Analysis of membranes photolabeled with lipid analogues. Reaction of phospholipids containing a disulfide group and a nitrene or carbene precursor with lipids and with gramicidin A

Photoaffinity labeling coupled to MS to identify peptide biological partners: Secondary reactions, for better or for worse?

Affinity photolabeling is a smart method to study noncovalent and transient interactions and provide a submolecular picture of the contacts between interacting partners. In this review, we will focus on the identification of peptide partners using photoaffinity labeling coupled to mass spectrometry in different contexts such as in vitro with a purified potential partner, in model systems such as model membranes, and with live cells using both targeted and nontargeted proteomics studies. Different biological partners will be described, among which glycoconjugates, oligonucleotides, peptides, proteins, and lipids, with the photoreactive label inserted either on the peptide of interest or on the potential partner. Particular attention will be paid to the observation and characterization of specific rearrangements following the photolabeling reaction, which can help characterize photoadducts and provide a better understanding of the interacting systems and environment.

Photolabeling Strategies to Study Membranotropic Peptides Interacting with Lipids and Proteins in Membranes

Membranotropic peptides is a class of peptides that exert their biological action at the level of cell membranes. Understanding how they interact with their different membrane binding partners (lipids, proteins, and/or glycoconjugates) is important to decipher their mechanism of action. Affinity photolabeling is a powerful method to study noncovalent interactions and provide a submolecular picture of the contacts between two interacting partners. In this review, we give a panorama of photolabeling-based studies of the interactions between membranotropic peptides and membranes using either photoreactive lipids or peptides.

Kinetics of peptide folding in lipid membranes

Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments.

Identification of PhIL1, a novel cytoskeletal protein of the Toxoplasma gondii pellicle, through photosensitized labeling with 5-[125I]iodonaphthalene-1-azide

The pellicle of the protozoan parasite Toxoplasma gondii is a unique triple bilayer structure, consisting of the plasma membrane and two tightly apposed membranes of the underlying inner membrane complex. Integral membrane proteins of the pellicle are likely to play critical roles in host cell recognition, attachment, and invasion, but few such proteins have been identified. This is in large part because the parasite surface is dominated by a family of abundant and highly immunogenic glycosylphosphatidylinositol (GPI)-anchored proteins, which has made the identification of non-GPI-linked proteins difficult. To identify such proteins, we have developed a radiolabeling approach using the hydrophobic, photoactivatable compound 5-[(125)I]iodonaphthalene-1-azide (INA). INA can be activated by photosensitizing fluorochromes; by restricting these fluorochromes to the pellicle, [(125)I]INA labeling will selectively target non-GPI-anchored membrane-embedded proteins of the pellicle. We demonstrate here that three known membrane proteins of the pellicle can indeed be labeled by photosensitization with INA. In addition, this approach has identified a novel 22-kDa protein, named PhIL1 (photosensitized INA-labeled protein 1), with unexpected properties. While the INA labeling of PhIL1 is consistent with an integral membrane protein, the protein has neither a transmembrane domain nor predicted sites of lipid modification. PhIL1 is conserved in apicomplexan parasites and localizes to the parasite periphery, concentrated at the apical end just basal to the conoid. Detergent extraction and immunolocalization data suggest that PhIL1 associates with the parasite cytoskeleton.

Development and application of diazirines in biological and synthetic macromolecular systems

Many different reagents and methodologies have been utilised for the modification of synthetic and biological macromolecular systems. In addition, an area of intense research at present is the construction of hybrid biosynthetic polymers, comprised of biologically active species immobilised or complexed with synthetic polymers. One of the most useful and widely applicable techniques available for functionalisation of macromolecular systems involves indiscriminate carbene insertion processes. The highly reactive and non-specific nature of carbenes has enabled a multitude of macromolecular structures to be functionalised without the need for specialised reagents or additives. The use of diazirines as stable carbene precursors has increased dramatically over the past twenty years and these reagents are fast becoming the most popular photophors for photoaffinity labelling and biological applications in which covalent modification of macromolecular structures is the basis to understanding structure-activity relationships. This review reports the synthesis and application of a diverse range of diazirines in macromolecular systems.

