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1
Raymond, Danielle M., and Bradley L. Nilsson. "Multicomponent peptide assemblies." Chemical Society Reviews 47, no. 10 (2018): 3659–720. http://dx.doi.org/10.1039/c8cs00115d.
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This review presents recent efforts in the development of multicomponent supramolecular peptide assemblies with a focus on multicomponent assemblies derived from β-sheet peptides, low molecular weight peptides, peptide amphiphiles, coiled coil peptides, collagen, and related systems.
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Lupaescu, Ancuta-Veronica, Ionel Humelnicu, Brindusa Alina Petre, Catalina-Ionica Ciobanu, and Gabi Drochioiu. "Direct evidence for binding of aluminum to NAP anti-amyloid peptide and its analogs." European Journal of Mass Spectrometry 26, no. 2 (September 24, 2019): 106–16. http://dx.doi.org/10.1177/1469066719877714.
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NAP (NAPVSIPQ) is a small peptide derived from the activity-dependent neuroprotective protein (ADNP), which provides neuroprotection against amyloid-β peptide toxicity associated with Alzheimer disease. Several metal ions are able to promote the formation of amyloid-β peptide oligomers and protofibrils in human brain tissue. Although the relationship between metal ions and amyloid-β peptide peptides is extensively investigated, that with the NAP peptide is less understood. Nevertheless, our previous research revealed unexpected iron binding to NAP peptide and its analogs. However, a link between aluminum ions, Alzheimer disease and amyloid-β peptide or NAP peptides still remains controversial. Therefore, we have investigated the possible binding of aluminum ions to NAP peptide and its four analogs. Indeed, MALDI-ToF mass spectrometry (MS), including MS/MS study, and Fourier transform infrared (FT-IR) spectroscopy revealed an unexpected pattern of aluminum ion binding to both NAP peptide and its analogs. Our results have been discussed with respect to NAP protection against Alzheimer disease-related neurotoxicity.
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Tsutsumi, Hiroshi, Kazuhiko Nakano, and Hisakazu Mihara. "Dihydrofolate reductase inhibitory peptides screened from a structured designed β-loop peptide library displayed on phage." Molecular BioSystems 11, no. 10 (2015): 2713–16. http://dx.doi.org/10.1039/c5mb00316d.
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Checco, James W., Dale F. Kreitler, Nicole C. Thomas, David G. Belair, Nicholas J. Rettko, William L. Murphy, Katrina T. Forest, and Samuel H. Gellman. "Targeting diverse protein–protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold." Proceedings of the National Academy of Sciences 112, no. 15 (March 30, 2015): 4552–57. http://dx.doi.org/10.1073/pnas.1420380112.
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Peptide-based agents derived from well-defined scaffolds offer an alternative to antibodies for selective and high-affinity recognition of large and topologically complex protein surfaces. Here, we describe a strategy for designing oligomers containing both α- and β-amino acid residues (“α/β-peptides”) that mimic several peptides derived from the three-helix bundle “Z-domain” scaffold. We show that α/β-peptides derived from a Z-domain peptide targeting vascular endothelial growth factor (VEGF) can structurally and functionally mimic the binding surface of the parent peptide while exhibiting significantly decreased susceptibility to proteolysis. The tightest VEGF-binding α/β-peptide inhibits the VEGF165-induced proliferation of human umbilical vein endothelial cells. We demonstrate the versatility of this strategy by showing how principles underlying VEGF signaling inhibitors can be rapidly extended to produce Z-domain–mimetic α/β-peptides that bind to two other protein partners, IgG and tumor necrosis factor-α. Because well-established selection techniques can identify high-affinity Z-domain derivatives from large DNA-encoded libraries, our findings should enable the design of biostable α/β-peptides that bind tightly and specifically to diverse targets of biomedical interest. Such reagents would be useful for diagnostic and therapeutic applications.
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Oppegård, Camilla, Gunnar Fimland, Lisbeth Thorbæk, and Jon Nissen-Meyer. "Analysis of the Two-Peptide Bacteriocins Lactococcin G and Enterocin 1071 by Site-Directed Mutagenesis." Applied and Environmental Microbiology 73, no. 9 (March 2, 2007): 2931–38. http://dx.doi.org/10.1128/aem.02718-06.
