BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics

Cross-linking combined with mass spectrometry is an emerging approach for studying protein structure and protein-protein interactions. However, unambiguous mass spectrometric identification of cross-linked peptides derived from proteolytically digested cross-linked proteins is still challenging. Here we describe the use of a novel cross-linker, bimane bisthiopropionic acid N-succinimidyl ester (BiPS), that overcomes many of the challenges associated with other cross-linking reagents. BiPS is distinguished from other cross-linkers by a unique combination of properties: it is photocleavable, fluorescent, homobifunctional, amine-reactive, and isotopically coded. As demonstrated with a model protein complex, RNase S, the fluorescent moiety of BiPS allows for sensitive and specific monitoring of the different cross-linking steps, including detection and isolation of cross-linked proteins by gel electrophoresis, determination of in-gel digestion completion, and fluorescence-based separation of cross-linked peptides by HPLC. The isotopic coding of BiPS results in characteristic ion signal "doublets" in mass spectra, thereby permitting ready detection of cross-linker-containing peptides. Under MALDI-MS conditions, partial photocleavage of the cross-linker occurs, releasing the cross-linked peptides. This allows differentiation between dead-end, intra-, and interpeptide cross-links based on losses of specific mass fragments. It also allows the use of the isotope doublets as mass spectrometric "signatures." A software program was developed that permits automatic cross-link identification and assignment of the cross-link type. Furthermore photocleavage of BiPS assists in cross-link identification by allowing separate tandem mass spectrometry sequencing of each peptide comprising the original cross-link. By combining the use of BiPS with MS, we have provided the first direct evidence for the docking site of a phosphorylated G-protein-coupled receptor C terminus on the multifunctional adaptor protein beta-arrestin, clearly demonstrating the broad potential and application of this novel cross-linker in structural and cellular biology.     

Immunohistochemical localization of oxytocin and vasopressin in the adrenal glands of rat,cow, hamster and guinea pig

Summary The distribution of oxytocin and vasopressin in the adrenals of rat, cow, hamster and guinea pig has been studied by use of immunohistochemical techniques. In all the species studied the adrenal cortex contained both peptides; the staining in the zona glomerulosa being more intense than that in zona fasciculata or zona reticularis. The medulla, however, showed considerable species variation. In the cow, both peptides appear to be present in the adrenergic and noradrenergic cells, though staining was particularly prominent in cortical islands interspersed within the medullary tissue. In the rat, groups of medullary cells positive for both peptides were found, though it was not possible to associate these groups with particular chromaffin cell types. In the hamster oxytocin was present only in adrenaline-containing cells, whereas vasopressin was present in all medullary cells. The guinea pig medulla, which contains only adrenaline-secreting cells, was positive for both peptides. The possibilities that vasopressin and oxytocin have an autocrine or paracrine role in functioning of the adrenal gland is discussed.     

Identification and characterization of N-glycosylated and phosphorylated variants of proenkephalin A-derived peptides in bovine adrenal medulla, spinal cord and ileum

Recent studies have shown that during its biosynthesis in bovine adrenal medulla, the opioid precursor proenkephalin A, may be both N-glycosylated and phosphorylated. To investigate whether these chemical modifications were common to proenkephalin A processing in other tissues, we have sought to characterize enkephalin-containing peptides from bovine adrenal medulla, spinal cord and ileum. The peptides were identified using antiserum L189, specific for the C-terminus of Met-enkephalin Arg6Gly7Leu8 (MERGL), and L152, specific for the C-terminus of Met-enkephalin Arg6Phe7 (MERF). Glycosylated MERGL-immunoreactive peptides of 23, 20, 16 and 13 kDa were identified in adrenal medulla using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and concanavalin A-Sepharose affinity chromatography. Sephadex G50 gel filtration fractionated the glycosylated peptides into two immunoreactive peaks. Similar peaks of concanavalin A-binding MERGL immunoreactivity were detected in extracts of spinal cord and ileum, although there were differences in relative proportions of the two peaks. Antiserum L152 identified phosphorylated N-terminally extended variants of MERF when boiling water extracts of adrenal medulla, spinal cord and ileum were separated by anion exchange chromatography. In adrenal medulla these peptides were more than 99% phosphorylated, whereas in both ileum and spinal cord there was a relatively higher proportion of the unphosphorylated peptide. The results indicate that N-glycosylation and phosphorylation of proenkephalin A occurs in adrenal medulla, spinal cord and ileum, although there are tissue-specific differences in the relative proportions of the modified and unmodified peptides.     