New mono- and tricyclopalladated dendritic systems with encapsulated catalytic sites

The preparation of a series of new macrocyclic carbodiazasilane molecules functionalized with the monoanionic [2,6-(CH2NMe2)2C6H3](-)[triple bond]N,C,N-pincer ligand has been accomplished. Palladation of these systems was possible through oxidative addition with [Pd(dba)2] affording exclusive formation of the meso diastereoisomer. The X-ray crystal structures of these novel ligands and of the palladium(II) complex 10 were determined and confirmed the stereochemistry of the organopalladium cage. Attachment of the para-OH functionalized carbodiazasilane macrocycle 16 to a central core led to the formation of the dendritic structure 18 which was palladated to afford the novel multimetallic dendritic system with encapsulated catalytic sites 1. This cyclopalladated carbosilane dendrimer (1) as well as the mononuclear organopalladium cage 10 can be conveniently converted into active Lewis acid catalysts for the aldol condensation reaction. The catalytic data showed higher reaction rates for the dendritic structure than for the corresponding mononuclear systems.

Synthesis of azidophospholipids and labeling of lysophosphatidylcholine acyltransferase from developing soybean cotyledons

A photoreactive substrate analog of lysophosphatidylcholine (LPC), 1-([(4-azidosalicyl)-12-amino)]dodecanoyl-sn-glycerol-3-phospho cholin e (azido-LPC) was synthesized. Fast atom bombardment mass spectrometry was employed to confirm the structures of azido-LPC and its intermediates. Azido-LPC was used to label putative acyl-CoA:LPC acyltransferase from microsomal membranes of developing soybean cotyledons. The synthesized substrate analog acts as a substrate for the target acyltransferases and phospholipases in the dark. When the microsomal membranes were incubated with the acyl acceptor analog and immediately photolyzed, LPC acyltransferase was irreversibly inhibited. Photoinactivation of the enzyme by the photoprobe decreased in the presence of LPC. Microsomal membranes were photolyzed with 125I-labeled azido-LPC and analyzed by SDS-PAGE followed by autoradiography. These revealed that the analog preferentially labeled 54- and 114-kDa polypeptides. Substrate protected the labeling of both the polypeptides. In our earlier report, the same polypeptides were also labeled with photoreactive acyl-CoA analogs, suggesting that these polypeptides could be putative LPC acyltransferase(s). These results demonstrated that the photoreactive phospholipid analog could be a powerful tool to label acyltransferases involved in lipid biosynthesis.

Molecular mechanism of membrane protein integration into the endoplasmic reticulum

As proteins are integrated into the membrane of the endoplasmic reticulum, some hydrophilic polypeptide segments are transported through the translocation channel, others remain in the cytosol, and hydrophobic transmembrane sequences are released into the lipid phase. We have addressed the molecular mechanism by which these events occur. We demonstrate that both the lumenal and the cytosolic domains of a membrane protein are synthesized while the ribosome is membrane bound, so that even cytosolic domains come in contact with the translocation channel. We also find that, before translation of the protein is terminated, transmembrane sequences can laterally exit the translocation channel and enter the lipid environment. These results have significant implications for the folding and assembly of membrane proteins.

Photolabeling of human serum albumin by 4-azido-2-([14C]-methylamino) trifluorobenzonitrile. A high-efficiency, long wavelength photolabel

N-alkyl derivatives of perfluoroarylazides are excellent candidates for photolabeling of proteins since they have absorption spectra in the 340-350 nm range permitting photolabel absorption without direct protein photolysis. The [14C]-N-methylamino derivative of 4-azido-tetrafluorobenzonitrile has been used to demonstrate that 80% of the photo-induced nitrene transient becomes covalently attached to HSA during photolysis. Multiwavelength detection of the photoprobe-protein separation by size exclusion chromatography is shown to be an effective tool for assessing the conjugation of the photoprobe to the protein.