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ABSTRACT The two peptides (Lcn-α and Lcn-β) of the two-peptide bacteriocin lactococcin G (Lcn) were changed by stepwise site-directed mutagenesis into the corresponding peptides (Ent-α and Ent-β) of the two-peptide bacteriocin enterocin 1071 (Ent), and the potencies and specificities of the various hybrid constructs were determined. Both Lcn and, to a lesser extent, Ent were active against all the tested lactococcal strains, but only Ent was active against the tested enterococcal strains. The two bacteriocins thus differed in their relative potencies to various target cells, despite their sequence similarities. The hybrid combination Lcn-α+Ent-β had low potency against all strains tested, indicating that these two peptides do not interact optimally. The reciprocal hybrid combination (i.e., Ent-α+Lcn-β), in contrast, was highly potent, indicating that these two peptides may form a functional antimicrobial unit. In fact, this hybrid combination (Ent-α+Lcn-β) was more potent against lactococcal strains than wild-type Ent was (i.e., Ent-α+Ent-β), but it was inactive against enterococcal strains (in contrast to Ent but similar to Lcn). The observation that Ent-α is more active against lactococci in combination with Lcn-β and more active against enterococci in combination with Ent-β suggests that the β peptide is an important determinant of target cell specificity. Especially the N-terminal residues of the β peptide seem to be important for specificity, since Ent-α combined with an Ent-β variant with Ent-to-Lcn mutations at positions 1 to 4, 7, 9, and 10 was >150-fold less active against enterococcal strains but one to four times more active against lactococcal strains than Ent-α+Ent-β. Moreover, Ent-to-Lcn single-residue mutations in the region spanning residues 1 to 7 in Ent-β had a more detrimental effect on the activity against enterococci than on that against lactococcal strains. Of the single-residue mutations made in the N-terminal region of the α peptide, the Ent-to-Lcn mutations N8Q and P12R in Ent-α influenced specificity, as follows: the N8Q mutation had no effect on activity against tested enterococcal strains but increased the activity 2- to 4-fold against the tested lactococcal strains, and the P12R mutation reduced the activity >150-fold and only ∼2-fold against enterococcal and lactococcal strains, respectively. Changing residues in the C-terminal half/part of the Lcn peptides (residues 20 to 39 and 25 to 35 in Lcn-α and Lcn-β, respectively) to those found in the corresponding Ent peptides did not have a marked effect on the activity, but there was an ∼10-fold or greater reduction in the activity upon also introducing Lcn-to-Ent mutations in the mid-region (residues 8 to 19 and 9 to 24 in Lcn-α and Lcn-β, respectively). Interestingly, the Lcn-to-Ent F19L+G20A mutation in an Lcn-Ent-β hybrid peptide was more detrimental when the altered peptide was combined with Lcn-α (>10-fold reduction) than when it was combined with Ent-α (∼2-fold reduction), suggesting that residues 19 and 20 (which are part of a GXXXG motif) in the β peptide may be involved in a specific interaction with the cognate α peptide. It is also noteworthy that the K2P and A7P mutations in Lcn-β reduced the activity only ∼2-fold, suggesting that the first seven residues in the β peptides do not form an α-helix.
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Schenk, Dale B., Peter Seubert, Ivan Lieberburg, and Jan Wallace. "β-Peptide Immunization." Archives of Neurology 57, no. 7 (July 1, 2000): 934. http://dx.doi.org/10.1001/archneur.57.7.934.
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Fujii, Daisuke, Kento Takase, Ami Takagi, Kei Kamino, and Yoshiaki Hirano. "Design of RGDS Peptide-Immobilized Self-Assembling β-Strand Peptide from Barnacle Protein." International Journal of Molecular Sciences 22, no. 3 (January 27, 2021): 1240. http://dx.doi.org/10.3390/ijms22031240.
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We designed three types of RGD-containing barnacle adhesive proteins using self-assembling peptides. In the present study, three types of RGD-containing peptides were synthesized by solid-phase peptide synthesis, and the secondary structures of these peptides were analyzed by CD and FT-IR spectroscopy. The mechanical properties of peptide hydrogels were characterized by a rheometer. We discuss the correlation between the peptide conformation, and cell attachment and cell spreading activity from the viewpoint of developing effective tissue engineering scaffolds. We created a peptide-coated cell culture substrate by coating peptides on a polystyrene plate. They significantly facilitated cell adhesion and spreading compared to a non-coated substrate. When the RGDS sequence was modified at N- or C-terminal of R-Y, it was found that the self-assembling ability was dependent on the strongly affects hydrogel formation and cell adhesion caused by its secondary structure.
