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Results for “post translational modification”

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PubMed1997

Functional expression of human mannan-binding proteins (MBPs) in human hepatoma cell lines infected by recombinant vaccinia virus: post-translational modification, molecular assembly, and differentiation of serum and liver MBP.

Human mannan-binding proteins (MBPs) occur in two forms, serum MBP (S-MBP) and liver MBP (L-MBP), both of which are synthesized in the liver from a single form of human MBP mRNA. To investigate further the mechanisms of post-translational modification, molecular assembly and differentiation of S-MBP and L-MBP in vitro, we expressed a full-length human MBP cDNA in three human hepatoma cell lines, using the vaccinia virus expression system. The expression of human MBP cDNA reproduced the native MBP differentiation of S-MBP and L-MBP in human hepatoma cells. The recombinant S-MBP was secreted into the medium, and the recombinant L-MBP retained in the cells. The former had the ability to activate the complement through the classical or lectin pathway but the latter did not. Furthermore, one notable difference between the two MBPs was the degree of oligomerization through interchain disulfide bonds between subunits. In addition, we showed that both S-MBP and L-MBP undergo hydroxylation of lysine and proline residues in collagen-like sequences, and that the hydroxylysine is glycosylated to form glucosylgalactosylhydroxylysine (GluGalHyl) and galactosylhydroxylysine (GalHyl). Hydroxylation was required for S-MBP to be assembled into large complexes, the apparent molecular sizes of which were estimated to be 200-1,300 kDa by SDS-PAGE under non-reducing conditions and gel filtration under non-denaturing conditions. The hydroxylation and subsequent glycosylation and oligomerization were inhibited by alpha,alpha'-dipyridyl, an inhibitor of collagen lysyl and prolyl hydroxylases. These results suggested that newly synthesized lectins undergo post-translational modifications unique to the two forms of MBP, S-MBP, and L-MBP, in human hepatocytes and hepatoma cells, and that the collagen-like domains of the MBPs play an important role in promoting molecular assembly.

Aged↗

PubMed2000

Evidence for differential post-translational modifications of slow myosin heavy chain during murine skeletal muscle development.

The contractile properties of muscle fibres are, in part, determined by the myosin heavy chain (MyHC) isoforms they express. Using monoclonal antibodies, we show that at least three forms of slow twitch MyHC accumulate sequentially during mouse fetal development and that slow MyHC maturation in slow fibres occurs before expression of the adult fast MyHCs in fast fibres. Expression of deletion derivatives of beta-cardiac MyHC cDNA shows that the slow MyHC epitopes that are detected in adult but not in young animals are located near the N-terminus. The same N-terminal region of various fast MyHC molecules contains a conserved epitope that can, on occasions, be observed when slow MyHC cDNA is expressed in non-muscle cells. The results raise the possibility that the N-terminal epitopes result from post-translational modification of the MyHC and that a sequence of slow and fast MyHC isoform post-translational modifications plays a significant role during development of murine muscle fibres.

Animals↗

PubMed2001

Global regulation of post-translational modifications on core histones.

Full-length masses of histones were analyzed by mass spectrometry to characterize post-translational modifications of bulk histones and their changes induced by cell stimulation. By matching masses of unique peptides with full-length masses, H4 and the variants H2A.1, H2B.1, and H3.1 were identified as the main histone forms in K562 cells. Mass changes caused by covalent modifications were measured in a dose- and time-dependent manner following inhibition of phosphatases by okadaic acid. Histones H2A, H3, and H4 underwent changes in mass consistent with altered acetylation and phosphorylation, whereas H2B mass was largely unchanged. Unexpectedly, histone H4 became almost completely deacetylated in a dose-dependent manner that occurred independently of phosphorylation. Okadaic acid also partially blocked H4 hyperacetylation induced by trichostatin-A, suggesting that the mechanism of deacetylation involves inhibition of H4 acetyltransferase activity, following perturbation of cellular phosphatases. In addition, mass changes in H3 in response to okadaic acid were consistent with phosphorylation of methylated, acetylated, and phosphorylated forms. Finally, kinetic differences were observed with respect to the rate of phosphorylation of H2A versus H4, suggesting differential regulation of phosphorylation at sites on these proteins, which are highly related by sequence. These results provide novel evidence that global covalent modifications of chromatin-bound histones are regulated through phosphorylation-dependent mechanisms.

