Chemical crosslinking of cell membranes

Thiol-disulphide independent in-cell trapping for the identification of peroxiredoxin 2 interactors

Hydrogen peroxide (H2O2) acts as a signalling molecule by oxidising cysteine thiols in proteins. Recent evidence has established a role for cytosolic peroxiredoxins in transmitting H2O2-based oxidation to a multitude of target proteins. Moreover, it is becoming clear that peroxiredoxins fulfil their function in organised microdomains, where not all interactors are covalently bound. However, most studies aimed at identifying peroxiredoxin interactors were based on methods that only detect covalently linked partners. Here, we explore the applicability of two thiol-disulphide independent in-cell trapping methodological approaches in combination with mass spectrometry for the identification of interaction partners of peroxiredoxin 2 (Prdx2). The first is biotin-dependent proximity-labelling (BioID) with a biotin ligase A (BirA*)-fused Prdx2, which has never been applied on redox-active proteins. The second is crosslinker co-immunoprecipitation with an N-terminally His-tagged Prdx2. During the initial characterisation of the tagged Prdx2 constructs, we found that the His-tag, but not BirA*, compromises the peroxidase and signalling activities of Prdx2. Further, the Prdx2 interactors identified with each approach showed little overlap. We therefore concluded that BioID is a more reliable method than crosslinker co-immunoprecipitation. After a stringent mass spec data filtering, BioID identified 13 interactors under elevated H2O2 conditions, including subunit five of the COP9 signalosome complex (CSN5). The Prdx2:CSN5 interaction was further confirmed in a proximity ligation assay. Taken together, our results demonstrate that BioID can be used as a method for the identification of interactors of Prdxs, and that caution should be exercised when interpreting protein-protein interaction results using tagged Prdxs.

Identification of VAPA and VAPB as Kv2 Channel-Interacting Proteins Defining Endoplasmic Reticulum-Plasma Membrane Junctions in Mammalian Brain Neurons

Membrane contacts between endoplasmic reticulum (ER) and plasma membrane (PM), or ER-PM junctions, are ubiquitous in eukaryotic cells and are platforms for lipid and calcium signaling and homeostasis. Recent studies have revealed proteins crucial to the formation and function of ER-PM junctions in non-neuronal cells, but little is known of the ER-PM junctions prominent in aspiny regions of mammalian brain neurons. The Kv2.1 voltage-gated potassium channel is abundantly clustered at ER-PM junctions in brain neurons and is the first PM protein that functions to organize ER-PM junctions. However, the molecular mechanism whereby Kv2.1 localizes to and remodels these junctions is unknown. We used affinity immunopurification and mass spectrometry-based proteomics on brain samples from male and female WT and Kv2.1 KO mice and identified the resident ER vesicle-associated membrane protein-associated proteins isoforms A and B (VAPA and VAPB) as prominent Kv2.1-associated proteins. Coexpression with Kv2.1 or its paralog Kv2.2 was sufficient to recruit VAPs to ER-PM junctions. Multiplex immunolabeling revealed colocalization of Kv2.1 and Kv2.2 with endogenous VAPs at ER-PM junctions in brain neurons from male and female mice in situ and in cultured rat hippocampal neurons, and KO of VAPA in mammalian cells reduces Kv2.1 clustering. The association of VAPA with Kv2.1 relies on a "two phenylalanines in an acidic tract" (FFAT) binding domain on VAPA and a noncanonical phosphorylation-dependent FFAT motif comprising the Kv2-specific clustering or PRC motif. These results suggest that Kv2.1 localizes to and organizes neuronal ER-PM junctions through an interaction with VAPs.SIGNIFICANCE STATEMENT Our study identified the endoplasmic reticulum (ER) proteins vesicle-associated membrane protein-associated proteins isoforms A and B (VAPA and VAPB) as proteins copurifying with the plasma membrane (PM) Kv2.1 ion channel. We found that expression of Kv2.1 recruits VAPs to ER-PM junctions, specialized membrane contact sites crucial to distinct aspects of cell function. We found endogenous VAPs at Kv2.1-mediated ER-PM junctions in brain neurons and other mammalian cells and that knocking out VAPA expression disrupts Kv2.1 clustering. We identified domains of VAPs and Kv2.1 necessary and sufficient for their association at ER-PM junctions. Our study suggests that Kv2.1 expression in the PM can affect ER-PM junctions via its phosphorylation-dependent association to ER-localized VAPA and VAPB.