The stability of collagen cross-links when derived from hydroxylsyl residues

The cross-linked cyanogen bromide peptide, (4×9), previously isolated after reduction of cartilage collagen, has been isolated without prior reduction of the collagen. The unreduced cross-link is cleaved by periodate allowing recovery of the component peptides. When isolated after borotritide reduction of the collagen, (4×9) contains a single residue of radioactive hydroxylysinohydroxynorleucine. Radioactivity in the cross-link remains in the component peptides when the cross-link is cleaved with periodate. Performic acid oxidation removes this radioactivity and produces an additional glutamic acid residue in each peptide. These data indicate that dehydrohydroxylysinohydroxynorleucine undergoes an Amadori rearrangement producing a more stable keto-amine form of the cross-link.     

Locus of a histidine-based, stable trifunctional, helix to helix collagen cross-link: stereospecific collagen structure of type I skin fibrils

The loci of the three amino acid residues that contribute their prosthetic groups to form the stable, nonreducible, trifunctional intermolecular cross-link histidinohydroxylysinonorleucine in skin collagen fibrils were identified. Two apparently homogeneous three-chained histidinohydroxylysinonorleucine cross-linked peptides were chromatographically isolated. They were obtained from a tryptic digest of denatured unreduced 6 M guanidine hydrochloride insoluble bovine skin collagen. Amino acid and sequence analyses demonstrated that the prosthetic groups of alpha 1(I)-chain Hyl-87, alpha 1(I)-chain Lys-16c, and alpha 2(I)-chain His-92 formed the cross-link. The latter results served to define the locus of the stable, nonreducible trifunctional moiety. Identical types of analyses were performed on the three-chained peptides isolated after bacterial collagenase digestion of the cross-linked tryptic peptides. This confirmed the initial identification and location of the three peptides linked by the cross-link. In addition, data reported here provide for a correction of the micromolecular structure for the alpha 2(I) chain. Stereochemical considerations concerning this trifunctional cross-link's specific locus indicate that the steric relationships between the alpha chains of skin and skeletal tissue collagens are fundamentally different and the intermolecular relationships in skin fibrils are specific for skin. The same molecular relationships also indicate that histidinohydroxylysinonorleucine links three molecules of collagen. The stereochemistry of cross-linking for skin collagen is in accordance with and explains the X-ray findings of a 65-nm periodicity found for this tissue [Stinson, R. H., & Sweeny, P. R. (1980) Biochim. Biophys. Acta 621, 158; Brodsky, B., Eikenberry, E. F., & Cassidy, K. (1980) Biochim. Biophys. Acta 621, 162].     

Mass-spectrometric characterization of two posttranslational modifications of cysteine dioxygenase

Recent crystal structures of cysteine dioxygenase (CDO) suggest the presence of two posttranslational modifications adjacent to the catalytic iron center: a thioether cross-link between Cys93 and Tyr157 and extra electron density at Cys164 which was variously explained as cystine or cysteine sulfinic acid. Purification of recombinant rat CDO yields “mature” and “immature” forms with distinct electrophoretic mobilities. We have positively identified and characterized the two modifications in the products of three sequential proteolytic digestions using liquid chromatography coupled with tandem mass spectrometry. The cross-link is unique to the mature form and was identified in an ion of m/z 3,225.403, consistent with a Tyr-Cys cross-link of peptides Gly80-Phe94 with His155-Phe167. The cross-link is liable to cleavage by in-source decay and the resulting separate peptides were sequenced by collision-induced dissociation tandem mass spectrometry. Mass-spectrometric analysis of these same and overlapping peptides in the presence or absence of reductants and alkylating agents identified the second modification to be a cystine formed between Cys164 and exogenous cysteine as proposed earlier. Both modifications have been shown to form in the presence of high levels of cysteine and iron. This and the presence of small amounts of an apparently off-pathway cystine at position Cys93 suggest that although these conditions promote CDO maturation, they may actually arise via nonenzymatic, nonphysiological processes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Pre- and postnatal aminopeptidase activities in the rat brain