Acetylation↗

PubMed1999

Extensive post-translational modification, including serine to D-alanine conversion, in the two-component lantibiotic, lacticin 3147.

Lacticin 3147 is a two-component bacteriocin produced by Lactococcus lactis subspecies lactis DPC3147. In order to further characterize the biochemical nature of the bacteriocin, both peptides were isolated which together are responsible for the antimicrobial activity. The first, LtnA1, is a 3,322 Da 30-amino acid peptide and the second component, LtnA2, is a 29-amino acid peptide with a mass of 2,847 Da. Conventional amino acid analysis revealed that both peptides contain the thioether amino acid, lanthionine, as well as an excess of alanine to that predicted from the genetic sequence of the peptides. Chiral phase gas chromatography coupled with mass spectrometry of amino acid composition indicated that both LtnA1 and LtnA2 contain D-alanine residues and amino acid sequence analysis of LtnA1 confirmed that the D-alanine results from post-translational modification of a serine residue in the primary translation product. Taken together, these results demonstrate that lacticin 3147 is a novel, two-component, D-alanine containing lantibiotic that undergoes extensive post-translational modification which may account for its potent antimicrobial activity against a wide range of Gram-positive bacteria.

Alanine↗

PubMed2003

A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications.

MOTIVATION: Tandem mass spectrometry combined with sequence database searching is one of the most powerful tools for protein identification. As thousands of spectra are generated by a mass spectrometer in one hour, the speed of database searching is critical, especially when searching against a large sequence database, or when the peptide is generated by some unknown or non-specific enzyme, even or when the target peptides have post-translational modifications (PTM). In practice, about 70-90% of the spectra have no match in the database. Many believe that a significant portion of them are due to peptides of non-specific digestions by unknown enzymes or amino acid modifications. In another case, scientists may choose to use some non-specific enzymes such as pepsin or thermolysin for proteolysis in proteomic study, in that not all proteins are amenable to be digested by some site-specific enzymes, and furthermore many digested peptides may not fall within the rang of molecular weight suitable for mass spectrometry analysis. Interpreting mass spectra of these kinds will cost a lot of computational time of database search engines. OVERVIEW: The present study was designed to speed up the database searching process for both cases. More specifically speaking, we employed an approach combining suffix tree data structure and spectrum graph. The suffix tree is used to preprocess the protein sequence database, while the spectrum graph is used to preprocess the tandem mass spectrum. We then search the suffix tree against the spectrum graph for candidate peptides. We design an efficient algorithm to compute a matching threshold with some statistical significance level, e.g. p = 0.01, for each spectrum, and use it to select candidate peptides. Then we rank these peptides using a SEQUEST-like scoring function. The algorithms were implemented and tested on experimental data. For post-translational modifications, we allow arbitrary number of any modification to a protein. AVAILABILITY: The executable program and other supplementary materials are available online at: http://hto-c.usc.edu:8000/msms/suffix/.

Algorithms↗

PubMed1995

Monoclonal and polyclonal antibodies detect a new type of post-translational modification of axonemal tubulin.

Polyclonal (PAT) and monoclonal (AXO 49) antibodies against Paramecium axonemal tubulin were used as probes to reveal tubulin heterogeneity. The location, the nature and the subcellular distribution of the epitopes recognized by these antibodies were, respectively, determined by means of: (i) immunoblotting on peptide maps of Paramecium, sea urchin and quail axonemal tubulins; (ii) immunoblotting on ciliate tubulin fusion peptides generated in E. coli to discriminate antibodies directed against sequential epitopes (reactive) from post-translational ones (non reactive); and (iii) immunofluorescence on Paramecium cells, using throughout an array of antibodies directed against tubulin sequences and post-translational modifications as references. AXO 49 monoclonal antibody and PAT serum were both shown to recognize epitopes located near the carboxyl-terminal end of both subunits of Paramecium axonemal tubulin, whereas the latter recognized additional epitopes in alpha-tubulin; AXO 49 and a fraction of the PAT serum proved to be unreactive over fusion proteins; both PAT and AXO 49 labelled a restricted population of very stable microtubules in Paramecium, consisting of axonemal and cortical ones, and their reactivity was sequentially detected following microtubule assembly; finally, both antibodies stained two upward spread bands in Paramecium axonemal tubulin separated by SDS-PAGE, indicating the recognition of various alpha- and beta-tubulin isoforms displaying different apparent molecular masses. These data, taken as a whole, definitely establish that PAT and AXO 49 recognize a post-translational modification occurring in axonemal microtubules of protozoa as of metazoa. This modification appears to be distinct from the previously known ones, and all the presently available evidence indicates that it corresponds to the very recently discovered polyglycylation of Paramecium axonemal alpha- and beta-tubulin.

