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At least 19 recordsLinked to original sources
PubMed1993

Peptidases in the CNS: formation of biologically active, receptor-specific peptide fragments.

Peptides function as chemical signals between cells of multicellular organisms, or different organisms, via specific receptors on target cells. Many hormones, neuromodulators, and growth factors are peptides. Because there is no known reuptake system for peptides at the nerve terminal, the biological activity of peptides in the extracellular space is regulated by enzymatic degradation and extracellular metabolism. For example, angiotensin I is processed extracellularly in the lung by angiotensin-converting enzyme (ACE; E.C. 3.4.15.1), a peptidyl dipeptidase, to form the potent vasoconstrictor hormone angiotensin II. When neuropeptides are released from neurons into the extracellular space, specific peptidases also can modulate the peptidergic signal by generating smaller, biologically active fragments via products with similar or dissimilar characteristics of the parent peptide. Therefore, receptor-binding selectivity of a released peptide hormone can be regulated by peptidases. Because peptidases may play a key role in the extracellular regulation of peptidergic signaling, alterations in peptidase activities by drugs or disease states may lead to disruptions in biological homeostasis. The subject of this article is the role of peptidases in the central nervous system in the formation of biologically active, receptor-specific peptides from peptide E, beta-endorphin, neurotensin, and cholecystokinin.

Amino Acid Sequence↗
PubMed1990

Fragment peptide library for classification and functional prediction of proteins.

From protein sequence comparison data found in the literature, a library was organized using peptide fragment sequences which are common to related proteins. Each of the fragments was then examined for its occurrence in all the protein superfamilies defined by the NBRF-PIR data base. We have selected those fragment peptides that appear exclusively in one or a few superfamilies, and thus made a library of fragment peptides that characterize specific superfamilies. Such characteristic peptides are, in general, five to seven residues long and contain unusually high proportions of glycine and cysteine. This collection is a useful resource for the classification and functional prediction of protein molecules.

Amino Acid Sequence↗
PubMed1977

Multiple sclerosis: sensitization of a myelin basic protein fragment (peptide T) encephalitogenic to primates. A preliminary report.

Myelin basic A1 protein is the sole antigen of the central nervous system capable of inducing experimental allergic encephalitis (EAE), but sensitization with peptide fragments of the molecule may also induce disease. Using the macrophage migration inhibition factor (MIF) assay we have compared sensitization to portions of the molecule active in inducing EAE in monkeys with results obtained concomitantly using the intact protein. Cellular sensitization to human myelin A1 protein, peptide L (residues 1-116), peptide T (residues 117-170), and petide Y (residues 154-170) was studied using the Thor-Rocklin MIF assay system. Lymphocytes of 10 normal subjects, 10 multiple sclerosis patients 0-3 weeks after onset, 10 4 weeks to 3 months after and 10 6 months or longer after onset of an acute exacerbation were assayed. Results of the investigation reveal evidence of cellular sensitization to myelin basic protein encephalitogenic peptide T occurring during attacks of multiple sclerosis. Peptide L, relatively nonencephalitogenic to primates, failed to induce a significant lymphocyte response, whereas peptide Y which is encephalitogenic gave irregular results.

Adult↗
PubMed1988

Effects of neuromedin B, gastrin-releasing peptide-10 and their fragment peptides on secretion of gastrointestinal and pancreatic hormones in dogs.

The effects of neuromedin B (NMB), gastrin-releasing peptide (GRP)-10 and their C-terminal fragment peptides on the pancreatic and gastrointestinal hormone release were studied in dogs. Intravenous bolus injections of NMB and GRP-10 (4.5 nmol/kg) into conscious dogs elicited a sharp and statistically significant rise in plasma gastrin and insulin levels, but only GRP-10 brought on a significant rise in the plasma glucagon and enteroglucagon levels. The degree of stimulation of gastrin and insulin secretion by NMB and GRP-10 was dose-dependent. With a dose of 4.5 nmol/kg, the minimum size of C-terminal fragment peptides of NMB and GRP-10 to stimulate gastrin secretion was NMB and GRP-10, respectively. Both NMB and GRP-10 (0.1-100 nmol/l) stimulated insulin release from the isolated canine pancreas. The glucagon release was stimulated by 10 and 100 nmol/l GRP-10 and was not stimulated by the same doses of NMB. The somatostatin release was not influenced by either peptide. It is concluded that 1) NMB and GRP-10 can stimulate gastrin and pancreatic hormone secretion, and the latter effect may be mainly due to a direct action on the islet cells; 2) the stimulatory effect of GRP-10 is stronger than that of NMB. The difference in the minimal active fragment between NMB and GRP-10 suggests that the amino acid of position 3 - NMB (Leu) and GRP-10 (His) - may play an important role in their biological activity.