The chemical synthesis of N-[1-(2-naphthol)]-phosphatidylethanolamine, a fluorescent phospholipid for excited-state proton transfer studies

A procedure for the preparation of N-[1-(2-naphthol)]-phosphatidylethanolamine (NAPH-PE) has been developed. The synthesis is based on the Schiff base formation between the NH2 of the phospholipid and the aldehyde moiety of 2-hydroxy-1-naphthaldehyde. Then selective reduction of the imine is used to obtain the stable secondary amine, NAPH-PE. Formation of the intermediate Schiff base and the final product is confirmed by 13C- and 1H-NMR. Similar to free 2-naphthol, the excited-state pKa (pKa*) of its phospholipid derivative appears to be significantly lower than the ground-state pKa. At pH 7.4, the excitation spectrum of NAPH-PE shows no deprotonated species in the ground-state, while the emission spectrum presents a significant contribution of this species. Thus the fluorescent phospholipid exhibits the typical behavior of excited-state proton-transfer probes. NAPH-PE is found to incorporate in dimyristoyllecithin (DML) vesicles. The emission spectrum of the probe inserted in the liposomes is affected by acetate used as a proton acceptor. These properties should also be manifest in other lipid bilayers (e.g., plasma membranes of cells) and used for excited-state proton transfer studies.

Evidence for the presence of water within the hydrophobic core of membranes

The photoreactive ganglioside derivative N-diazirinyl-lyso-GM1 was incorporated into liposomes and calf brain microsomes. After photoactivation at 350 nm it was found to dimerize with phospholipids such as phosphatidylcholine and phosphatidylserine and with cholesterol. The predominant covalent reaction product, however, was the alcohol, resulting from the reaction with water. It amounted to about 45% of the covalent reaction products in calf brain microsomes and to about 58% in pure phosphatidylcholine liposomes. Based on the temperature dependence of the photoreaction of N-diazirinyl-lyso-GM1 in liposomes consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphoryl-choline or 1,2-distearoyl-sn-glycero- 3-phosphorylcholine and on affinity labeling experiments with cholera toxin we propose that the predominant reaction of N-diazirinyl-lyso-GM1 with water is due to the presence of water within the hydrophobic core of artificial and biological membranes.

GTP interacts through its ribose and phosphate moieties with different subunits of the eukaryotic initiation factor eIF-2

We have previously shown that a GTP derivative bearing p-azidoaniline at the gamma-phosphate group specifically labels the gamma-subunit of eukaryotic initiation factor eIF-2. In the present study a new GTP derivative carrying the photoreactive group at the ribose moiety of GTP was applied for affinity labeling of eIF-2 in different initiation complexes. Using this GTP analogue the beta-subunit of eIF-2 was found to be specifically labeled in all complexes investigated. It is concluded that GTP interacts with both the beta- and gamma-subunit of eIF-2: the guanosine moiety is in contact with the beta-subunit and the gamma-phosphate group with the gamma-subunit.

Hydrophobic labelling of membrane-embedded proteins with lipophilic reagents. Incorporation of [125I]INA and [125I]TID into B lymphocyte membrane immunoglobulins

Hydrophobic labelling is frequently used in the study of membrane-inserted domains of intrinsic proteins. However, the published procedures, fail to incorporate sufficient radioactivity into membrane immunoglobulins of B lymphocytes to permit investigation of their subunit structures and associations with other proteins. In order to increase the specific radioactivity of [125I]iodonaphthylazide ([125I]INA), an improved method for the synthesis of the reagent was developed. In addition, the optimal conditions for labelling B lymphocytes with [125I]INA and the commercially available reagent 3-(trifluoromethyl)-3-(3'-[125I]iodophenyl)diazirine ([125I]TID) were elaborated. Under these optimized conditions, Ig molecules labelled with [125I]INA and [125I]TID were isolated and analysed in detail by SDS-PAGE. The usefulness of the two reagents for the investigation of lipid-embedded domains of membrane proteins is discussed.

F0 part of the ATP synthase from Escherichia coli. Influence of subunits a, and b, on the structure of subunit c

Four different sets of proteoliposomes were prepared from F0, subunit c, a complex of subunits a and c (ac complex) and an ac complex supplemented with subunit b. Only liposomes containing intact F0 or all subunits of F0 were active in proton translocation and F1 binding [Schneider, E. and Altendorf, K. (1985) EMBO J. 4, 515-518]. The conformation of subunit c in the different preparations was analyzed by labelling the proteoliposomes with the hydrophobic photoactivatable reagent 3-(trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine ([125I]TID). Subsequent isolation and Edman degradation of this polypeptide revealed distinct radioactive labelling patterns over the entire amino acid sequence. In the F0 complex and in the ac complex subunit c retains a labelling pattern which is related to that found in TID-labelled membrane vesicles of Escherichia coli [Hoppe et al. (1984) Biochemistry 23, 5610-5616]. In the absence of subunit a, considerably more and different amino acid residues of subunit c are modified. The labelling data are discussed in relation to structural aspects of F0 and functional properties of proteoliposomes reconstituted with F0 or individual subunits.

