Selective labelling of the hydrophobic segments of intrinsic membrane proteins with a lipophilic photogenerated carbene

Surface-modified bacteria: synthesis, functionalization and biomedical applications

The past decade has witnessed a great leap forward in bacteria-based living agents, including imageable probes, diagnostic reagents, and therapeutics, by virtue of their unique characteristics, such as genetic manipulation, rapid proliferation, colonization capability, and disease site targeting specificity. However, successful translation of bacterial bioagents to clinical applications remains challenging, due largely to their inherent susceptibility to environmental insults, unavoidable toxic side effects, and limited accumulation at the sites of interest. Cell surface components, which play critical roles in shaping bacterial behaviors, provide an opportunity to chemically modify bacteria and introduce different exogenous functions that are naturally unachievable. With the help of surface modification, a wide range of functionalized bacteria have been prepared over the past years and exhibit great potential in various biomedical applications. In this article, we mainly review the synthesis, functionalization, and biomedical applications of surface-modified bacteria. We first introduce the approaches of chemical modification based on the bacterial surface structure and then highlight several advanced functions achieved by modifying specific components on the surface. We also summarize the advantages as well as limitations of surface chemically modified bacteria in the applications of bioimaging, diagnosis, and therapy and further discuss the current challenges and possible solutions in the future. This work will inspire innovative design thinking for the development of chemical strategies for preparing next-generation biomedical bacterial agents.

Simple purification of small-molecule-labelled peptides via palladium enolate formation from β-ketoamide tags

Palladium enolates derived from β-ketocarbonyl compounds serve as key intermediates in various catalytic asymmetric reactions. We found that the palladium enolate formed from β-ketoamide is stable in air and moisture and we applied this property to develop a peptide purification system using β-ketoamide as a small affinity tag in aqueous media. A solid-supported palladium complex successfully captured β-ketoamide-tagged molecules as palladium enolates and released them in high yield upon acid treatment. Optimum conditions for the catch and release of tagged peptides from a mixture of untagged peptides were established. To demonstrate the value of this methodology in identifying the binding site of a ligand to its target protein, we purified and identified a peptide containing the ligand-binding site from the tryptic digest of cathepsin B labelled with a covalent cathepsin B inhibitor containing a β-ketoamide tag.

Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins

Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.

Photoaffinity labelling strategies for mapping the small molecule-protein interactome

Nearly all FDA approved drugs and bioactive small molecules exert their effects by binding to and modulating proteins. Consequently, understanding how small molecules interact with proteins at an molecular level is a central challenge of modern chemical biology and drug development. Complementary to structure-guided approaches, chemoproteomics has emerged as a method capable of high-throughput identification of proteins covalently bound by small molecules. To profile noncovalent interactions, established chemoproteomic workflows typically incorporate photoreactive moieties into small molecule probes, which enable trapping of small molecule-protein interactions (SMPIs). This strategy, termed photoaffinity labelling (PAL), has been utilized to profile an array of small molecule interactions, including for drugs, lipids, metabolites, and cofactors. Herein we describe the discovery of photocrosslinking chemistries, including a comparison of the strengths and limitations of implementation of each chemotype in chemoproteomic workflows. In addition, we highlight key examples where photoaffinity labelling has enabled target deconvolution and interaction site mapping.

Diazirines as potent electrophilic nitrogen sources: application to the synthesis of pyrazoles

Even after more than 50 years since its discovery, the electrophilic potential of diazirines was never truly exploited. This longstanding limitation has been resolved. N-Monosubstituted diaziridines and hydrazones are obtained by nucleophilic additions. They release, under hydrolysis conditions, the corresponding monosubstituted hydrazines. The latter were converted to pyrazoles in high yields. The adamantanone can be recovered in 80-100% yields. This work demonstrates the potential of diazirines as electrophilic nitrogen sources with recoverable protecting groups.

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.

Modification of ovine opsin with the photosensitive hydrophobic probe 1-azido-4-[125I]iodobenzene. Labelling of the chromophore-attachment domain

The hydrophobic photosensitive probe 1-azido-4-[125I]iodobenzene (AIB) partitioned preferentially into photoreceptor disc membranes and, upon u.v. irradiation, became covalently bound to opsin and phospholipid. The labelling of both protein and phospholipid was linearly related to AIB concentration. The amount of probe incorporated into protein was not significantly different when membranes were irradiated at -100 degrees, 4 degrees or 25 degrees C, but irreversible aggregation of monomeric opsin was dramatically reduced by performing the photolysis at -100 degrees C. Labelling of opsin after irradiation at -100 degrees or 4 degrees was not significantly reduced by the presence of lysine in the aqueous buffer, indicating that significant amounts of reactive species did not enter the aqueous phase. The incorporation into phospholipid, unlike that into opsin, decreased as the temperature of irradiation increased. Some labelling of opsin occurred on incubation with pre-photoactivated AIB, indicating that reaction may also occur with reactive species of longer lifetimes than the nitrene. Proteolysis of labelled opsin with Staphylococcus aureus V8 proteinase yielded two radiolabelled membrane-bound fragments. The location of the modified sites (cysteine, tryptophan, tyrosine, lysine and histidine residues: all nucleophiles) in the smaller fragment was entirely consistent with putative models for the protein derived from other studies.