Analysis of cell-cell contact mediated by Ig superfamily cell adhesion molecules

Cell-cell adhesion is a fundamental requirement for all multicellular organisms. The calcium-independent cell adhesion molecules of the immunoglobulin superfamily (IgSF-CAMs) represent a major subgroup. They consist of immunoglobulin folds alone or in combination with other protein modules, often fibronectin type-III folds. More than 100 IgSF-CAMs have been identified in vertebrates and invertebrates. Most of the IgSF-CAMs are cell surface molecules that are membrane-anchored either by a single transmembrane segment or by a glycosylphosphatidylinositol (GPI) anchor. Some of the IgSF-CAMs also occur in soluble form, e.g., in the cerebrospinal fluid or in the vitreous fluid of the eye, due to naturally occurring cleavage of the GPI anchor or the membrane-proximal peptide segment. Some IgSF-CAMs, such as NCAM, occur in various forms that are generated by alternative splicing. This unit contains a series of protocols that have been used to study the function of IgSF-CAMs in vitro and in vivo.

Metabolism of diazirine-modified N-acetylmannosamine analogues to photo-cross-linking sialosides

Terminal sialic acid residues often mediate the interactions of cell surface glycoconjugates. Sialic acid-dependent interactions typically exhibit rapid dissociation rates, precluding the use of traditional biological techniques for complex isolation. To stabilize these transient interactions, we employ a targeted photo-cross-linking approach in which a diazirine photo-cross-linker is incorporated into cell surface sialylated glycoconjugates through the use of metabolic oligosaccharide engineering. We describe three diazirine-modified N-acetylmannosamine (ManNAc) analogues in which the length of the linker between the pyranose ring and the diazirine was varied. These analogues were each metabolized to their respective sialic acid counterparts, which were added to both glycoproteins and glycolipids. Diazirine-modified sialic acid analogues could be incorporated into both α2-3 and α2-6 linkages. Upon exposure to UV irradiation, diazirine-modified glycoconjugates were covalently cross-linked to their interaction partners. We demonstrate that all three diazirine-modified analogues were capable of competing with endogeneous sialic acid, albeit to varying degrees. We found that larger analogues were less efficiently metabolized, yet could still function as effective cross-linkers. Notably, the addition of the diazirine substituent interferes with metabolism of ManNAc analogues to glycans other than sialosides, providing fidelity to selectively incorporate the cross-linker into sialylated molecules. These compounds are nontoxic and display only minimal growth inhibition at the concentrations required for cross-linking studies. This report provides essential information for the deployment of photo-cross-linking analogues to capture and study ephemeral, yet essential, sialic acid-mediated interactions.

Molecular assembly of cystic fibrosis transmembrane conductance regulator in plasma membrane

Based on electrophysiological measurements, it has been argued that the active form of cystic fibrosis trans-membrane conductance regulator (CFTR) Cl(-) channel is a multimer. It has also been demonstrated that this multimerization is likely due to PDZ domain-interacting partners. Here we demonstrate that although CFTR in vitro can self-associate into multimers, which depends on PDZ-based interactions, this may not be the case in cell membrane. Using chemical cross-linking, we demonstrated that CFTR exists as a higher order complex in cell membrane. However, this higher order complex is predominantly CFTR dimers, and the PDZ-interacting partners (Na(+)/H(+) exchanger regulatory factor-1 (NHERF1) and NHERF2) constitute approximately 2% of this complex. Interestingly solubilizing membrane expressing CFTR in detergents such as Triton X-100, Nonidet P-40, deoxycholate, and SDS tended to destabilize the CFTR dimers and dissociate them into monomeric form. The dimerization of CFTR was tightly regulated by cAMP-dependent protein kinase-dependent phosphorylation and did not depend on the active form of the channel. In addition, the dimerization was not influenced by either the PDZ motif or its interacting partners (NHERF1 and NHERF2). We also demonstrated that other signaling-related proteins such as Gbeta and syntaxin 1A can be in this higher order complex of CFTR as well. Our studies provide a deeper understanding of how the CFTR assembly takes place in native cell membrane.

A 28 kDa mitochondrial protein is radiolabelled by crosslinking with a 125I-labelled presequence

A 13-residue peptide containing the first 12 amino acids of the N-terminal part of the signal sequence of yeast cytochrome c oxidase subunit IV is shown by chemical crosslinking to interact with a mitochondrial protein. This result is obtained with mitochondria from four different origins. Submitochondrial localization experiments suggest that the 28 kDa labelled component is present on the outer face of the inner membrane. Since such addressing peptides are imported into mitochondria through the same machinery as protein precursors, the 28 kDa protein might be a component of the translocation apparatus.