Transbilayer migration (flip-flop) of 12-(4-azido-2-nitrophenoxy)stearoyl glucosamine in large unilamellar phospholipid vesicles

The ability of the glycolipid photoprobe, 12-(4-azido-2-nitrophenoxy)-stearoyl[1-14C]glucosamine (12-APS-GlcN), to undergo transbilayer flip-flop and intermembrane transfer between liposomes was examined. It was found that probe which was incorporated into membranes during the preparation of large unilamellar vesicles (LUVs) could be rapidly and completely extracted by incubation of these donor vesicles (in the liquid-crystalline state) with probe-free acceptor vesicles.

Stability of transmembrane regions in bacteriorhodopsin studied by progressive proteolysis

Proteinase K digestions of bacteriorhodopsin were carried out with the aim of characterizing the membrane-embedded regions of the protein. Products of digestions for two, eight or 24 hours were separated by high-pressure liquid chromotography. A computerized search procedure was used to compare the amino acid analyses of peptide-containing peaks with segments of the bacteriorhodopsin sequence. Molecular weight distributions of the products were determined by sodium dodecylsulfate-urea polyacrylamide gel electrophoresis. The structural integrity of the protein after digestion was monitored through the visible absorption spectrum, by X-ray diffraction of partially dried membranes, and by following release of biosynthetically-incorporated 3H leucine from the digested membranes. During mild proteolysis, bacteriorhodopsin was cleaved near the amino and carboxyl termini and at two internal regions previously identified as being accessible to the aqueous medium. Longer digestion resulted in cleavage at new sites. Under conditions where no fragments of bacteriorhodopsin larger than 9000 mol wt were observed, a significant proportion of the digested membranes retained diffraction patterns similar to those of native purple membranes. The harshest digestion conditions led to complete loss of the X-ray diffraction patterns and optical absorption and to release of half the hydrophobic segments of the protein from the membrane in the form of small soluble peptides. Upon cleavage of aqueous loop regions of the protein, isolated transmembrane segments may experience motion in a direction perpendicular to the plane of the membrane, allowing them access to protease.

Transmembrane topology of acetylcholine receptor subunits probed with photoreactive phospholipids

The domains of the acetylcholine receptor subunits that contact the lipid phase were investigated by hydrophobic photolabeling of receptor-rich membrane fragments prepared from Torpedo marmorata and Torpedo californica electric organs. The radioactive arylazido phospholipids used carry a photoreactive group, either at the level of the lipid polar head group (PCI) or at the tip of the aliphatic chain (PCII), and thus probe respectively the "superficial" and "deep" regions of the lipid bilayer. The four subunits of T. marmorata and T. californica acetylcholine receptor reacted with both the PCI and PCII probes and thus are all exposed to the lipid phase. Ligands known to stabilize different conformations of the acetylcholine receptor (nicotinic agonists, snake alpha-toxin, and noncompetitive blockers) did not cause any significant change in the labeling pattern. The acetylcholine receptor associated 43 000-dalton v1 protein did not react with any of the probes. A striking difference in labeling between T. marmorata and T. californica acetylcholine receptors occurred at the level of the alpha-subunit when the superficial PCI probe was used. An approximately 5-fold higher labeling of the alpha-subunit as compared to the beta-, gamma-, and delta-subunits was observed by using receptor-rich membranes from T. marmorata but not from T. californica. The same difference persisted after purification of the labeled receptors from the two species and was restricted to an 8000-dalton C-terminal tryptic peptide. The only mutation observed in this region of the complete alpha-subunit sequence of the two species is the substitution of cysteine-424 in T. marmorata by serine-424 in T. californica.(ABSTRACT TRUNCATED AT 250 WORDS)

Phospholipids involved in specific binding of 12-O-(5-azido-2-nitrobenzoyl)phorbol-13-acetate to epidermal microsomes, a photolabeling study

The preparation of 12-O-(5-azido-2-nitro)benzoylphorbol-13-acetate (NABPA) is described. It is used as a photoaffinity probe to study the biochemical components involved in the specific binding of phorbol esters to an epidermal particulate fraction (microsomes) from NMRI mice: without irradiation NABPA binds in a saturable and high affinity manner (KD = 12 nM; Rt = 2.6 pmol/mg protein) to microsomes; after irradiation (at 350 nm) specific photolabeling (representing specific binding of NABPA) is found of phospholipids (phosphatidyl-serine (PS) and -ethanolamine(PE)), but not of protein. The results are discussed in the context of protein kinase C being a receptor for phorbol esters.

