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At least 919 records · Page 51Linked to original sources
PubMed2000

Ideally amphipathic beta-sheeted peptides at interfaces: structure, orientation, affinities for lipids and hemolytic activity of (KL)(m)K peptides.

Designed to model ideally amphipathic beta-sheets, the minimalist linear (KL)(m)K peptides (m=4-7) were synthesized and proved to form stable films at the air/water interface, they insert into compressed dimyristoylphosphatidylcholine monolayers and interact with egg phosphatidylcholine vesicles. Whatever the interface or the lateral pressure applied to the films, FT-IR and polarization-modulated IRRAS spectroscopy developed in situ on the films indicated that all the peptides totally fold into intermolecular antiparallel beta-sheets. Calculated spectra of the amide region allowed us to define the orientation of the beta-strands compared to the interface. It is concluded that such beta-sheets remain flat-oriented without deep perturbation of zwitterionic phospholipids. Dansyl labelling at the N-terminus indicates that all the peptides are monomeric at a low concentration in aqueous buffer and bind to lipids with similar Dns burying. The affinities for zwitterionic lecithin mono- and bilayers, quantitatively estimated from buffer to lipid partition constants, monotonically increased with peptide length, indicating that hydrophobicity is a limiting parameter for lipid and membrane affinities. Peptides induced permeability increases on zwitterionic liposomes, they are strongly hemolytic towards human erythrocytes and their activity increases concurrently with length. Taking into account the lipid affinity, a hemolytic efficiency can be defined: at the same amount of peptide bound, this efficiency strongly increases with the peptide length. It is proposed that the first determinant step of membrane disturbance is the invasion of the outer membrane leaflet by these ideally amphipathic beta-sheeted structures lying flat at the interface, like large rafts depending on the number of beta-strands.

Amino Acid Sequence↗
PubMed1988

Brain natriuretic peptide-32: N-terminal six amino acid extended form of brain natriuretic peptide identified in porcine brain.

Brain natriuretic peptide (BNP) is a newly identified peptide of 26 residues, which has a remarkable homology to but is distinct from atrial natriuretic peptide. The peptide exerts natriuretic-diuretic activity as well as potent chick rectum relaxant activity. By using radioimmunoassay specific to BNP and immunoaffinity chromatography, we have isolated from porcine brain a novel peptide of 32 residues carrying a BNP structure at the C-terminus. The amino acid sequence of this peptide was determined to be: Ser-Pro-Lys-Thr-Met- Arg-Asp-Ser-Gly-Cys-Phe-Gly-Arg-Arg-Leu-Asp-Arg-Ile-Gly-Ser-Leu-Ser-Gly- Leu- Gly-Cys-Asn-Val-Leu-Arg-Arg-Tyr. This peptide is an N-terminal six amino acid extended form of BNP and henceforth is designated BNP-32. BNP and BNP-32 are found to be major forms of BNP family in porcine brain.

Amino Acid Sequence↗
PubMed1988

High-performance liquid chromatography of amino acids, peptides and proteins. LXXXV. Evaluation of the use of hydrophobicity coefficients for the prediction of peptide elution profiles.

The gradient elution behaviour of five synthetic decapeptide analogues has been investigated using an octadecylsilica stationary phase and trifluoroacetic acid-water-acetonitrile mobile phases. The influence of gradient time and flow-rate on the relative retentions and bandwidths of these peptides was assessed using quantitative expressions derived from linear solvent strength theory and general plate height theory. Linear relationships between logarithmic median capacity factors, log k, and the mole fraction of organic solvent modifier, phi, were observed over the experimental range of conditions used. The slopes of these plots were different for all peptides, which indicates that divergences will occur in the prediction of peptide retention times due to conformation dependent changes in hydrophobic contact area occupancy at the stationary phase surface. However, the differences in S values (tangent to the curve obtained in a plot of log k versus phi) for these peptides were not substantial enough to seriously affect the prediction of peptide retention times at one gradient slope from those observed at another. In addition, significant differences existed between experimental and theoretical peak capacity data of these peptide analogues of similar molecular weight and overall polarity, particularly at lower flow-rates or longer residence times. These results once again demonstrate that additional diffusional and interactive processes occur during the reversed-phase separation of peptides and proteins which are not yet adequately formalized by current chromatographic theory.

Amino Acids↗
PubMed1987

Size-exclusion high-performance liquid chromatography of peptides. Requirement for peptide standards to monitor column performance and non-ideal behaviour.