In situ cross-linking of cartilage proteoglycans

Although the in vitro interactions between purified cartilage matrix components have been studied extensively, little is known about these interactions in situ. In this study, cartilage was treated with a cross-linking reagent with a span of 1.2 nm between its reactive terminal groups in order to preserve the native relationships between closely associated matrix components throughout extraction, purification, and preparation for electron microscopy. After in situ cross-linking, electron microscopy and gel chromatography revealed that about one-half of the guanidine hydrochloride extractable proteoglycans were polymeric, usually with two to five proteoglycan subunits in each polymer. Cross-linking consistently involved the thin segments of the proteoglycan subunits. Some of the proteoglycan polymers were capable of binding hyaluronic acid and were parts of aggregates under associative conditions. SDS-polyacrylamide gel electrophoresis revealed that link proteins were present within the polymers, and studies in which purified proteoglycans were cross-linked in vitro confirmed that the link proteins increased the proportion of polymeric proteoglycans. These findings suggest that individual proteoglycans within cartilage have intimate associations with other proteoglycans that are mediated by link proteins.

Detection by chemical cross-linking of bovine brain synapsin I self-association

Synapsin I is believed to play an important role in the regulation of neurotransmitter release, since it is able to bind to synaptic vesicles, to the cytoskeleton and to membrane proteins; in addition, it bundles F-actin and microtubules. These properties, which are controlled by phosphorylation, could be explained if synapsin has different and multiple binding sites or if synapsin I is able to form polymers by self-association. In this study we present experimental evidence that synapsin I at low concentration forms self-associated dimers, as revealed after mild treatments with cross-linking agents. We have especially studied here the effects of copper/o-phenanthroline, a zero-length cross-linking agent which forms covalent links by oxidative formation of S-S bridges between adjacent cysteines. The time course and concentration-dependence of synapsin-dimer formation are studied; interestingly, these experiments could suggest a different behaviour of the two polypeptides. Limited proteolysis of phosphorylated synapsin I by V8 protease, alpha-chymotrypsin or collagenase, performed on the isolated dimer and monomer, allows us to localize tentatively in the central hydrophobic core of the molecule the cysteine residues the oxidation of which by copper/o-phenanthroline gives rise to synapsin dimers.

N-(3-(p-azido-m-[125I]iodophenyl)propionyl)-succinimide--a heterobifunctional reagent for the synthesis of radioactive photoaffinity ligands: synthesis of a carrier-free 125I-labeled cardiac glycoside photoaffinity label

A new heterobifunctional reagent, N-(3-(p-azido-m-iodophenyl)propionyl)-succinimide (AIPPS), was synthesized and chemically characterized. The radiochemical form of the reagent, [125I]AIPPS, should be of general use as a photoactive reagent for the derivatization of free amino groups on a large variety of biologically active compounds, including many hormones. Amino-containing ligands can be derivatized with [125I]AIPPS in a method which is similar to that used for the 125I-labeled Bolton-Hunter reagent (N-(3-(p-hydroxyphenyl)propionyl)-succinimide). The added advantage with [125I]AIPPS, however, is that the ligand derivative is made both photoactive and radioactive in a single step. As an example of how this reagent can be used, we have prepared carrier-free [125I]AIPPS and reacted it with the amino-containing cardiac glycoside, 4-amino-4,6-dideoxyglucosyl digitoxigenin (GluD). The radioiodinated cardiac glycoside, [125I]AIPP-GluD, was purified by thin-layer chromatography and was carrier-free with a specific radioactivity of 2175 Ci/mmol. [125I]AIPP-GluD was an effective photoaffinity label for Na,K-ATPase as shown by specific photoaffinity labeling of purified canine kidney enzyme and human erythrocyte enzyme.

State of aggregation of the (Ca2+ + Mg2+)-ATPase studied using chemical cross-linking

We have studied cross-linking of the (Ca2+ + Mg2+)-ATPase in sarcoplasmic reticulum and in reconstituted systems, using glutaraldehyde, cupric-1,10-phenanthroline and 3,3'-dithiobis (sulphosuccinimidylpropionate). All reagents produce extensive cross-linking, forming aggregates too large to enter polyacrylamide gels. Only traces of cross-linked dimeric ATPase species are formed. Saturation transfer electron spin resonance spectra of spin-labelled sarcoplasmic reticulum cross-linked with glutaraldehyde are also consistent with the formation of extensively cross-linked aggregates in the membrane. The results are interpreted in terms of dynamic clusters of ATPase molecules in the membrane, probably in the form of rows of ATPase molecules.