Labeling of phospholipids in vesicles and human erythrocytes by photoactivable fatty acid derivatives

The photoactivable glycolipid probes, 2-(4-azido-2-nitrophenoxy)palmitoyl[1-14C]glucosamine (compound A) and 12-(4-azido-2-nitrophenoxy)stearoyl[1-14C]glucosamine (compound B) were synthesized essentially as described before [Iwata, K. K. et al. (1978) Prog. Clin. Biol. Res. 22, 579-589]. These probes were used to label phospholipid vesicles and erythrocyte membranes. A chromatographic method was developed to quantify the individual probe-phospholipid adducts involving both phosphatidylcholine, phosphatidylethanolamine, and phosphatidylserine. For both membranes as well as for both probes a phospholipid labeling pattern was obtained which appeared to reflect the relative content of fatty acid double bonds in each phospholipid class. The distinct labeling of phosphatidylserine in intact erythrocytes strongly suggested that the probes spontaneously and rapidly redistributed between the two halves of the membrane bilayer. In addition, both probes yielded an extensive labeling of the membrane proteins. Analysis by dodecylsulfate-polyacrylamide gel electrophoresis and autoradiography has indicated that the protein labeling pattern was different, depending on whether the 'shallow' probe (compound A) or 'depth' probe (compound B) were used.

Group-directed modification of bacteriorhodopsin by arylisothiocyanates. Labeling, identification of the binding site and topology

Group-directed hydrophobic modification of membrane-integrated protein segments by arylisothiocyanates is applied to bacteriorhodopsin. Labeling of purple membrane with phenylisothiocyanate and 4-N,N'-dimethylamino-azobenzene-4'-isothiocyanate results in covalent modification of a unique lysine epsilon-amino group of bacteriorhodopsin. Lysine residue 41, located in the amino-terminal chymotryptic fragment, has been identified as the arylisothiocyanate binding site by established sequencing techniques. The phenylisothiocyanate binding site is not accessible for the aqueously soluble analog p-sulfophenylisothiocyanate. Furthermore, the acid-induced bathochromic shift of the bound chromophore reagent is not observed following acidification of 4-N,N'-dimethylamino-azobenzene-4'-isothiocyanate-labeled purple membrane. The modification thus occurs in the hydrophobic membrane domain, providing further evidence for intramembraneous disposition of the modified protein segment. Light-induced proton translocation is preserved in reconstituted vesicles containing either phenylisothiocyanate-modified or 4-N,N'-dimethylamino-azobenzene-4'-isothiocyanate-modified bacteriorhodopsin.

Labeling of intramembrane segments of the alpha-subunit and beta-subunit of pure membrane-bound (Na+ + K+)-ATPase with 3-trifluoromethyl-3-(m-[125I]iodophenyl)diazirine

The photoactivatable carbene precursor 3-trifluoromethyl-3-(m-[125I]iodophenyl)diazirine ( [125I]TID) was tested as a probe for labeling lipid-embedded segments of the proteins of pure membrane bound (Na+ + K+)-ATPase. The probe labeled the alpha-subunit (100 kDa), its major tryptic and chymotryptic fragments of 78 kDa, 58 kDa, and 46 kDa, and the beta-subunit (38 kDa) from within the lipid bilayer to nearly the same specific activity. The labeling was resistant to extensive proteolysis and the distribution of label among the proteolytic fragments and the two subunits was independent of a 47-fold variation in concentration of [125I]TID. The data show that several transmembrane segments are distributed along the sequence of the alpha-subunit and that also the beta-subunit traverses the bilayer. [125I]TID provides a more uniform labeling of the transmembrane segments of the alpha-subunit and beta-subunit than that obtained with other hydrophobic reagents. This will facilitate further studies of the primary structure and folding pattern of the Na+,K+-pump proteins in the membrane.