodynamic properties of protein-containing lipid bilayers. The basis of this work is a theoretical model for pure lipid bilayer phase transitions developed earlier by Scott. Simple assumptions on the nature of the lipid conformations near a protein strongly affect the predicted properties of the model. Here we consider (a) random protein-lipid contacts, (b) enhanced contact between protein and lipid with a number of gauche bonds, and (c) enhanced contact between protein and all-trans but tilted lipid chains. Comparison of predicted results with experimental data seems to favor point c above but, by itself point c does not work well at larger protein concentrations. The results are discussed in the light of spectroscopic data, lipid-protein (plus annular lipid) miscibility, and interprotein forces.     

Spin-label ESR studies of lipid-protein interactions in thylakoid membranes

Lipid-protein interactions in thylakoid membranes, and in the subthylakoid membrane fractions containing either photosystem 1 or photosystem 2, have been studied by using spin-labeled analogues of the thylakoid membrane lipid components, monogalactosyldiacylglycerol, phosphatidylglycerol, and phosphatidylcholine. The electron spin resonance spectra of the spin-labeled lipids all consist of two components, one corresponding to the fluid lipid environment in the membranes and the other to the motionally restricted membrane lipids interacting directly with the integral membrane proteins. Spectral subtraction has been used to quantitate the fraction of the membrane lipids in contact with the membrane proteins and to determine the selectivity between the different lipid classes for the lipid-protein interaction. The fractions of motionally restricted lipid in the thylakoid membrane are 0.36, 0.39, and 0.53, for the spin-labeled monogalactosyldiacylglycerol, phosphatidylcholine, the phosphatidylglycerol, respectively. Spin-labeled monogalactosyldiacylglycerol exhibits very little preferential interaction over phosphatidylchline, which suggests that part of the role of monogalactosyldiacylglycerol in thylakoid membranes is structural, as is the case for phosphatidylcholine in mammalian membranes. Spin-labeled phosphatidylglycerol shows a preferential interaction over the corresponding monogalactosyldiacylglycerol and phosphatidylcholine analogues, in contrast to the common behavior of this lipid in mammalian systems. This pattern of lipid selectivity is preserved in both the photosystem 1 and photosystem 2 enriched subthylakoid membrane fractions.     

Energetics of complementary side-chain packing in a protein hydrophobic core

The energetics of complementary packing of nonpolar side chains in the hydrophobic core of a protein were analyzed by protein engineering experiments. We have made the mutations Ile----Val, Ile----Ala, and Leu----Ala in a region of the small bacterial ribonuclease barnase where the major alpha-helix packs onto the central beta-sheet. The destabilization resulting from the creation of cavities was determined by measuring the decrease in free energy of folding from reversible denaturation induced by urea, guanidinium chloride, or heat. The different methods give consistent and reproducible results. The loss in free energy of folding for the mutant proteins is 1.0-1.6 kcal/mol per methylene group removed. This exceeds by severalfold the values obtained from model experiments of the partitioning of relevant side chains between aqueous and nonpolar solvents. Much of this discrepancy arises because two surfaces are buried when a protein folds--both the amino acid side chain in question and the portions of the protein into which it packs. These experiments directly demonstrate that the interior packing of a protein is crucial in stabilizing its three-dimensional structure: the conversion of leucine or isoleucine to alanine in the hydrophobic core loses half the net free energy of folding of barnase with a concomitant decrease in yield of the expressed recombinant protein.     

Circular dichroism studies on lipid-protein complexes of a hydrophobic myelin protein

Circular dichroism spectra of lipophilin (a hydrophobic protein purified from human central nervous system myelin) were analyzed by the method of Chen et al. (1974) to obtain information on its secondary structure in aqueous and lipid environments. When introduced into phosphatidylcholine vesicles by dialysis from 2-chloroethanol, the protein possessed about 75% alpha helix. A new water-soluble form of lipophilin also containing over 70% alpha helix was obtained by a similar dialysis in the absence of lipid. This product had a higher helical content than two other water-soluble preparations derived by dialysis from phenol-acetic acid-urea. Interaction of all three aqueous forms of the protein with lysolecithin micelles resulted in increases in total helical content or in the average length of helical segments. The amount of beta sheet was at a minimum for lipophilin incorporated into vesicles, where the presence of lipid also provided some protection against thermal denaturation.     

Energetics of cell-cell and cell-biopolymer interactions

The energy vs distance balance of cell suspensions (in the presence and in the absence of extracellular biopolymer solutions) is studied, not only in the light of the classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory (which considered just the electrostatic (EL) and Lifshitz-van der Waals (LW) interactions), but also by taking electron-acceptor/electron-donor, or Lewis acid-base (AB) and osmotic (OS) interactions into account. Since cell surfaces, as well as many biopolymers tend to have strong monopolar electron-donor properties, they are able to engage in a strong mutual AB repulsion when immersed in a polar liquid such as water. The effects of that repulsion have been observed earlier in the guise of hydration pressure. The AB repulsion is, at close range, typically one or two orders of magnitude stronger than the EL repulsion, but its rate of decay is much steeper. In most cases, AB interactions are quantitatively the dominant factor in cell stability (when repulsive) and in "hydrophobic interactions" (when attractive). OS interactions exerted by extracellularly dissolved biopolymers are weak, but their rate of decay is very gradual, so OS repulsions engendered by biopolymer solutions may be of importance in certain long-range interactions. OS interactions exerted by biopolymers attached to cells or particles (e.g., by glycocalix glycoproteins), are very short-ranged and usually are negligibly small in comparison with the other interaction forces, in aqueous media.     

Energetics of cell-cell and cell-biopolymer interactions

The energy vs distance balance of cell suspensions (in the presence and in the absence of extracellular biopolymer solutions) is studied, not only in the light of the classical Derjaguin-Landau-Verwey-Over-beek (DLVO) theory (which considered just the electrostatic (EL) and Lifshitz-van der Waals (LW) interactions), but also by taking electron-acceptor/electron-donor, or Lewis acid-base (AB) and osmotic (OS) interactions into account. Since cell surfaces, as well as many biopolymers tend to have strong monopolar electron-donor properties, they are able to engage in a strong mutual AB repulsion when immersed in a polar liquid such as water. The effects of that repulsion have been observed earlier in the guise of hydration pressure. The AB repulsion is, at close range, typically one or two orders of magnitude stronger than the EL repulsion, but its rate of decay is much steeper. In most cases, AB interactions are quantitatively the dominant factor in cell stability (when repulsive) and in “hydrophobic interactions” (when attractive). OS interactions exerted by extracellularly dissolved biopolymers are weak, but their rate of decay is very gradual, so OS repulsions engendered by biopolymer solutions may be of importance in certain long-range interactions. OS interactions exerted by biopolymers attached to cells or particles (e.g., by glycocalix glycoproteins), are very short-ranged and usually are negligibly small in comparison with the other interaction forces, in aqueous media.