A series of five synthetic peptide polymers with the sequence Ac-(G-L-G-A-K-G-A-G-V-G)n-amide, where n = 1-5, was employed to assess the resolving power of high-performance size-exclusion columns in peptide separations. The peptide standards showed great versatility in monitoring both ideal (no interactions of solutes with the column material) and non-ideal (hydrophobic and/or ionic interactions of solutes with the column material) size-exclusion behaviour in volatile and non-volatile mobile phases. The effectiveness of adding salts or organic solvents to overcome non-specific interactions of solutes with the column materials was well illustrated by the standards. In addition, the advantageous use of non-ideal size-exclusion behaviour was highlighted. The ability to predict the position and/or elution order of peptides during size-exclusion chromatography (SEC) requires peptides to be separated by a pure size-exclusion process. Although the peptide standards demonstrated similar ideal size-exclusion profiles in non-denaturing medium on all the columns studied, this study suggested that, if the conformational character of a peptide-protein mixture in a particular mobile phase is uncertain and ideal size-exclusion behaviour is required, SEC should be carried out under highly denaturing conditions.

Acetonitriles↗
PubMed1991

Peptide maps at picomolar levels obtained by reversed-phase high-performance liquid chromatography and pre-column derivatization with phenyl isothiocyanate. Microsequencing of Phenylthiocarbamyl Peptides.

A new reversed-phase high-performance liquid chromatography approach to the production of analytical peptide maps by pre-column derivatization using phenylisothiocyanate is described. Tryptic peptide digests were derivatized with phenyl isothiocyanate to form the phenylthiocarbamyl peptides followed by reversed-phase high-performance liquid chromatographic analysis. The phenylthiocarbamyl peptides were separated by reversed-phase high-performance liquid chromatography with the conventional gradient elution system of water-acetonitrile containing trifluoroacetic acid. The sensitivity of detection of these peptide derivatives was within the range 5-10 pmol with a constant baseline at 254-260 nm. The isolated phenylthiocarbamyl peptides can be subjected to automatic Edman degradation. The effectiveness of this method was exemplified by microsequencing of phenylthiocarbamyl peptides isolated from tryptic digests of three different proteins: alpha-lactalbumin, beta-lactoglobulin and a lambda light-chain immunoglobulin.

Alkylation↗
PubMed2002

Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis.

Recognition by the T-cell receptor (TCR) of immunogenic peptides presented by class I major histocompatibility complexes (MHCs) is the determining event in the specific cellular immune response against virus-infected cells or tumor cells. It is of great interest, therefore, to elucidate the molecular principles upon which the selectivity of a TCR is based. These principles can in turn be used to design therapeutic approaches, such as peptide-based immunotherapies of cancer. In this study, free energy simulation methods are used to analyze the binding free energy difference of a particular TCR (A6) for a wild-type peptide (Tax) and a mutant peptide (Tax P6A), both presented in HLA A2. The computed free energy difference is 2.9 kcal/mol, in good agreement with the experimental value. This makes possible the use of the simulation results for obtaining an understanding of the origin of the free energy difference which was not available from the experimental results. A free energy component analysis makes possible the decomposition of the free energy difference between the binding of the wild-type and mutant peptide into its components. Of particular interest is the fact that better solvation of the mutant peptide when bound to the MHC molecule is an important contribution to the greater affinity of the TCR for the latter. The results make possible identification of the residues of the TCR which are important for the selectivity. This provides an understanding of the molecular principles that govern the recognition. The possibility of using free energy simulations in designing peptide derivatives for cancer immunotherapy is briefly discussed.

Algorithms↗
PubMed2002

Detection of low-molecular-mass plasma peptides in the cavernous and systemic blood of healthy men during penile flaccidity and rigidity--an experimental approach using the novel differential peptide display technology.

OBJECTIVES: To use Differential Peptide Display (DPD) technology to evaluate the patterns of low-molecular-mass peptides and small proteins in the systemic and cavernous blood taken from healthy adult male volunteers during the penile stages of flaccidity and rigidity. Results from basic research implicate a role of various peptides in the control of mammalian penile erectile tissue. Nevertheless, it is not yet known which particular peptides are essential in the regulation of penile flaccidity, tumescence, rigidity, and detumescence. METHODS: Five healthy male subjects were exposed to visual and tactile erotic stimuli to elicit penile erection. Whole blood was simultaneously aspirated from the corpus cavernosum and cubital vein during penile flaccidity and rigidity. Plasma aliquots were subjected to DPD analysis by means of matrix-assisted-laser-desorption-ionization mass mapping and electrospray-ionization quadrupole--time-of-flight mass spectrometry. RESULTS: High-resolution two-dimensional peptide mass mapping revealed differences in the systemic and cavernous plasma samples related to penile flaccidity and rigidity. Distinct signals were recognized in the cavernous but not in the systemic plasma obtained during flaccidity. These signals were not registered in the plasma samples obtained from the corpus cavernosum during rigid erection. Although one signal was identified as the blood coagulation-activating peptide XIIIa, the remaining two signals could not be related to any known peptide. These signals may represent unknown local peptidergic factors that might be involved in the regulation of penile flaccidity. CONCLUSIONS: Our study demonstrates that DPD is a feasible method for detecting differences in the cavernous and systemic blood in relation to the different functional conditions of the penile erectile tissue. Additional studies using DPD should include the analysis of blood samples taken from the cavernous meshwork of healthy subjects during penile tumescence and detumescence to establish DPD as a valuable tool in contemporary corpus cavernosum basic research.