Animals↗

PubMed1987

Identification of the post-translational modifications of the core-specific lectin. The core-specific lectin contains hydroxyproline, hydroxylysine, and glucosylgalactosylhydroxylysine residues.

The core-specific lectin (CSL) synthesized and secreted by rat hepatocytes and the rat hepatoma H-4-II-E shows affinity for mannose and N-acetylglucosamine residues in the "core" region of asparagine-linked oligosaccharides. The CSL undergoes two stages of post-translational modification which result in an increase in its Mr from 24,000 to 26,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. We have determined that the lectin undergoes hydroxylation of proline and lysine and that the hydroxylysine is glycosylated to form glucosylgalactosylhydroxylysine (GlcGalHyLys). CSL metabolically labeled with [3H]lysine and [3H]proline contains hydroxylated forms of proline and lysine. The mature form of the lectin can also be metabolically labeled with [3H]galactose. alpha,alpha'-Dipyridyl, an inhibitor of collagen prolyl and lysyl hydroxylases, prevents the metabolic incorporation of [3H]galactose and the post-translational increases in the Mr of the CSL, indicating that both events are dependent upon hydroxylation of proline and lysine. Virtually all of the hydroxylysine present in the CSL is recovered as glucosylgalactosylhydroxylysine after alkaline hydrolysis. The post-translational modifications of the CSL place it in a select family of secreted proteins which contain collagen-like sequences, including the pulmonary surfactant proteins, complement component C1q, and the 18 S asymmetric form of acetylcholinesterase.

2,2'-Dipyridyl↗

PubMed2003

Post-translational modification of flagellin determines the specificity of HR induction.

Flagellin, a constituent of the flagellar filament, is a potent elicitor of hypersensitive cell death in plant cells. Flagellins of Pseudomonas syringae pvs. glycinea and tomato induce hypersensitive cell death in their non-host tobacco plants, whereas those of P. syringae pv. tabaci do not remarkably induce it in its host tobacco plants. However, the deduced amino acid sequences of flagellins from pvs. tabaci and glycinea are identical, indicating that post-translational modification of flagellins plays an important role in determining hypersensitive reaction (HR)-inducibility. To investigate genetically the role of modification of flagellin in HR-induction, biological and phytopathological phenotypes of a flagella-defective Delta fliC mutant and Delta fliC mutants complemented by the introduction of the flagellin gene (fliC) from different pathovars of P. syringae were investigated. The Delta fliC mutant of pv. tabaci lost flagella, motility, the ability to induce HR cell death in non-host tomato cells and virulence toward host tobacco plants, whereas all pv. tabaci complemented by the introduction of the fliC gene of pvs. tabaci, glycinea or tomato recovered all the abilities that the Delta fliC mutant had lost. These results indicate that post-translational modification of flagellins is strongly correlated with the ability to cause HR cell death.

Apoptosis↗

PubMed1985

High post-translational modification levels in type II procollagen are not a consequence of slow triple-helix formation.

The kinetics of triple helix formation of newly synthesized type II procollagen in chick embryo sternal cartilage cells were determined. The data obtained were in agreement with a model for triple helix formation in cellulo proposed recently (Bruckner et al., 1981). The time required to produce fully triple helical type II procollagen in cartilage cells was only 30% longer than for type I procollagen in tendon cells. Therefore, the several-fold increase in post-translational modification observed for type II collagen as compared to type I collagen cannot be attributed solely to slow helix formation but rather is a result of higher levels of enzymic activity of post-translational modification present in cartilage cells.

Animals↗

PubMed2006

Peptide sequence tag-based blind identification of post-translational modifications with point process model.