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Plaisancié, Pascale, Rachel Boutrou, Monique Estienne, Gwénaële Henry, Julien Jardin, Armelle Paquet, and Joëlle Léonil. "β-Casein(94-123)-derived peptides differently modulate production of mucins in intestinal goblet cells." Journal of Dairy Research 82, no. 1 (October 22, 2014): 36–46. http://dx.doi.org/10.1017/s0022029914000533.
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We recently reported the identification of a peptide from yoghurts with promising potential for intestinal health: the sequence (94-123) of bovine β-casein. This peptide, composed of 30 amino acid residues, maintains intestinal homoeostasis through production of the secreted mucin MUC2 and of the transmembrane-associated mucin MUC4. Our study aimed to search for the minimal sequence responsible for the biological activity of β-CN(94-123) by using several strategies based on (i) known bioactive peptides encrypted in β-CN(94-123), (ii) in silico prediction of peptides reactivity and (iii) digestion of β-CN(94-123) by enzymes of intestinal brush border membranes. The revealed sequences were tested in vitro on human intestinal mucus-producing HT29-MTX cells. We demonstrated that β-CN(108-113) (an ACE-inhibitory peptide) and β-CN(114-119) (an opioid peptide named neocasomorphin-6) up-regulated MUC4 expression whereas levels of the secreted mucins MUC2 and MUC5AC remained unchanged. The digestion of β-CN(94-123) by intestinal enzymes showed that the peptides β-CN(94-108) and β-CN(117-123) were present throughout 1·5 to 3 h of digestion, respectively. These two peptides raised MUC5AC expression while β-CN(117-123) also induced a decrease in the level of MUC2 mRNA and protein. In addition, this inhibitory effect was reproduced in airway epithelial cells. In conclusion, β-CN(94-123) is a multifunctional molecule but only the sequence of 30 amino acids has a stimulating effect on the production of MUC2, a crucial factor of intestinal protection.
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Del Borgo, Mark P., Ketav Kulkarni, and Marie-Isabel Aguilar. "Unique Functional Materials Derived from β-Amino Acid Oligomers." Australian Journal of Chemistry 70, no. 2 (2017): 126. http://dx.doi.org/10.1071/ch16511.
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The unique structures formed by β-amino acid oligomers, or β-peptide foldamers, have been studied for almost two decades, which has led to the discovery of several distinctive structures and bioactive molecules. Recently, this area of research has expanded from conventional peptide drug design to the formation of assemblies and nanomaterials by peptide self-assembly. The unique structures formed by β-peptides give rise to a set of new materials with altered properties that differ from conventional peptide-based materials; such new materials may be useful in several bio- and nanomaterial applications.
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Fox, Robert I., and Ho-Il Kang. "Mechanism of Action of Antimalarial Drugs: Inhibition of Antigen Processing and Presentation." Lupus 2, no. 1_suppl (February 1993): 9–12. http://dx.doi.org/10.1177/0961203393002001031.
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Recent studies have elucidated the steps involved in the association of antigenic peptides with major histocompatibility complex (MHC) encoded proteins and have suggested how antimalarial compounds might influence this important site of immune activation. These steps of antigen presentation in the macrophage (or other antigen-presenting cells) include: (a) the partial proteolytic degradation of endogenous and exogenous proteins into peptides within the lysosome; (b) the synthesis of MHC class II (i.e. HLA-D associated) α, β, and invariant (Ii) chains in the endoplasmic reticulum; (c) the initial association of α-Ii and β-li chains in the endoplasmic reticulum and the transport of these complexes to the primary endosome; (d) the fusion of lysosomal vacuoles and endosomal vacuoles, allowing the mixtures of lysosomal enzymes, peptides, α–Ii and β–Ii; (e) the displacement of Ii chains by peptides to form α–β–peptide complexes in the endosome; and (f) the migration of α–β–peptide complexes to the macrophage cell surface where they can stimulate CD4 T cells, resulting in release of cytokines. A low pH is required for digestion of the protein by acidic hydrolases in the lysosome, for assembly of the α–β–peptide complex and for its transport to the cell surface. Chloroquine and hydroxychloroquine are weak diprotic bases that can diffuse across the cell membrane and raise the pH within cell vesicles. This background provides the underlying basis for the theory that antimalarials may act to prevent autoimmunity by the following putative mechanism. Antimalarial compounds may: (a) stabilize the α-Ii and β-Ii interactions and prevent low-affinity peptides from forming α–β–peptide complexes; and (b) interfere with the efficient movement of α-Ii, β-Ii and α–β–peptide complexes to the correct locations within the cell cytoplasm or to the cell surfaces. Decreased presentation of autoantigenic peptides by macrophages might then lead to downregulation of autoimmune CD4+ T cells and diminish release of cytokines associated with clinical and laboratory signs of autoimmune disease.