Adult↗
PubMed1999

Molecular mimicry between a viral peptide and a myelin oligodendrocyte glycoprotein peptide induces autoimmune demyelinating disease in mice.

Semliki Forest Virus (SFV) induces an encephalomyelitis followed by demyelination in the brains of C57Bl6/J (B6) mice. To investigate the role of molecular mimicry in the pathogenesis of postviral demyelination, alignment algorithms were used and amino acid homologies between immunogenic epitopes of SFV and myelin autoantigens, myelin basic protein (MBP), myelin proteolipid protein (PLP) and myelin oligodendrocyte glycoprotein (MOG) were identified. Immunization of B6 mice with SFV proteins induced significant lymphocyte proliferation to SFV E2 peptides and to MOG peptide, 18-32 (which had molecular mimicry with E2 115-129), but not to MBP or PLP peptides. Both MOG 18-32 and E2 115-129, induced a later-onset chronic EAE-like disease that correlated with the presence of multifocal vacuolation in the CNS white matter. This histopathology was reminiscent of the secondary demyelination seen following SFV infection. Serum antibody responses to the peptides appeared late after immunizations and some samples cross-reacted with other myelin peptides, as well as with the mimicked MOG peptides. These findings suggest that following a CNS viral infection, antibody response to an epitope of virus that exhibits molecular mimicry with a peptide of MOG may contribute to autoimmune mediated injury to CNS myelin.

Acute Disease↗
PubMed2001

Effect of peptide-carrier coupling on peptide-specific immune responses.

Synthetic peptides are covalently linked to immunogenic carrier proteins to enhance the anti-peptide immune response. To investigate whether the method of conjugation influences the immune response, we evaluated two distinctly different choices of linker for a peptide-carrier construct. HPG-30, a synthetic peptide derived from the p17 gag protein of human immunodeficiency virus 1, was covalently linked to keyhole limpet hemocyanin by either glutaraldehyde or a maleimide ester. Glutaraldehyde linkage enhanced the anti-peptide antibody and native protein response compared to maleimide. The maleimide-linked conjugate was more effective at inducing a peptide-specific cellular response. Thus, manipulation of the conjugation method can modify the magnitude and character of the immune response to a synthetic peptide vaccine.

Amino Acid Sequence↗
PubMed1981

The use of 2-dimensional CNBr peptide maps for the analysis of crosslinked peptides in bone collagen.

CNBr peptides from insoluble bovine cortical bone collagen were analyzed using a 2-D mapping technique. The major type 1 collagen CNBr peptides were detected by fluorography after general-labelling with 3H-NaBH4 in dimethyl-formamide. These maps were similar to those visualized by coomassie blue staining and demonstrated a proportional decrease of alpha 1CB6. New groups of peptides, different from those normally present in soluble type I collagen were detected. Some of these peptides were slightly larger and more acidic than alpha 1CB6 and were highly labelled when the demineralized bone was specifically labelled for the presence of aldehydes and crosslinks with 3H-NaBH4 in a phosphate buffer, pH 7.4. Based on the size and charge characteristics of these specifically labelled peptides, they were tentatively identified as crosslinking peptides containing different combinations of alpha 1CB6, alpha 1CB0,1 and alpha 1CB5. The specificity of the labelling method using 3H-NaBH4 in phosphate buffer was demonstrated by the detection of other known crosslinked peptides and by the virtual absence of label in alpha 1CB7, CB8, and CB3. We feel that this simple methodological approach developed in these experiments will prove to be very useful in the analysis of collagen crosslinks present in insoluble collagens derived from normal tissues of various ages as well as from pathological states.

Animals↗
PubMed1997

Augmentation of immune response by an analog of the antigenic peptide in a human T-cell clone recognizing mutated Ras-derived peptides.