Amino Acid Sequence↗
PubMed2000

Cooperative assembly of a nativelike ubiquitin structure through peptide fragment complexation: energetics of peptide association and folding.

Peptide fragments corresponding to the N- and C-terminal portions of bovine ubiquitin, U(1-35) and U(36-76), are shown by NMR to associate in solution to form a complex of modest stability (Kassn approximately 1.4 x 10(5) M(-1) at pH 7.0), with NMR features characteristic of a nativelike structure. The complex undergoes cold denaturation, with temperature-dependent estimates of stability from NMR indicating a DeltaC(p) degrees for fragment complexation in good agreement with that determined for native ubiquitin, suggesting that fragment association results in the burial of a similar hydrophobic surface area. The stability of the complex shows appreciable pH dependence, suggesting that ionic interactions on the surface of the protein contribute significantly. However, denaturation studies of native ubiquitin in the presence of guanidine hydrochloride (Gdn.HCl) show little pH dependence, suggesting that ionic interactions may be "screened" by the denaturant, as recently suggested. Examination of the conformation of the isolated peptide fragments has shown evidence for a low population of nativelike structure in the N-terminal beta-hairpin (residues 1-17) and weak nascent helical propensity in the helical fragment (residues 21-35). In contrast, the C-terminal peptide (36-76) shows evidence in aqueous solution, from some Halpha chemical shifts, for nonnative phi and psi angles; nonnative alpha-helical structure is readily induced in the presence of organic cosolvents, indicating that tertiary interactions in both native ubiquitin and the folded fragment complex strongly dictate its structural preference. The data suggest that the N-terminal fragment (1-35), where interaction between the helix and hairpin requires the minimum loss of conformational entropy, may provide the nucleation site for fragment complexation.

Animals↗
PubMed1992

Antagonistic effect of a vasoactive intestinal peptide fragment, vasoactive intestinal peptide(1-11), on guinea pig trachea smooth muscle relaxation.

The conformation of various regions of vasoactive intestinal peptide (VIP) has been analyzed by semiempirical methods, CD, and NMR spectroscopy, indicating that residues 11-21 are most likely to be helical, whereas the amino-terminal portion VIP(1-11) could exhibit two beta-turn structures. VIP(1-11) inhibits 125I-VIP binding to intact guinea pig tracheal epithelial cells and the VIP-induced smooth muscle response. However, the endecapeptide exhibits no effect on the muscle tone. All these data suggest that VIP(1-11) may be a useful tool in studying VIP receptor recognition, its regulation, and cellular functions.

Amino Acid Sequence↗
PubMed1998

Thermodynamics of the reconstitution of tuna cytochrome c from two peptide fragments.

Two peptide fragments from tuna cytochrome c (cyt c), N-fragment (residues 1-44 containing the heme) and C-fragment (residues 45-103), combine to form a 1:1 fragment complex. This was clearly proved by ion-spray mass spectrometry. It was found from CD and NMR spectra that the structure of the fragment complex formed is similar to that of an intact cyt c, although each isolated fragment itself is unstructured. Binding constants and enthalpies upon the complex formation were directly observed by isothermal titration calorimetry. Thermodynamic parameters (deltaG(o)b, deltaHb, deltaS(o)b, and deltaC(b)p)) associated with the complex formation were determined at various pHs and temperatures. DeltaHb was found to be almost independent of pH values. The change in heat capacity accompanying the complex formation (deltaC(b)p) was directly determined from the temperature dependence of deltaHb. In addition, the change in heat capacity and enthalpy upon tuna cyt c unfolding were determined by differential scanning calorimetry. Thermodynamic parameters for the unfolding/dissociation process of the fragment complex were compared with those for cyt c unfolding at pH 3.9 and 303 K. In a comparison of two unfolding processes, the heat capacity change of each was very close to the other, while both the unfolding enthalpy and entropy of the fragment complex were larger than those of tuna cyt c. These thermodynamic data suggest that the internal interactions between polar groups (hydrogen bonding) and nonpolar groups (van der Waals interactions) are preserved in the fragment complex as well as in the native state of cyt c.

Animals↗
PubMed2006

A machine learning approach to predicting peptide fragmentation spectra.