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Lee, Jung Kwon, Eunice C. Y. Li-Chan, Imelda W. Y. Cheung, You-Jin Jeon, Ju-Young Ko, and Hee-Guk Byun. "Neuroprotective Effect of β-secretase Inhibitory Peptide from Pacific Hake (Merluccius productus) Fish Protein Hydrolysate." Current Alzheimer Research 16, no. 11 (December 6, 2019): 1028–38. http://dx.doi.org/10.2174/1567205016666191113122046.
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Background: Various methodologies have been employed for the therapeutic interpolation of the progressive brain disorder Alzheimer’s disease. Thus, β-secretase inhibition is significant to prevent disease progression in the early stages. Objective: This study seeks to purify and characterize a novel β-secretase inhibitory peptide from Pacific hake enzymatic hydrolysate. Methods: A potent β-secretase inhibitory peptide was isolated by sequential purifications using Sephadex G-25 column chromatography and octadecylsilane (ODS) C18 reversed-phase HPLC. A total of seven peptides were synthesized using the isolated peptide sequences. SH-SY5Y cells stably transfected with the human ‘‘Swedish’’ amyloid precursor protein (APP) mutation APP695 (SH-SY5YAPP695swe) were used as an in-vitro model system to investigate the effect of Leu-Asn peptide on APP processing. Results: The β-secretase inhibitory activity (IC50) of the purified peptide (Ser-Leu-Ala-Phe-Val-Asp- Asp-Val-Leu-Asn) from fish protein hydrolysate was 18.65 μM and dipeptide Leu-Asn was the most potent β-secretase inhibitor (IC50 value = 8.82 µM). When comparing all the seven peptides, the inhibition pattern of Leu-Asn dipeptide was found to be competitive by Lineweaver-Burk plot and Dixon plot (Ki value = 4.24 µM). The 24 h treatment with Leu-Asn peptide in SH-SY5Y cells resulted in reducing the β-amyloid (Aβ) production in a dose-dependent manner. Conclusion: Therefore, the results of this study suggest that β-secretase inhibitory peptides derived from marine organisms could be potential candidates to develop nutraceuticals or pharmaceuticals as antidementia agents.
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Clark, David C., Linda J. Smith, and Lesley C. Chaplin. "The Effect of Dephosphorylation on the Conformation of Peptides from β-Casein." Collection of Czechoslovak Chemical Communications 57, no. 2 (1992): 425–28. http://dx.doi.org/10.1135/cccc19920425.
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Peptides β(1-28) and β(1-52) incorporating residues 1-28 and 1-52 of β-casein were prepared by proteolysis of the protein using plasmin and chymotrypsin respectively. Analysis of the circular dichroism spectra of the isolated peptides revealed that limited levels of α-helix were formed only by peptide β(1-52) and then only in the presence of >40% trifluoroethanol (TFE). Partial dephosphorylation of the peptides by treatment with alkaline phosphatase resulted in the formation of significant levels of α-helix in both peptides in the presence of TFE. However, no α-helix was detected in either peptide in the absence of TFE.
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Urban, Jennifer M., Janson Ho, Gavin Piester, Riqiang Fu, and Bradley L. Nilsson. "Rippled β-Sheet Formation by an Amyloid-β Fragment Indicates Expanded Scope of Sequence Space for Enantiomeric β-Sheet Peptide Coassembly." Molecules 24, no. 10 (May 23, 2019): 1983. http://dx.doi.org/10.3390/molecules24101983.