Cytogenetic evaluations in human lymphocytes exposed to methyl acetimidate, a lysine-specific protein crosslinking agent

The cytogenetic effects of methyl acetimidate (MAI), a lysine-specific protein crosslinking reagent, were investigated using human peripheral lymphocytes in culture. Lymphocytes were treated with the chemical either prior to PHA exposure or 2-3 days following mitogenic stimulation and assessed for perturbations in cellular proliferation and induction of SCEs. Severe reductions in the mitotic index (MI) and pronounced decreases in the proportion of metaphases proceeding beyond M(1) were observed following G0 exposure to MAI concentrations of as low as 2 mM; with complete suppression of mitotic activity in all cultures exposed to levels of 3 mM MAI or greater. Concentrations resulting in severe depression in MI caused only moderate increases in SCEs. Cells exposed to less than 10 mM MAI during the late S-G2 stages of the cell cycle and harvested at the first metaphase following treatment exhibited profound mitotic delay, impaired prophase to metaphase transitions and abnormal mitotic configurations. These findings demonstrate that protein-specific crosslinking agents may induce a wide spectrum of adverse cytogenetic outcomes in both cycling and noncycling lymphocytes.

Structural studies on membrane-bound and soluble growth-hormone-binding proteins of rabbit liver

Covalent cross-linking techniques have been used to investigate the structural characteristics of the growth-hormone (GH) receptor in a variety of rabbit liver cell membrane preparations (particulate and soluble). Two classes of GH-binding protein have been identified which differ in their Mr by gel filtration and susceptibility to precipitation with poly(ethylene glycol) (PEG). The first, a PEG-precipitable (Mr approximately 300,000) protein, contained Mr-65,000 and Mr-40,000 binding proteins linked by disulphide bonds. It was present in aqueous extracts derived from microsomal membranes but was not present in cytosol preparations. The second, a PEG-non-precipitable protein (Mr approximately 100,000) was composed of a non-disulphide-linked primary GH-binding subunit of Mr 60,000-66,000. This binding protein was present in all rabbit liver cell fractions and/or preparations. Both binding-protein classes contained intramolecular disulphide bonds. It is not clear whether the Mr-approximately 100,000 form, or perhaps higher-Mr species which have not been identified by cross-linking studies, represents the native, endogenous, form of the GH receptor present in particulate microsomal or plasma membranes. Accordingly, although these data have identified two classes of GH-binding protein, especially a primary GH-binding subunit of Mr 60,000-66,000, they indicate that, unlike studies on the insulin receptor, covalent cross-linking techniques alone are not sufficient to delineate the complete subunit structure of the native and endogenous form of the GH receptor.

Chemical crosslinking of alpha subunits in the F1 adenosine triphosphatase of Escherichia coli

The arrangement of the subunits in the F1 adenosine triphosphatase of Escherichia coli has been investigated using bifunctional chemical crosslinking agents to covalently link adjacent subunits in the enzyme molecule. The synthesis of the new cleavable crosslinking agent 2,2'-dithiobis(succinimidyl propionate) is described. The crosslinked products resulting from the reaction of the enzyme with 2,2'- and 3,3'-dithiobis(succinimidyl propionate), 3,3'-dithiobis(sulfosuccinimidyl propionate), disuccinimidyl tartrate, dimethyl adipimidate, 1-ethyl-3[3-(dimethylamino)propyl]carbodiimide, and 1,2:3,4-diepoxybutane were analyzed by "three-dimensional" polyacrylamide gel electrophoresis in which they were resolved first in a two-dimensional system. Following cleavage of the crosslinking bridge in the separated products, the constituent subunits were identified by a further one-dimensional gel electrophoresis step. This procedure greatly improved the precision with which crosslinked subunits could be identified. It largely overcame problems due to abnormal migration of crosslinked species on gel electrophoresis and to the formation of multiple species of the same crosslinked subunit dimers. The following crosslinked subunit dimers were identified: alpha alpha, alpha beta, beta gamma, alpha delta, beta epsilon, and gamma epsilon. The trimer alpha alpha delta was recognized. The formation of alpha alpha over alpha beta dimers was favored when more polar crosslinking agents were used. The constraints placed by the finding of adjacent alpha subunits upon current models for the arrangement of the subunits in the F1 ATPase are discussed.