UNLABELLED: An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental spectra with theoretical spectra from peptides in a peptide database is very time consuming and may lead to high false positive rate. In this paper, we introduce a new approach that is both efficient and effective for blind PTM identification. Our work consists of the following phases. First, we develop a novel tree decomposition based algorithm that can efficiently generate peptide sequence tags (PSTs) from an extended spectrum graph. Sequence tags are selected from all maximum weighted antisymmetric paths in the graph and their reliabilities are evaluated with a score function. An efficient deterministic finite automaton (DFA) based model is then developed to search a peptide database for candidate peptides by using the generated sequence tags. Finally, a point process model-an efficient blind search approach for PTM identification, is applied to report the correct peptide and PTMs if there are any. Our tests on 2657 experimental tandem mass spectra and 2620 experimental spectra with one artificially added PTM show that, in addition to high efficiency, our ab-initio sequence tag selection algorithm achieves better or comparable accuracy to other approaches. Database search results show that the sequence tags of lengths 3 and 4 filter out more than 98.3% and 99.8% peptides respectively when applied to a yeast peptide database. With the dramatically reduced search space, the point process model achieves significant improvement in accuracy as well. AVAILABILITY: The software is available upon request.

Algorithms↗

PubMed2004

The effect of post-translational modifications on the hemorrhagic activity of snake venom metalloproteinases.

Metalloproteinases (MPs) are Zn(+)-dependent endoproteolytic enzymes, abundant in crotalid and viperid snake venoms. Most snake venom metalloproteinases (svMPs) are active on extracellular matrix components and this effect is thought to result in bleeding as a consequence of the basement membrane disruption in capillaries. Jararhagin and ACLH are hemorrhagic svMPs from Bothrops jararaca and Agkistrodon contortrix laticinctus venom, respectively. Both enzymes demonstrate proteolytic activity on fibrinogen and fibronectin and jararhagin inhibits collagen-induced platelet aggregation in vitro. This work describes the expression, purification and successful refolding of the recombinant ACLH zymogen (rPRO-ACLH) as well as the catalytic domain of jararhagin (rCDJARA). The heterologous proteins were produced in E. coli, an in vivo expression system that does not make post-translational modifications. The recombinant refolded proteins did not show any hemorrhagic activity in mice skin, as well as the native deglycosylated jararhagin and ACLH. However, they preserved their proteolytic activity on fibrinogen and fibronectin. It seems that the hemorrhagic properties of these hemorrhagins are dependent on post-translational modifications, whereas their proteolytic activity is not dependent on such modifications.

Agkistrodon↗

PubMed1978

Effects of a post-translational modification mutation on different developmentally regulated glycosidases in Dictyostelium discoideum.

We have studied the effect of a post-translational modification mutation upon four developmentally regulated glycosidases of Dictyostelium discoideum. The presence of the modA mutation affects the intracellular level of these multimeric enzymes differently. The level of alpha-glucosidase is unaffected in the modA mutant. The mutant cell contains only a very small fraction of the wild type beta-glucosidase-1 activity. The alteration in modification renders beta-glucosidase-1 holoenzyme thermolabile and susceptible to degradation in vivo. alpha-Mannosidase-1 and N-acetylglucosaminidase are found at approximately 1/3 of the wild type level in the modA mutant. Degradation of holoenzyme does not appear to be responsible for the low level of these activities. We propose that alpha-mannosidase-1 and N-acetylglucosaminidase subunits are being degraded prior to subunit assembly. We conclude the modification bestows different properties upon the various glycosidases.

Acetylglucosaminidase↗

PubMed2006

Role of post-translational modifications in regulating c-Myc proteolysis, transcriptional activity and biological function.