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In 1953, Pauling and Corey predicted that enantiomeric β-sheet peptides would coassemble into so-called “rippled” β-sheets, in which the β-sheets would consist of alternating l- and d-peptides. To date, this phenomenon has been investigated primarily with amphipathic peptide sequences composed of alternating hydrophilic and hydrophobic amino acid residues. Here, we show that enantiomers of a fragment of the amyloid-β (Aβ) peptide that does not follow this sequence pattern, amyloid-β (16–22), readily coassembles into rippled β-sheets. Equimolar mixtures of enantiomeric amyloid-β (16–22) peptides assemble into supramolecular structures that exhibit distinct morphologies from those observed by self-assembly of the single enantiomer pleated β-sheet fibrils. Formation of rippled β-sheets composed of alternating l- and d-amyloid-β (16–22) is confirmed by isotope-edited infrared spectroscopy and solid-state NMR spectroscopy. Sedimentation analysis reveals that rippled β-sheet formation by l- and d-amyloid-β (16–22) is energetically favorable relative to self-assembly into corresponding pleated β-sheets. This work illustrates that coassembly of enantiomeric β-sheet peptides into rippled β-sheets is not limited to peptides with alternating hydrophobic/hydrophilic sequence patterns, but that a broader range of sequence space is available for the design and preparation of rippled β-sheet materials.
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Maruthainar, K., Y. Peng-Loh, and D. G. Smyth. "The processing of β-endorphin and α-melanotrophin in the pars intermedia of Xenopus laevis is influenced by background adaptation." Journal of Endocrinology 135, no. 3 (December 1992): 469–78. http://dx.doi.org/10.1677/joe.0.1350469.
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ABSTRACT β-Endorphin-and α-melanotrophin (α-MSH)-related peptides were extracted from the pars intermedia of Xenopus laevis maintained for 2, 4 or 6 weeks on a white background and for the same periods on a black background. The peptides were resolved under dissociating conditions by gel exclusion chromatography on Sephadex G-50 and they were detected by radioimmunoassay with antibodies to β-endorphin, α,N-acetyl β-endorphin and α-MSH. The β-endorphin-related peptides separated into two fractions of different molecular size. Further purification of the peptides in each fraction was by ion exchange chromatography on SP-Sephadex C-25 and by high-pressure liquid chromatography. The α-MSH-related peptides were resolved by gel exclusion and ion exchange chromatography. The purified β-endorphin- and α-MSH-immunoreactive peptides were identified by comparison of their chromatographic properties with the corresponding peptides from porcine pituitary or by comparison with synthetic peptides. The major form of β-endorphin in the pars intermedia of the frog adapted to a white background was identified as α,N-acetyl β-endorphin (1–8); it was accompanied by a small quantity of acetylated peptides with molecular size similar to β-endorphin. In contrast, the pars intermedia of the frogs adapted to a black background contained approximately equal amounts of α,N-acetyl β-endorphin (1–8) and the larger forms of β-endorphin. The higher molecular weight forms were identified as the α,N-acetyl derivatives of β-endorphin (1–26), (1–27) and (1–31); however after 6 weeks of white adaptation the sole remaining peptide in this group was the 26-residue peptide. An additional β-endorphin immunoreactive peptide, provisionally identified as β-endorphin (10–26), was present in both black- and white-adapted animals; the amounts of this peptide increased during white adaptation. Major differences in the processing of α-MSH were also observed. In the frogs adapted to a black background des-acetyl α-MSH greatly predominated over the acetyl form whereas after 6- weeks adaptation to a white background the acetylated peptide proved to be the principal component. The results demonstrate that the proteolytic processing of β-endorphin and the acetylation of α-MSH in Xenopus laevis are influenced by background adaptation. The formation of β-endorphin (1–8) appears to reflect the action of an endopeptidase that acts at the single arginine residue present at position 9. This cleavage does not appear to take place in mammalian β-endorphins where position 9 is occupied by lysine. Journal of Endocrinology (1992) 135, 469–478
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Kulkarni, Ketav, Sepideh Motamed, Nathan Habila, Patrick Perlmutter, John S. Forsythe, Marie-Isabel Aguilar, and Mark P. Del Borgo. "Orthogonal strategy for the synthesis of dual-functionalised β3-peptide based hydrogels." Chemical Communications 52, no. 34 (2016): 5844–47. http://dx.doi.org/10.1039/c6cc00624h.
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We describe a new class of hydrogelator based on helical β3-peptide foldamers carrying a bioactive payload. The β3-peptides self-assemble to form a nanofibrous mesh resulting in a stable hydrogel. Co-incubation with different β3-peptide monomers allowed tuning of cell adherence.
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Skelton, Nicholas J., Tamas Blandl, Stephen J. Russell, Melissa A. Starovasnik, and Andrea G. Cochran. "β‒hairpin polypeptides by design and selection." Spectroscopy 17, no. 2-3 (2003): 213–30. http://dx.doi.org/10.1155/2003/148024.