T-cells that recognize mutated p21 Ras are relevant to immune surveillance systems against cancer. We report here evidence that immune responses of a T-cell clone recognizing mutated p21 Ras can be augmented by an analog peptide. Using spleen cells from a gastric cancer patient, we established the CD4+ alpha beta Th1-like clone C27 that recognizes wild-type (3EYKLVVVGAGGVGKS17) and mutated p21 Ras protein molecules and peptides, in an HLA-DR1-restricted manner. C27 responded prominently to mutated Ras peptides carrying Val or Ala at position 12, as compared to wild-type and other mutated peptides. C27 also exhibited a much stronger response to a mutated p21 Ras whole-protein molecule-carrying Val at position 12, as compared with the wild-type protein. The proliferative response and production of GM-CSF, TNF-alpha, and IFN-gamma by C27 were further augmented by replacing the possible first DR anchor 4Tyr of the mutated Ras peptide with Trp, a more potent anchor residue for the DR1 molecule. Enhancement of peptide antigenicity by substituting the HLA anchor residue of an antigenic peptide recognized by tumor-reactive T-cells may prove to be a novel strategy for antigen-specific cancer immunotherapy.

Adjuvants, Immunologic↗
PubMed2002

Purification of anti-MUC1 antibodies by peptide mimotope affinity chromatography using peptides derived from a polyvalent phage display library.

A polyvalent, lytic phage display system (T7Select415-1b) displaying a random peptide library has been investigated for its ability to discover novel mimotopes reactive with the therapeutic monoclonal antibody C595. Sequence analysis of enriched phage lead to the identification of a predominant sequence RNREAPRGKICS, and two other consensus sequences RXXP and RXP. The novel synthetic peptide RNREAPRGKICS was linked to beaded agarose and the performance as a mimotope affinity chromatography matrix evaluated. Antibody purified using the novel matrix was found to be of higher specific reactivity than antibody purified using the conventional epitope matrix (peptide APDTRPAPG). The RNREAPRGKICS peptide binding to C595 demonstrated a higher equilibrium association constant (K(A)=0.75 x 10(6)) than the epitope peptide (K(A)=0.16 x 10(6)). Circular dichroism showed that the novel peptide had a more highly ordered structure at 4 degrees C and room temperature, than the epitope peptide.

Amino Acid Sequence↗
PubMed1998

New method to study the effects of peptide sequence on the dissociation energetics of peptide ions.

A new method has been developed to study the dissociation patterns of singly protonated peptides by using a quadrupole ion trap mass spectrometer. The new approach involves using boundary-activated dissociation to characterize the ease of dissociation of peptide ions. Insight can be gained into the effect of specific peptide sequences on the dissociation energetics of protonated peptides. Increased knowledge of the effects of specific sequences on the dissociation patterns of peptide ions should improve the ability to interpret complex spectra from tandem mass spectrometry (MS/MS) experiments. This method has confirmed the previously observed increase in the energy needed for the dissociation of peptide ions containing basic residues. In addition, this technique has revealed the effect of the location of proline residues on the dissociation energetics of peptides with this amino acid.

Algorithms↗
PubMed1997

T cells can be activated by peptides that are unrelated in sequence to their selecting peptide.

We tested the ability of CD4+ T cells, selected in the thymus by reaction with class II protein bound to a single peptide, to react with the same class II protein bound to other peptides. The T cells reacted with all peptides tested, including one that was quite unlike the selecting peptide in T cell receptor binding residues. The receptors on class II/peptide-reactive T cells from class II/single peptide mice were similar but not identical to some of those from normal animals. Thus, class II bound to a single peptide selects a subset of T cells that is related to that selected by class II bound to many peptides.

Amino Acid Sequence↗
PubMed2005

Continuous pH/salt gradient and peptide score for strong cation exchange chromatography in 2D-nano-LC/MS/MS peptide identification for proteomics.

Tryptic digests of human serum albumin and human lung epithelial cell lysates were used as test samples in a novel proteomics study. Peptides were separated and analyzed using 2D-nano-LC/MS/MS with strong cation exchange (SCX) and reversed-phase chromatography and continuous gradient elution. The peptide elution conditions combined simultaneous pH gradient with ammonium acetate salt gradient elution modes. A novel empirical SCX peptide elution score was developed, which accounts for both the number of basic and acidic residues and, in part, their location within a sequence of a peptide. Average scores calculated for the fractionated peptide sequences correlated well with the pH of SCX elution fractions. Multiple peptides with identical amino acid sequences, but differing in cysteine tags possessing different positive charge and different SCX elution properties, were obtained by subjecting the samples to reduction and alkylation with different cysteine alkylating reagents: iodoacetamide, 4-vinylpyridine, and (3-acrylamidopropyl) trimethylammonium chloride. The structurally similar peptides were used as elution standards.