Topology of beef heart cytochrome c oxidase from studies on reconstituted membranes

The orientation of purified beef heart cytochrome c oxidase, incorporated into vesicles by the cholate dialysis procedure [Carroll, R.C., & Racker, E. (1977) J. Biol. Chem. 252, 6981], has been investigated by functional and structural approaches. The level of heme reduction obtained by using cytochrome c along with the membrane-impermeant electron donor ascorbate was 78 +/- 2% of that obtained with cytochrome c and the membrane-permeant reagent N,N,N',N'-tetramethyl-p-phenylenediamine. Electron transfer from cytochrome c is known to occur exclusively from the outer surface of the mitochondrial inner membrane (C side), implying that at least 78% of the oxidase molecules are oriented in the same way in these vesicles as in the intact mitochondria. Trypsin, which cleaves subunit IV near its N terminus, modifies only 5-7% of this subunit in intact vesicles. This removal of the N-terminal residues has been shown to occur only in mitochondrial membranes with their inner side (M side) exposed. Diazobenzene [35S]sulfonate [( 35S]DABS) likewise modifies subunit IV only in submitochondrial particles. Labeling of intact membranes with [35S]DABS resulted in incorporation of only 4-8% of the total counts that could be incorporated into this subunit in membranes made leaky to the reagent by addition of 2% Triton X-100. Therefore, both the functional and structural data show that at least 80% and probably more of the cytochrome c oxidase molecules are oriented with their C domain outermost and M domains in the lumen of vesicles prepared by the cholate dialysis method.(ABSTRACT TRUNCATED AT 250 WORDS)

Exposure of acetylcholine receptor to the lipid bilayer

All four subunits of the acetylcholine receptor in membrane fragments isolated from T. californica have been labeled with a photolabile hydrophobic probe, [3H]adamantanediazirine, which selectively labels regions of integral membrane proteins in contact with the hydrocarbon core of the lipid bilayer. As all of the homologous subunits are exposed to the lipid bilayer, it is probable that they each interact with the surrounding membrane in a similar fashion.

Lactoperoxidase-catalyzed iodination of sodium and potassium ion-activated adenosine triphosphatase in the Madin-Darby canine kidney epithelial cell line and canine renal membranes

Experiments are described in which the large chain of (Na+ + K+)-ATPase is labeled by lactoperoxidase-catalyzed iodination either at its extracytoplasmic surface exclusively or at both its extracytoplasmic and its cytoplasmic surfaces simultaneously. The former was accomplished by labeling intact cells of the Madin-Darby canine kidney line, and the latter by labeling open membrane vesicles, also from canine kidney. A comparison of the specific radioactivities for the large chain from the open membranes and the large chain from the Madin-Darby canine kidney cells reveals that the former was labeled approximately 5-fold more extensively. This indicates that the large chain of (Na+ + K+)-ATPase is situated in the membrane such that more of its mass protrudes into the cytoplasm than into the extracytoplasmic environment.

Identification of hydrophobic regions of the calcium-transport ATPase from sarcoplasmic reticulum after photochemical labeling with adamantane diazirine

The Ca-ATPase from skeletal muscle sarcoplasmic reticulum was labeled with [3H]adamantane diazirine. Adamantane diazirine is a hydrophobic photoactivated probe that partitions into the cell membrane and can be used to identify regions of proteins that are embedded within the membrane. Digestion of the labeled protein with trypsin and separation of the labeled tryptic fragments by SDS-polyacrylamide-gel electrophoresis indicated that all of the major tryptic fragments were labeled by the probe. The presence of glutathione in the sample buffer during photolysis did not alter the pattern of labeling, indicating that adamantane diazirine labeled the Ca-ATPase from within the lipid bilayer. These results indicate that the Ca-ATPase polypeptide must cross the membrane at least 3 times.

Selective labeling of the hydrophobic core of membranes with 3-(trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine, a carbene-generating reagent

The synthesis of a new photoactivatable probe, 3-(trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine ([125I]-TID), with a high specific radioactivity (10 Ci mmol-1) is described. It was tested as a probe for the hydrophobic core of membranes. TID partitions strongly in favor of the lipid phase of membranes, and the photogenerated carbene labels intrinsic membrane proteins in a highly selective manner. This conclusion was reached from the distribution of radioactivity among the proteins of [125I]TID-labeled human erythrocyte membranes. By far the most heavily labeled protein is band 3 [nomenclature of Fairbanks, G., Steck, T. L., & Wallach, F. G. H. (1971) Biochemistry 10, 2606-2617] while the labeling of glycophorin is approximately 5 times less than that of band 3. There is little or no labeling of known extrinsic proteins.