Research concerning the functional role of brain peptides is performed, in part, by studying peptidase enzymes which might be involved in brain peptide processing or inactivation. Aminopeptidase (AP) activity has been proposed as a candidate regulator of the degradation of these peptides. In this paper, changes in Lys- and Leu-aminopeptidase activities in rat brain hemispheres, cerebellum and medulla were examined in 20 day fetuses and one day postnatal subjects. Aminopeptidase activities were studied by measuring the rate of hydrolysis of the artificial substrates Lys- and Leu-2-naphthylamides (fluorimetrically detected in triplicate). Both enzyme activities increase from the last fetal stage up to the first day of birth in all the brain areas examined except for the case of Leu-AP activity in the medulla. It is suggested that these activities play a part in the neurochemical changes that take place during rat brain maturation, possibly by regulating the activity of several neuroactive peptides.     

Isolation of polypeptides containing the intermolecular cross-link , '-dihydroxylysinonorleucine from dentin collagen

Insoluble dentin collagen was reduced with sodium borotritiide and then sequentially cleaved with cyanogen bromide and trypsin. Separation and purification of the labeled peptides were accomplished by gel filtration and ion-exchange chromatography. Two peptides were obtained containing 38 and 26 residues each, respectively. Both contained stoichiometric amounts of the collagen intermolecular cross-link δ,δ′-dihydroxylysinonorleucine. Their compositions are reported. The data indicate that one of the branches on each of the H-shaped peptides might be identical and the other branch on each is derived from different loci on the collagen molecule. Neither crosslink peptide involves the N-terminal portion of collagen.     

Immunohistochemical localization of Met-enkephalin, Met-enkephalin-Arg6-Gly7-Leu8, Met-enkephalin-Arg6-Phe7 and Leu-enkephalin in human adrenal medulla and pheochromocytomas

Immunohistochemical localization of Met-enkephalin, Met-enkephalin-Arg6-Gly7-Leu8, Met-enkephalin-Arg6-Phe7 and Leu-enkephalin was studied in human adrenal medulla and pheochromocytomas at the light and electron microscopic levels. Both adrenal medulla and pheochromocytomas (4 adrenal, 1 extra-adrenal) showed scattered or clustered cells which contained all of the above peptides and suggested the production of proenkephalin A. The presence of these peptides predominantly in the secretory granules suggested that proenkephalin A is processed to final products mainly in the secretory granules. The localization of Met-enkephalin-Arg6-Gly7-Leu8 and Met-enkephalin-Arg6-Phe7 in cisternae of rough endoplasmic reticula indicated their actual production in pheochromocytomas.     

Localization of the alpha-chain cross-link acceptor sites of human fibrin

The potential cross-link acceptor sites of fibrin were specifically labeled with the fluorescent, substitute cross-link donor monodansyl cadaverine (MDC). Several fluorescent alpha-chain peptides generated from enzymatic and cyanogen bromide (CNBr) cleavage of the labeled fibrin were identified by sodium dodecyl sulfate disc gel electrophoresis; they were isolated and then characterized by amino acid analysis, NH2-terminal sequence analysis, and chromatographic and electrophoretic analyses of their digestion products. Ancrod cleavage of MDC-labeled fibrin produced a series of six alpha-chain peptides of molecular weights 34,000 to 12,000, each of which contained an MDC-labeled acceptor site, and an NH2-terminal alpha-chain derivative of molecular weight 37,500. The latter remains disulfide bound in the residual fibrin and has two MDC-labeled sit-s which are separable by CNBr cleavage. Mild plasmin digestion of MDC-labeled fibrin generated fluorescent alpha-chain peptides of molecular weights 45,000, 42,000, 35,000, 23,000, 21,000, and 2,500 in the supernatant and a nonfluorescent NH2-terminal alpha-chain derivative of molecular weight 25,000 which remained in the insoluble residual fibrin. The alignment of these plasmic supernatant peptides was determined from NH2-terminal sequence analyses which indicated that an MDC acceptor site was located at approximately residue 255 of the Aalpha-chain. Cleavage of the MDC-labeled alpha-chain by CNBr, however, localized most of its fluorescence (approximately 80%) to a fragment of molecular weight 29,000 which had the same NH2-terminal sequence as the labeled plasmic peptide of molecular weight 21,000. Both peptides were cleaved by ancrod into two acceptor site-containing peptides of approximately equal fluorescence. The preliminary NH2-terminal sequence analyses of these peptides, when combined with the above findings, indicated that these two other cross-link acceptor sites are in a peptide segment which comprises the middle 17% of the Aalpha-chain.     