Amino Acid Sequence↗
PubMedDate not supplied

Synthesis of peptide-oligonucleotide conjugates with single and multiple peptides attached to 2'-aldehydes through thiazolidine, oxime, and hydrazine linkages.

2'-Deoxyoligonucleotides and 2'-O-methyloligoribonucleotides carrying one or more 2'-aldehyde groups were synthesized and coupled to peptides containing an N-terminal cysteine, aminooxy, or hydrazide group to give peptide-oligonucleotide conjugates incorporating single or multiple peptides in good yield. The facile conjugation method allows specific coupling in aqueous solution of unprotected oligonucleotides containing aldehyde groups to unprotected N-terminally modified peptides and other small molecules. A 12-mer 2'-O-methyloligoribonucleotide complementary to the HIV-1 TAR RNA stem-loop and containing two conjugated copies of an 8-mer model laminin peptide was hardly affected in TAR RNA binding and showed a similar level of inhibition of HIV-1 Tat-dependent in vitro transcription compared to the unconjugated 2'-O-methyloligoribonucleotide. Advantages of this conjugation method include (1) the ability to attach more than one peptide or other small molecule to oligonucleotide at defined nucleoside residue locations; (2) a conjugation route that does not affect significantly oligonucleotide binding to RNA structures; and (3) three alternative, facile, and mild conjugation reaction types that do not require use of a large excess of peptide reagent.

Aldehydes↗
PubMedDate not supplied

Signal peptide mimics conjugated to peptide nucleic acid: a promising solution for improving cell membrane permeability.

The specific binding ability and biostability of PNA (peptide nucleic acid) with DNA or RNA make PNA not only a good tool for the studies of molecular biology but also the candidate for gene-targeting drugs. However, the main obstacle for its potential usage as a therapeutic is the low cell uptake caused by the poor cell membrane permeability. In this paper the hydrophobic pentadecapeptide and two signal peptide mimics, hexa- and decapeptides ending with a positively charged amino acid, were proposed as the linked carrier for the transportation of PNA T10 through the cell membrane; stable spin label was coupled to the peptide-PNA conjugate so that the ESR measurements can be used for the assessment of their transmembrane movements. The syntheses of spin-labeled peptide-PNA conjugates were carried out on MBHA resin with Boc strategy. The cell membrane permeability of the spin-labeled conjugates of peptides and PNA can be determined with ESR, during the incubation of erythrocyte with the samples. According to ESR measurements, the three conjugates exhibit enhanced uptake into erythrocytes. The hexa- and decapeptide-modified PNA showed suitable water solubility. The peptide-PNA conjugates retained their binding ability to complementary DNA. The results suggest that peptide modification of PNA might be a promising solution for improving cell membrane permeability toward PNA.

Amino Acid Sequence↗
PubMed1995

Binding to protein targets of peptidic leads discovered by phage display: crystal structures of streptavidin-bound linear and cyclic peptide ligands containing the HPQ sequence.

The streptavidin-bound crystal structures of two disulfide-bridge cyclic peptides (cyclo-Ac-[CHPQGPPC]-NH2 and cyclo-Ac-[CHPQFC]-NH2) and of a linear peptide (FSHPQNT) were determined, as well as the structure of apostreptavidin (streptavidin-sulfate). Both the linear and disulfide-bridged cyclic peptides studied share a common HPQ conformation and make common interactions with streptavidin, although significant differences in structures and interactions occur for flanking residues among the complexes. The conformation of the linear peptide in the crystal structure of streptavidin-FSHPQNT was found to differ from that in the same complex published [Weber, P. C., Pantoliano, M. W., & Thompson, L. D. (1992) Biochemistry 31, 9350-9354]. In the present investigation, the HPQNT portion of the ligand is well-defined with some density defining the Phe, whereas in the investigation of Weber et al. only the HPQ segment of the bound peptide could be interpreted. Both bound cyclic peptides adopt a beta-turn involving an H-bond between the His main chain carbonyl and the main chain amide NH of the i+3 residue. In the streptavidin-bound cyclo-Ac-[CHPQFC]-NH2 structure, there is an additional H-bond, indicative of alpha-helix, between the main chain His carbonyl and the main chain C-terminal Cys amide NH group. Binding interactions for both cyclic and linear peptides include direct H-bonds, H-bonds mediated by tightly bound water molecules, and hydrophobic interactions. The above structures and that of streptavidin-biotin in the literature are compared and discussed in the context of structure-based ligand design.

Amino Acid Sequence↗