Permanent suppression of phase separation cataract in calf lens using amine modification agents

Low temperature induced opacification (cold cataract) of the nucleus of young mammalian lenses is associated with a phase separation of proteins in the lens cell cytoplasm. Calf lenses were treated with a variety of imido-esters and N-hydroxysuccinimide-esters, which react specifically with amino groups. Many potent inhibitors of phase separation cataract were identified which lower the opacification temperature by 6 degrees C or more. Lenses generally remain clear, colorless and soft. Furthermore, suppression of the cold cataract temperature is permanent upon removal of excess reagent.

Identification of the calmodulin-binding components in bovine lens plasma membranes

Lens membranes, purified from calf lenses, have been labeled by covalent cross-linking to membrane-bound 125I-calmodulin with dithiobis(succinimidyl propionate). Electrophoretic analysis in sodium dodecyl sulfate demonstrated two major 125I-containing products of Mr = 49 000 and 36 000. That the formation of these two components was specifically inhibited by unlabeled calmodulin, or calmodulin antagonists, would indicate that the formation of these components was calmodulin-specific. The size of these two 125I-labeled components was unchanged over a range of 125I-calmodulin or dithiobis(succinimidyl propionate) concentrations indicating that they represent 1:1 complexes between 125I-calmodulin (Mr = 17 000) and Mr-32 000 and Mr-19 000 lens membrane components respectively. Although formation of both cross-linked components exhibited an absolute dependence on Mg2+, the autoradiographic intensity of these components was enhanced when Ca2+ was included with Mg2+ during the cross-linking reaction. Labeling was maximal in 10 mM MgCl2 and approximately 1 microM Ca2+. Treatment of lens membranes with chymotrypsin resulted in the cleavage of MP26 (the major lens membrane protein), with the appearance of a major proteolytic fragment of Mr = 22 000. This proteolysis was not associated with any significant change in either the size or amount of the 125I-calmodulin-labeled membrane components. These results suggest that calmodulin interacts with two membrane proteins, but not significantly with MP26, in the intact lens cell membrane. Our results indicate the need to maintain caution in interpreting direct calcium plus calmodulin effects on MP26 and lens cell junctions.

Photo-induced dimerization of anthracene phospholipids for the study of the lateral distribution of lipids in membranes

It is shown that photo-induced cross-linking reaction between anthracene-labelled phospholipids can be used for studying, at a molecular level, their lateral distribution in bilayer structures. A simple and versatile method is proposed. It is based on the property of anthracene to form covalently bound dimers upon irradiation in the near ultraviolet (360 nm) and on the possibility of separating the lipid photo-dimers from the lipid monomers by thin-layer chromatography. Identification of the photo-dimers is easily achieved since, upon illumination at a shorter wavelength (250-280 nm), they partially dissociate to the native monomer molecules. The feasibility of the method was tested by checking the effects of cations (sodium, calcium) on the homogeneity of 1/1 mixtures of anthracene-phosphatidylcholine, i.e. 1-acyl-2-[9-(2-anthryl)-nonanoyl]-sn-glycero-3-phosphocholin e (Anthr-PC) with anthracene-phosphatidic acid (Anthr-PA) and with anthracene-phosphatidylglycerol (Anthr-PG) in the form of liposomes. These lipids were anthracene-labelled by acylation of their glycerol backbone at the sn-2 position with the synthetic 9-(2-anthryl)-nonanoic acid. Data presented indicate a good miscibility of these lipids in the presence of sodium. For each lipid mixture, the lipid heterodimers were clearly identified and, quantitatively, they dominated the lipid homodimers, as expected for a regular distribution of the lipids in the 1/1 mixture. Addition of calcium ions to the lipid suspensions did not alter the miscibility properties of Anthr-PC and Anthr-PG. In contrast, calcium triggered a clear-cut phase separation in the Anthr-PC/Anthr-PA mixture as, in this case, only traces of the heterodimer form of the lipids remained observable on the chromatogram. The three anthracene-phospholipids, pure or mixed together, exhibit a clear-cut gel-to-liquid phase transition which was detectable by fluorescence intensity measurements. The analysis of the corresponding phase-transition temperatures confirms, at a 'macroscopic' level, the effects of sodium and calcium on the mixing properties of the anthracene phospholipids which were revealed at a 'microscopic' level by the dimerization procedure.