Reversible inactivation of (Na+ + K+)-ATPase by use of a cleavable bifunctional reagent.

1. Purified (Na+ + K+)-ATPase, prepared from rabbit kidney outer medulla, is incubated with the bifunctional NH2-directed reagent dimethyl 3,3'-dithiobis-propionimidate. This results in a cross-link between the subunits of the enzyme and a simultaneous reduction of the (Na+ + K+)-ATPase and K+-stimulated p-nitrophenylphosphatase activities. 2. The most abundant cross-link product is a dimer of the two different subunits of the enzyme. 3. Reduction of the disulfide cross-link by dithioerythritol results in partial recovery of the original subunit structure of the enzyme and of the (Na+ + K+)-ATPase and K+-stimulated p-nitrophenylphosphatase activities. 4. These results suggest that a free mobility of the subunits of the (Na+ + K+)-ATPase system relative to each other is essential for proper functioning of both enzyme activities.     

Immunohistochemical studies for multiple peptide-immunoreactivities and co-localization of Met-enkephalin-Arg6-Gly7-Leu8, neuropeptide Y and somatostatin in human adrenal medulla and pheochromocytomas

Three normal human adult adrenal medullas and 12 cases of pheochromocytomas were studied for immunohistochemical localization of various peptides. Met-enkephalin-Arg6-Gly7-Leu8 (MEAGL) was present in all cases of pheochromocytomas. The normal adrenal medulla showed cells immunoreactive for MEAGL, neuropeptide tyrosine (NPY) and proopiomelanocortin derived N-terminal fragment (NTF). MEAGL and NPY were co-localized in some adrenal medullary cells. Pheochromocytomas showed striking multiple immunoreactivities regardless of histologic types, pleomorphic or organoid. Ten cases showed immunoreactivities for more than two peptides. All cases showed immunoreactivity for MEAGL and 9 cases showed NPY positive cells. Some tumor cells contain both MEAGL and NPY in the cytoplasm. Six cases were positive for somatostatin. Some tumor cells were shown to contain both MEAGL and SS. The appearance of SS and other peptides was considered to be related to the neoplastic transformation of the adrenal medulla.     

A structural model for desmosine cross-linked peptides.

Desmosine-enriched peptides were isolated from a thermolysin digest of bovine ligamentum nuchae elastin and a partial sequence was determined. A 'two-cross-link' model is proposed in which a second cross-link, perhaps lysinonorleucine, joins two peptide chains approx. 35 amino acid residues removed from the desmosine. Implied in this model is a certain asymmetry or directionality which places restrictions on the 'sense' of the peptide chains (either always parallel or anti-parallel) in order to align the cross-linking sites. Imposing such restrictions raises the possibility of specific alignment of elastin precursor molecules by microfibrillar proteins and/or aligning peptides on the precursor molecules themselves.     

Functional characteristics of neuropeptides in the dorsal medulla oblongata and vagus nerve

The dorsomedial medulla plays an integral role in the processing of primary sensory afferent information from the respiratory, cardiovascular, and gastrointestinal systems. A correlation has also been made between the topographical organization of these vagal afferent fibers in the dorsal medulla and the distribution of a variety of neuropeptides and their receptors in this brain region. In this paper, the evidence for the presence of several neuropeptides and their receptors in the dorsomedial medulla and intra- and/or extracranial segments of the vagus nerve is presented. The possible physiological significance of these peptides and their putative receptors in the vagus nerve is also addressed, with emphasis on angiotensin II and its cardiovascular actions in this region.     