The Myc proteins play a central role in cellular proliferation, differentiation, apoptosis and tumorigenesis. Although it is clear that multiple molecular mechanisms mediate these functions, it is unclear how individual mechanisms contribute and if different mechanisms work in concert or separately in mediating the diverse biological functions of c-Myc. Similarly, the role of post-translational modifications in regulating c-Myc molecular and biological properties has remained uncertain, despite over 20 years of research. In particular, phosphorylation of the N-terminal transcriptional regulatory domain has been shown to have a variety of consequences ranging from dramatic effects on apoptosis, tumorigenesis and c-Myc proteolysis to negligible effects on cellular transformation and transcriptional activity. This review attempts to provide a comprehensive and critical evaluation of the accumulated evidence to address the complex and controversial issues surrounding the role of post-translational modifications in c-Myc function, focusing on phosphorylation and ubiquitination of the N-terminal transcriptional regulatory domain. An overall model emerges that suggests phosphorylation and ubiquitination play critical roles in cell cycle progression, cell growth, apoptosis and tumorigenesis that are mediated by phosphorylation-dependent transcriptional activation of distinct sets of target genes and synchronized proteolysis.

Animals↗

PubMed2006

Post-translational modifications of human thrombin-activatable fibrinolysis inhibitor (TAFI): evidence for a large shift in the isoelectric point and reduced solubility upon activation.

Thrombin-activable fibrinolysis inhibitor (TAFI) is distinct from pancreatic procarboxypeptidase B in several ways. The enzymatic activity of TAFIa is unstable and decays with a half-life of a few minutes. During this study, we observed that (i) the isoelectric point (pI) of TAFI shifts dramatically from pH 5 toward pH 8 upon activation and (ii) TAFIa is significantly less soluble than TAFI. The structural bases for these observations were investigated by characterizing all post-translational modifications, including attached glycans and disulfide connectivity. The analyses revealed that all five potential N-glycosylation sites were utilized including Asn22, Asn51, Asn63, Asn86 (located in the activation peptide), and Asn219 (located in the catalytic domain). Asn219 was also found in an unglycosylated variant. Four of the glycans, Asn51, Asn63, Asn86, and Asn219 displayed microheterogeneity, while the glycan attached to Asn22 appeared to be homogeneous. In addition, bisecting GlcNAc attached to the trimannose core was detected, suggesting an origin other than the liver. Monosaccharide composition and LC-MS/MS analyses did not produce evidence for O glycosylation. TAFI contains eight cysteine residues, of which two, Cys69 and Cys383, are not involved in disulfides and contain free sulfhydryl groups. The remaining six cystines form disulfides, including Cys156-Cys169, Cys228-Cys252, and Cys243-Cys257. This pattern is homologous to pancreatic procarboxypeptidase B, and it is therefore unlikely that permutations in the cysteine connectivity are responsible for the enzymatic instability. LC-MS/MS analyses covering more than 90% of the TAFI amino acid sequence revealed no additional modifications. When these results are taken together, they suggest that the inherent instability of TAFIa is not caused by post-translational modifications. However, after activation, TAFIa loses 80% of the attached glycans, generating a large shift in pI and a propensity to precipitate. These changes are likely to significantly affect the properties of TAFIa as compared to TAFI.

Carboxypeptidase B2↗

PubMed2026

Comprehensive multi-post-translational modifications profiling reveals age-associated remodeling in skeletal muscle.

Sarcopenia, characterized by the progressive loss of skeletal muscle mass and function, is a major hallmark of aging. Post-translational modifications (PTMs) play essential roles in regulating protein activity and cellular homeostasis; however, how multiple PTMs are remodeled during skeletal muscle aging remains incompletely characterized. Here, we performed comprehensive multi-layered proteomic profiling of skeletal muscle from young (3-month-old) and aged (24-month-old) mice, systematically quantifying the global proteome together with five major PTMs: acetylation, phosphorylation, N-glycosylation, O-glycosylation, and ubiquitination. In total, we identified 5 337 proteins and mapped thousands of PTM sites, generating an integrated atlas of age-associated proteomic and PTM remodeling in skeletal muscle. Pathway enrichment analyses revealed distinct modification-specific patterns: acetylation and phosphorylation were predominantly associated with metabolic and mitochondrial-related pathways; N-glycosylation was enriched in immune- and secretory pathway-related processes; O-glycosylation was associated with muscle contraction-related pathways; and ubiquitination was preferentially linked to cytoskeletal organization in muscle cells. Correlation analyses further uncovered diverse association patterns among different PTMs across protein- and modification-level datasets. Phosphorylation and ubiquitination exhibited consistent positive associations, whereas acetylation and ubiquitination showed both inverse and concordant co-variation patterns across subsets of proteins. Phosphorylation and O-glycosylation displayed heterogeneous association patterns across different proteins, and acetylation and phosphorylation demonstrated positive correlations with distinct age-associated directional changes across protein subsets. Together, these results provide a comprehensive, multi-dimensional view of age-associated remodeling of the skeletal muscle proteome and multiple PTM layers, offering a valuable resource for understanding molecular alterations accompanying muscle aging and sarcopenia.