Isolation and partial characterization of membrane protein constituents of human neutrophil receptors for chemotactic formylmethionyl peptides

Plasma membranes of human neutrophils were solubilized in buffer containing a nonionic detergent and applied to a formylmethionylleucylphenylalanine (fMet-Leu-Phe)-Sepharose column that was washed and eluted with the chemotactic peptide fMet-Leu-Phe. Analysis of the eluate by filtration on Bio-Gel P150 in sodium dodecyl sulfate (NaDodSO4) buffer and by NaDodSO4-polyacrylamide gel electrophoresis revealed three predominant membrane proteins of approximate molecular weight 94 000 (MP-1), 68 000 (MP-2), and 40 000 (MP-3), of which MP-2 accounted for 74--93% of the total protein. Purified MP-1 and MP-2 contained an above average content of hydrophobic amino acids, while MP-2 and MP-3 had an above average content of acid and/or amide amino acids and a below average content of basic amino acids. MP-2 and MP-3, but not MP-1, bound [3H]fMet-Leu-Phe in equilibrium dialysis chambers. Both MP-2 and MP-3 exhibited high-affinity sites with a valence of 0.2--0.3 and mean KA values of 9 x 10(8) and 2 x 10(7) M-1, respectively, and low-affinity sites with a valence of 0.3--0.5 and mean KA values of 3 x 10(7) and 2 x 10(6) M-1 (n = 3). The specificity of the binding of fMet-Leu-Phe was suggested by the failure of MP-2 and MP-3 to bind lipid chemotactic factors and to adhere to a Sepaharose column to which had been coupled chemotactic fragments of the fifth component of complement. A series of synthetic formylmethionyl peptides exhibited the same rank order of potency as inhibitors of the binding of [3H]fMet-Leu-Phe by MP-2 and as stimuli of neutrophil chemotaxis. Membrane proteins isolated by fMet-Leu-Phe-Sepharose affinity chromatography may represent constituents of specific human neutrophil receptors for chemotactic peptides.

Photolabelling of membrane proteins with photoactive phospholipids

Photoactive probes have been introduced recently to study the hydrophobic sector of integral membrane proteins. A simple procedure to synthesize a new series of highly radioactive aryl azido-phospholipids is presented. They effectively exchange with the boundary lipids and, on illumination, the cross-link to several membrane proteins with high efficiency. The procedure and analysis of labelling of ATPase from sarcoplasmic reticulum is reported as an example. The advantages in using these photoactive phospholipids are discussed together with some information obtained on their use.

Internal and external membrane proteins of the cyanobacterium, Synechococcus cedrorum

The protein composition and architecture of the photosynthetic membranes from the cyanobacterium, Synechococcus cedrorum, were analyzed with the aid of site-specific labels. Using membranes labeled with 35S, about 50 membrane proteins can be detected by sodium dodecyl sulfate acrylamide gel electrophoresis. Approximately half of the proteins are accessible to modification by the impermeant probe, lactoperoxidase, indicating that they have surface-exposed domains. At least six of these external proteins can be removed by EDTA washing; the correspondence in molecular weights between five of these EDTA-extractable proteins and those of typical chloroplast coupling factor preparations may indicate that they are subunits of a membrane-bound ATPase. The photoactive, lipophilic compound, [125I]iodonaphthyl azide, was used to label protein domains in contact with the lipid bilayer. Iodonaphthyl azide modification led to a labelling pattern significantly different from that seen with lactoperoxidase. In particular, proteins in the 13000--20000 dalton range that were labeled poorly or not at all by lactoperoxidase were heavily modified by iodonaphthyl azide. Photosystem I and II particles, extracted from the membrane by digitonin treatment, were iodinated by lactoperoxidase after isolation. The PS I particles acted as a relatively tight complex, with most of the proteins remaining inaccessible to surface modification. The PS II particles, on the other hand, responded as a more open structure, with most of the subunits yielding to lactoperoxidase iodination. Similar studies on a highly fluorescent, temperature-sensitive mutant of S. cedrorum revealed a different organization of the PS II complex. This mutant, when grown at 40 degrees C, inserts a 51 kdalton polypeptide in place of a 53 kdalton protein. This protein also replaces the 53 kdalton species in the PS II complex of the mutant after 40 degrees C growth. The structure of this complex is altered in that more sites become accessible to lactoperoxidase. This is particularly true of the 51 kdalton protein, which is barely labeled by wild-type PS II complexes.