Immunolocalization of allatostatin-like neuropeptides and their putative receptor in eyestalks of the tiger prawn, Penaeus monodon

Allatostatin (AST)-like immunoreactivity (IR) was localized in the eyestalk of Penaeus monodon by immunohistochemistry using four anti-AST antibodies. Depending on the antisera, AST-like immunoreactivity was detected in neuronal bodies of the lamina ganglionalis, cell bodies anterior to the medulla externa and cell bodies on the anterior and posterior of the medulla terminalis. Neuronal processes in neuropiles of the medulla externa, medulla terminalis, sinus gland and nerve fibers in the optic nerve were also recognized. No IR in cell bodies or in nerve fibers was found in the medulla interna. Strong AST-like immunoreactivity was found in hundreds of cells of the X organ. The localization of AST-like peptides suggests that they function as neurotransmitters and/or neuromodulators. Antiserum to the Drosophila AST receptor (Dar-2) recognized a single protein in P. monodon eyestalk protein extracts that was identical in size to that found in Drosophila protein extracts. Using this antiserum the putative P. monodon AST receptor was localized to the sinus gland in both juvenile and adult eyestalks. To our knowledge this is the first demonstration of a neuropeptide receptor localized to the crustacean sinus gland. This suggests that ASTs may function directly on the sinus gland as a neuromodulator. In juvenile eyestalks, the putative AST receptor was also localized to neuronal X organ cells of the medulla terminalis in males but not in females. The significance of this sex-specific receptor localization is unclear but emphasizes that ASTs function within the nervous system of the eyestalk.     

Cross-linking of collagen. Location of pyridinoline in bovine articular cartilage at two sites of the molecule.

The location of pyridinoline in 18-month-old bovine articular cartilage was investigated by fractionation of CNBr-derived peptides by ion-exchange chromatography and gel filtration. Two peptides, PCP1 and PCP2, were isolated and were shown to contain stoichiometric amounts of pyridinoline. From its amino acid composition and sequence studies, peptide PCP1 was shown to comprise two C-terminal non-helical chains (CB14) linked through pyridinoline to the alpha 1(II)-CB12 portion of the helix. The CB14 chains appeared to be labile at their C-terminal ends, resulting in lower-than-expected amounts of homoserine, and only the N-terminal portion of the peptide was sequenced. Similar studies of peptide PCP2 showed that it contained two N-terminal non-helical chains (CB4) linked to the alpha 1(II)-CB9,7 portion of the helix. The isolated peptides therefore confirmed the function of pyridinoline in stabilizing the 4D stagger of adjacent molecules. The possibility that the cross-link could act both as an intra- and an inter-microfibrillar cross-link was considered. A mechanism of formation of pyridinoline was postulated that, together with other evidence, appears to support the view that, in cartilage, pyridinoline acts primarily as an intramicrofibrillar cross-link and does not contribute to increased stability during maturation through lateral aggregation and bonding of filaments.     

Structure, flexibility, and repair of two different orientations of the same alkyl interstrand DNA cross-link

Interstrand DNA cross-links are the principal cytotoxic lesions produced by chemotherapeutic bifunctional alkylating agents. Using an N(4)C-ethyl-N(4)C interstrand DNA cross-link to mimic this class of clinically important cancer chemotherapeutic agents, we have characterized the repair, structure, and flexibility of DNA that contains this cross-link in two different orientations. Plasmid DNAs in which the cytosines of single CpG or GpC steps are covalently linked were efficiently processed by repair proficient and homologous recombination deficient strains of Escherichia coli. Repair in a nucleotide excision repair (NER) deficient strain was less efficient overall and displayed a 4-fold difference between the two cross-link orientations. Both the structure and flexibility of DNA containing these cross-links were examined using a combination of (1)H NMR, restrained molecular dynamics simulations, and atomic force microscopy (AFM). The NMR structure of a decamer containing a CpG interstrand cross-link shows the cross-link easily accommodated within the duplex with no disruption of hydrogen bonding and only minor perturbations of helical parameters. In contrast, disruptions caused by the GpC cross-link produced considerable conformational flexibility that precluded structure determination by NMR. AFM imaging of cross-link-containing plasmid DNA showed that the increased flexibility observed in the GpC cross-link persists when it is embedded into much larger DNA fragments. These differences may account for the different repair efficiencies seen in NER deficient cells.     