Accurate peptide identification from tandem mass spectrometry experiments is the cornerstone of proteomics. Although various approaches for matching database sequences with experimental spectra have been developed to date (e.g. Sequest, Mascot) the sensitivity and specificity of peptide identification have not yet reached their full potential. This is in part due to the tradeoffs between robustness and accuracy of the existing methods with respect to the non-uniform nature of peptide fragmentation and bond cleavages induced by different mass spectrometers. Accordingly, it is expected that new approaches to de novo predicting peptide fragmentation spectra will enable more accurate peptide identification. To address this problem, here we used a data-driven approach to learn peptide fragmentation rules in mass spectrometry, in the form of posterior probabilities, for various fragment-ion types of doubly and triply charged precursor ions. We show that the accuracy of our neural-network based methodology is useful for subsequent peptide database searches and that the most useful rules of fragmentation significantly differ across ion and precursor types.

Amino Acids↗
PubMed2005

Bioconjugates for tunable peptide fragmentation: free radical initiated peptide sequencing (FRIPS).

The free radical initiator Vazo 68 is coupled to a peptide and electrosprayed into an ion trap mass spectrometer. On collisional activation, the Vazo 68-peptide conjugate generates a free radical, which can be collisionally activated to cleave the peptide backbone. Mostly z-type fragments are formed, as in CAD of other radical peptides and ECD fragmentation. We present data for the Angiotensin II-Vazo 68 conjugate and discuss possible sites of H atom abstraction from the peptide. This experimental methodology for generating peptide fragments is a useful step toward the development of a completely gas-phase approach to protein sequencing.

Angiotensin II↗
PubMed1994

1H NMR analysis of fibril-forming peptide fragments of transthyretin.

Peptide fragments of the protein transthyretin, previously shown to form cross beta-sheet amyloid-like fibrils in vitro, were investigated using 1H 1D and 2D NMR techniques. TTR 10-20, TTR 105-115 as well as a substituted analogue, (TTR 105-115Met111) all formed amyloid-like fibrils readily in 20-30% acetonitrile/water at room temperature. It was found that the presence of fibrils in the peptide solutions did not affect the observable NMR spectra, which may have been due to the line-broadening that would be associated with these macromolecular species. 1H NMR spectra were thus representative of the monomeric form of the peptide in solution. Information from D2O exchange, 3JNH-alpha H coupling measurements, temperature coefficients and NOESY experiments suggested that these peptides have some propensity for turn or helix but were predominantly unstructured. There was no indication of the monomeric species existing predominantly in an extended form, suggesting that the formation of beta-sheet based fibrils does not require preformed extended structures. TTR 105-115Met111 displayed slight structural differences from TTR 105-115 which may be related to the fibril-forming propensity of the corresponding mutant TTR.

Amino Acid Sequence↗
PubMed2001

Evidence for an initiation site for hen lysozyme folding from the reduced form using its dissected peptide fragments.

We prepared two dissected fragments of hen lysozyme and examined whether or not these two fragments associated to form a native-like structure. One (Fragment I) is the peptide fragment Asn59-homoserine-105 containing Cys64-Cys80 and Cys76-Cys94. The other (Fragment II) is the peptide fragment Lys1-homoserine-58 connected by two disulfide bridges, Cys6-Cys127 and Cys30-Cys115, to the peptide fragment Asn106-Leu129. It was found that the Fragment I immobilized in the cuvette formed an equimolar complex with Fragment II (K(d) = 3.3x10(-4) M at pH 8 and 25 degrees C) by means of surface plasmon resonance. Moreover, from analyses by circular dichroism spectroscopy and ion-exchange chromatography of the mixture of Fragments I and II at pH 8 under non-reducing conditions, it was suggested that these fragments associated to give the native-like structure. However, the mutant Fragment I in which Cys64-Cys80 and Cys76-Cys94 are lacking owing to the mutation of Cys to Ala, or the mutant fragment in which Trp62 is mutated to Gly, did not form the native-like species with Fragment II, because the mutant Fragment I derived from mutant lysozymes had no local conformation due to mutations. Considering our previous results where the preferential oxidation of two inside disulfide bonds, Cys64-Cys80 and Cys76-Cys94, occurred in the refolding of the fully reduced Fragment I, we suggest that the peptide region corresponding to Fragment I is an initiation site for hen lysozyme folding.

Animals↗
PubMed1999

Controlled cleavage of KLH1 and KLH2 by the V8 protease from Staphylococcus aureus reassociation, electrophoretic and transmission electron microscopy study of peptide fragments.