Animals↗

PubMed2005

Electron capture dissociation mass spectrometry in characterization of post-translational modifications.

Electron capture dissociation (ECD) represents a significant advance in tandem mass spectrometry for the identification and characterization of post-translational modifications (PTMs) of polypeptides. In comparison with the conventional fragmentation techniques, such as collisionally induced dissociation and infrared multi-photon dissociation, ECD provides more extensive sequence fragments, while allowing the labile modifications to remain intact during backbone fragmentation. This unique attribute offers ECD as an attractive alternative for detection and localization of PTMs. The success and rapid adoption of ECD recently led to the culmination of The 1st International Uppsala Symposium on Electron Capture Dissociation of Biomolecules and Related Phenomena (October 19-22, 2003, Stockholm, Sweden). Herein, we present a general overview of the ECD technique as well as selected applications in characterization of post-translationally modified polypeptides.

Electrons↗

PubMed1995

Recombinant endothelial nitric oxide synthase: post-translational modifications in a baculovirus expression system.

Nitric oxide synthesized by the endothelial isoform of nitric oxide synthase (ecNOS) is importantly involved in the homeostatic control of blood pressure and platelet aggregation. The different members of the nitric oxide synthase protein family have several biochemical features in common but serve distinct physiological functions and are the products of distinct genes. The ecNOS is further distinguished by its subcellular distribution in the endothelial cell membrane, and the enzyme undergoes several post-translational modifications, including myristoylation, palmitoylation, and phosphorylation. Overall, however, the ecNOS has remained less well characterized because of the challenges involved in isolating sufficient quantities of this membrane-associated protein from native or cultured endothelial cells. In this report, we describe the purification and characterization of ecNOS expressed in a heterologous system in recombinant baculovirus-infected insect Sf9 cells. Recombinant ecNOS is targeted to the Sf9 cell membrane and comprises approximately 10% of the total cellular protein, allowing purification to homogeneity in a single-step procedure to yield a stable protein that retains the essential features of the native enzyme. Using biosynthetic labeling and immunoprecipitation, we show that recombinant ecNOS is myristoylated, palmitoylated, and phosphorylated when expressed in insect Sf9 cells. The interpretation of structural and enzymological studies of recombinant ecNOS will be facilitated by the apparent fidelity of its biosynthesis and post-translational modification in insect Sf9 cells.

Amino Acid Oxidoreductases↗

PubMed1999

Post-translational modifications of ICA512, a receptor tyrosine phosphatase-like protein of secretory granules.

The autoantigen of type I diabetes ICA512 is a receptor tyrosine phosphatase-like protein enriched in the secretory granule membranes of neurons and peptide secreting endocrine cells. While the function of ICA512 remains unknown, it is thought to link regulated neuropeptide and peptide hormone secretion with signal transduction pathways involving tyrosine phosphorylation/dephosphorylation. To characterize further its biochemical properties, we conducted studies in the bovine pituitary, an abundant source of native ICA512, as well as in fibroblasts transfected with various human ICA512 cDNA constructs. Based on these studies we have established that the signal peptide of ICA512 encompasses residues 1-34 and that the ectodomain of ICA512 undergoes multiple post-translation modifications, including N-glycosylation. Newly synthesized ICA512 appears first as a pro-protein of 110 kDa that is then converted by post-translational modifications into a 130-kDa species. Cleavage of pro-ICA512 at a consensus for furin-like convertases generates a 60-66-kDa ICA512 transmembrane fragment (amino acids 449-979). Such processing ICA512 is not restricted to neuroendocrine cells, as it can also occur in transfected fibroblasts. Finally, the predicted N-terminal fragment of ICA512 resulting from this cleavage (amino acids 35-448) or parts thereof are present in the neurosecretosomes of posterior pituitary, raising the possibility that they may be secreted upon exocytosis of secretory granules.

Amino Acid Sequence↗