Identification of pro-opiomelanocortin and the secretion of its peptide fragments in the adrenals of the bull

Immunoreactive alpha-, beta- and gamma-endorphins and beta-lipotropin--C-terminal peptide fragments of pro-opiomelanocortin (POMC)--were discovered and measured by RIA in the bovine adrenal medulla and cortex. These peptides were also discovered in perfusates of the adrenal gland. POMC proper and some intermediate forms of its processing not differing in electrophoretic mobility from the respective molecular forms of hypophyseal POMC were identified in the medulla and cortex of the adrenals by the immunoblotting technique with the use of antiserum to beta-lipoprotein. It is concluded that POMC gene is expressed in the adrenal medulla and cortex and that as a result of POMC processing a noticeable amount of its peptide fragments is formed and secreted in adrenal cells. The authors thus suggest the presence of existence of the pituitary-unrelated mechanisms of adrenal function control with participation of POMC peptides synthesized in the adrenals.     

Expression of Trophic Peptides and Their Receptors in Chromaffin Cells and Pheochromocytoma

Pheochromocytomas are catecholamine-producing tumors arising from chromaffin cells of the adrenal medulla or extra-adrenal location. Along with catecholamines, tumoral cells produce and secrete elevated quantities of trophic peptides which are normally released in a regulated manner by the normal adrenal medulla. Among these peptides, the amounts of pituitary adenylate cyclase-activating polypeptide (PACAP), adrenomedullin (AM), and neuropeptide Y (NPY) are particularly high. These peptides can exert endocrine, paracrine or autocrine effects in numerous cell types. In particular, they have been shown to be involved in cell proliferation and survival, catecholamine production and secretion, and angiogenesis. Some of these processes are exacerbated in pheochromocytomas, raising the possibility of the involvement of trophic peptides. Here, we review the expression levels of NPY, PACAP, and AM and theirs receptors in chromaffin cells and pheochromocytomas, and address their possible implication in the adrenal medulla tumorigenesis and malignant development of pheochromocytomas.     

Localization of substance P-like,leucine-enkephalin-like,methionine-enkephalin-like,and FMRFamide-like immunoreactivity in the eyestalk of the fiddler crab,Uca pugilator

Summary The occurrence and distribution of substance P (SP)-like, methionine-(Met)- and leucine-(Leu)-enkephalinlike, and FMRFamide-like immunoreactivities were determined in the neuroendocrine complex of the eyestalk of the fiddler crab, Uca pugilator, by immunocytochemistry. SP-like immunoreactivity was found in the optic peduncle, sinus gland, medulla externa, medulla interna, lamina ganglionaris, and retinular cells. Met-enkephalin-like and Leuenkephalin-like immunoreactivity was observed in most of the retinular cells, optic peduncle, sinus gland, medulla terminalis, and lamina ganglionaris. However, Met-enkephalin-like, but no Leu-enkephalin-like, immunoreactivity was seen in the medulla terminalis X-organ. FMRFamide-like immunoreactivity could be seen in all parts of the eyestalk except in the sinus gland, lamina ganglionaris, and retinular cells. FMRF-amide-like activity was especially strong in the three chiasmatic regions connecting the optic ganglia. The possibility that these four peptides may function as neuroregulators in the fiddler crab is discussed.This investigation was supported in part by Grant No. PCM-8300064 from the National Science Foundation to MF and Biomedical Research Support Grant No. 2 SO7RRO5373 SUB from the University of Kansas Medical Center to LLV