The reassociation behaviour of protease V8-cleaved peptides from KLH1 and KLH2, the two hemocyanin isoforms from the giant keyhole limpet Megathura crenulata, has been studied by transmission electron microscopy of negatively stained specimens and SDS/PAGE. Reassociation of the complete mixture of protease cleavage products and of combinations of peptide fragments purified by HPLC was performed in the presence of 100 mm CaCl2 and 100 mm MgCl2 at pH 7.4, over a period of 1 to 4 weeks. The V8 protease splits KLH1 into peptide fragments containing the functional units abc, def, defg, defgh, g and h. This mixture of peptide fragments reassociated to form helical tubular polymers, with a diameter of approximately 25 nm. The single functional units g and h were not incorporated into the polymer. An essentially identical polymer was formed from the re-mixed HPLC-purified fragments abc, def and defg alone. As with uncleaved subunit, the tubular polymer of V8-cleaved KLH1 forms bundles. The combination of peptides def and defg led to the formation of short arc-like filamentous structures, which aggregated but showed little tendency to associate into larger polymers. The KLH1 peptide fragments abc and def alone, did not reassociate and in combination their potential to form polymers was very low. With KLH2, the V8 protease generated peptide fragments containing the functional units abc, defg, defgh and h, which in combination slowly reassociated to form a tubular polymer significantly different to that obtained from the KLH1 V8 fragments. The three-functional unit fragment abc from KLH2 showed no tendency to polymerize and the combination of peptides defg + defgh generated only disordered aggregates, with some indication of malformed tubules. The combination of biochemical and electron microscopical methods enabled the characterization of these polymers with respect to peptide composition and higher order structure.

Electrophoresis, Polyacrylamide Gel↗
PubMed1999

Minithioredoxin: a folded and functional peptide fragment of thioredoxin.

A peptide fragment comprising the first 83 residues from the N-terminus of E. coli thioredoxin is purified by hydroxylamine cleavage of the intact protein. At physiological pH, the secondary and tertiary structure contents of the peptide are 70 and 35%, respectively, compared to the intact protein. Peptide 83 is able to display dual biological functions of thioredoxin, namely, a substrate for the enzyme E. coli thioredoxin-reductase and a processivity factor of T7 DNA polymerase. At present, peptide 83 represents the minimum functional and folding unit of thioredoxin. The highly conserved residue Phe 81 appears to play an important role in the folding of peptide 83, as judged from the packing analysis. Peptide 83 also mimics a particular kinetic folding intermediate of thioredoxin in terms of spectral properties and may serve as an equilibrium peptide model for the former.

Anilino Naphthalenesulfonates↗
PubMed1999

Amino acids and peptides. LV. Application of 2-adamantyl derivatives as protecting groups to the synthesis of peptide fragments related to Sulfolobus solifataricus ribonuclease. II.

Segment condensations were performed to construct peptide fragments related to Sulfolobus solifataricus Ribonuclease. At each condensation step, the new protecting groups were stable. The protected peptide fragments were treated with a low-high HF procedure to give the desired peptide fragments. These peptide fragments were also prepared by the solid-phase method, and the obtained peptides were compared with those obtained by the solution method. The peptide fragments obtained by the solution method were identical with those obtained by the solid-phase method on analytical HPLC, indicating that the new protecting groups could be easily removed by HF, and no racemization occurred during the synthesis of the protected peptides.

Adamantane↗
PubMed2003

Biophysical studies and anti-growth activities of a peptide, a certain analog and a fragment peptide derived from alpha-fetoprotein.

A chemically synthesized 34-amino acid peptide, an analog, and a fragment of the peptide have been purified and studied. Biophysical studies were carried out to determine some of the metal ion binding properties of the original peptide and an analog of this parent peptide, in which the two histidine residues were replaced by alanines. As shown by visible absorption spectroscopy, Co (II) forms a complex with the parent peptide, but not with the analog peptide, and one or two histidines in the parent peptide are ligands for Co (II) ion binding. The effects on disulfide bond formation in the peptide by Zn (II) and Co (II) ions were also examined for this analog. Anti-growth assays were performed using the original cysteine-containing peptide with Zn (II) ion complexed to the peptide through the two cysteine residues. These rat uterine growth assays showed that the complexing of Zn (II) ion to the peptide maintained the anti-growth activity of the peptide, while gel-filtration experiments showed the zinc ions maintained the peptide in its anti-growth form indefinitely in solution. A saliently important part of this research was the discovery that a fragment of the peptide consisting of a middle sequence of 14 amino acids was found to have significant anti-growth activity in the rat uterine assay. Its activity suggested that this fragment might be considered a viable candidate for testing in anti-cancer protocols.

Amino Acid Sequence↗