Membrane asymmetry. A survey and critical appraisal of the methodology. I. Methods for assessing the asymmetric orientation and distribution of proteins

This and the companion article are aimed at surveying the methods used for the study of membrane asymmetry. The techniques employed for the assessment of the asymmetric distribution and orientation of membrane proteins are reviewed in this article, whereas those pertaining to the unequal distribution of lipids are detailed in the companion paper. The use of immunological techniques and lectins, functions of proteins and their perturbations, chemical reagents, enzymatic isotopic labeling and enzymatic cleavage of membrane proteins and physical techniques are discussed and illustrated using recent examples of their application. Whenever appropriate, problems involving crypticity and non-availability or non-reactivity of functional sites, relevant chemical functions or protein fragments to appropriate ligands, reagents or modifying enzymes are envisaged and possible modification of the exposure of proteins during preparation of ghosts and other drawbacks are discussed, the use of different techniques and control experiments in conjunction is recommended for a more realistic assessment of the distribution and orientation of proteins.

Membrane asymmetry. A survey and critical appraisal of the methodology. II. Methods for assessing the unequal distribution of lipids

In the companion paper, I have reviewed the techniques employed for assessment of the asymmetric distribution and orientation of membrane proteins. This article deals with methods applicable to the investigation of the unequal distribution of lipids between the two membrane leaflets. Among the techniques I will discuss are the use of immunological techniques and lectins, chemical reagents, enzymatic isotopic labeling and degradation of membrane lipids, exchange proteins and physical techniques. Whenever appropriate, problems of crypticity and non-availability of lipids to interact with the appropriate ligands, reagents, modifying enzymes or exchange proteins have been envisaged. It appears that in many case, highly discordant results, sometimes with the same biological material, have been obtained. Some of the difficulties encountered presumably stem from the reported existence of non-bilayer arrangements and isotropic movement of lipids as evidenced by freeze-fracture and NMR studies. Other problems may be related to the induction of such arrangements, especially the inverted micellar arrangement, by the modifying agents, particularly degradation enzymes or exchange proteins when they cause severe unilateral modification of the lipids of the exposed leaflet. In addition, the situation is complicated by the role of the induced increase in the flip-flop rate under different experimental conditions and by modification of the rearrangement of lipid molecules as a result of the metabolic state of the cell or ghost preparation and of the reactivity of lipids as a consequence of temperature changes. Here, more so than with proteins, one must be cautious in interpreting experimental results. Moreover, it would appear that the use of different techniques in conjunction and the consequent comparison of results should be recommended. It has been emphasized that 'general rules' do not hold and that each new material should be assay again. To give one example, it is not pertinent to state that proteins enhance the flip-flop rate in lipid vesicles (and hence in membranes). This holds true for glycophorin from erythrocyte membrane, but could not be proved when mitochondrial cytochrome oxidase was used. There seems to be no rule for the distribution of lipids between the two leaflets of different membranes. For example, even for different strains of the same bacterial species, highly divergent results have been reported. It is generally (and probably under the influence of different studies with erythrocytes) believed that in mammalian plasma membranes, choline phospholipids are enriched in the outer leaflet and aminophospholipids in the inner leaflet. Though this contention may prove to be correct, different instances of contradictory results have been given in the text. This shows that if rules do exist, they remain to be discovered or established...

Molecular cloning of a human histocompatibility antigen cDNA fragment

A clone (pHLA-1) containing HLA-specific cDNA was constructed by reverse transcription of partially purified HLA mRNA from the human lymphoblastoid cell line LKT. The identity of pHLA-1 was established by its ability to hybridize to HLA heavy chain mRNA and by nucleotide sequence analysis. The pHLA-1 cDNA insert (approximately 525 base pairs) corresponds to the COOH-terminal 46 amino acids of an HLA-A, -B, or -C antigen (15 residues from the hydrophobic region and the remainder from the COOH-termial hydrophilic region), together with a portion of the 3' untranslated region of the mRNA.

Photogenerated reagents for membranes: selective labeling of intrinsic membrane proteins in the human erythrocyte membrane

1-[3H]Spiro[adamantane-4,4'-diazirine], a lipophilic, photoactivatable reagent designed to label those segments of intrinsic proteins that lie within the lipid bilayer of biological membranes, has been evaluated. The reagent labels the intrinsic proteins of human erythrocyte membranes far more heavily than it labels the extrinsic proteins. This result, together with a detailed analysis of the label distribution in several well-characterized membrane proteins [Goldman, D.W., Pober, J.S., White, J., & Bayley, H. (1979) Nature (London) 280, 841], demonstrates that labeling with adamantanediazirine is a convenient and rapid method both for distinguishing intrinsic from extrinsic membrane proteins and for locating within intrinsic proteins those amino acid residues that are in contact with the hydrocarbon core of the lipid bilayer.