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We have developed polypeptide scaffolds that readily adopt aβ‒hairpin conformation (a pair of antiparallel strands connected by a turn) in solution. The study of such peptides allows us to understand the factors that govern stability and folding of these motifs in proteins, and permits mimicry of functionally important regions of proteins. Spectroscopic and biophysical methods have been used to characterize the conformational preferences and stability of these peptides, with a strong emphasis on using restraints generated from1H NMR spectroscopy to determine their three‒dimensional structure. By optimization of inter‒strand interactions, we have developed highly stable disulfide‒cyclized and linearβ‒hairpin peptides. In particular, tryptophan residues at non‒hydrogen bonded strand sites (NHB) are highly stabilizing. A variety of turn types have been presented from these scaffolds, suggesting that they might generally be useful in turn presentation. Interestingly,β‒hairpin peptides (containing a disulfide and a NHB tryptophan) have recently been discovered as antagonists of protein–protein interactions from naïve peptide libraries displayed on phage. Comparison of one suchβ‒hairpin peptide with anα‒helical peptide of very similar sequence provides further insight into the role that residue type and context play in determining polypeptide conformation.
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Puri, Rajinder N., and John W. Porter. "Isolation, purification, and characterization of a peptide that contains the β-ketoacyl reductase, enoyl reductase, and β-hydroxyacyl dehydrase activities of the pigeon liver fatty acid synthetase." Canadian Journal of Biochemistry and Cell Biology 63, no. 1 (January 1, 1985): 50–56. http://dx.doi.org/10.1139/o85-007.
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Controlled proteolytic cleavage of pigeon liver fatty acid synthetase with elastase (4% w/w) for 5 h yields two peptides that are designated II and IV. After 5 h of proteolysis the incubation mixture containing these peptides retains all of the component enzyme activities of the fatty acid synthetase complex. The two peptides are then separated by chromatography on an Affi-Gel Blue column. Gel filtration of the fraction containing peptide II yields a homogeneous peptide as shown by polyacrylamide gel electrophoresis in the presence and absence of sodium dodecyl sulfate. The molecular weight of this peptide has been estimated to be 130 000 by sodium dodecyl sulfate – polyacrylamide gel electrophoresis, size exclusion chromatography, and amino acid analysis. The sedimentation coefficient for peptide II is approximately 7.4S. Peptide II contains the domains for the β-ketoacyl and enoyl reductases and β-hydroxyacyl dehydrase activities of the fatty acid synthetase complex.
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Hoover, David M., Zhibin Wu, Kenneth Tucker, Wuyuan Lu, and Jacek Lubkowski. "Antimicrobial Characterization of Human β-Defensin 3 Derivatives." Antimicrobial Agents and Chemotherapy 47, no. 9 (September 2003): 2804–9. http://dx.doi.org/10.1128/aac.47.9.2804-2809.2003.
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ABSTRACT Human β-defensin 3 (hBD3) is a highly basic 45-amino-acid protein that acts both as an antimicrobial agent and as a chemoattractant molecule. Although the nature of its antimicrobial activity is largely electrostatic, the importance of the molecular structure on this activity is poorly understood. Two isoforms of hBD3 were synthesized: the first with native disulfide linkages and the second with nonnative linkages. In a third synthetic peptide, all cysteine residues were replaced with α-aminobutyric acid, creating a completely linear peptide. A series of six small, linear peptides corresponding to regions of hBD3 with net charges ranging from +4 to +8 (at pH 7) and lengths ranging from 9 to 20 amino acids were also synthesized. The linear full-length peptide showed the highest microbicidal activity against Escherichia coli and Staphylococcus aureus, while all three full-length forms showed equal activity against Candida albicans. The linear peptide also showed high activity against Enterococcus faecium and Pseudomonas aeruginosa. Peptides corresponding to the C terminus showed higher activities when tested against E. coli, with the most active peptides being the most basic. However, only the peptide corresponding to the N terminus of hBD3 showed any activity against S. aureus and C. albicans. Further, N-terminal deletion mutants of native hBD3 showed diminished activities against S. aureus. Thus, the antimicrobial properties of hBD3 derivatives are determined by both charge and structure.
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Peng, Zhenghong. "NMR conformational analysis on cyclic decapeptide template molecule." Canadian Journal of Chemistry 77, no. 8 (August 1, 1999): 1394–404. http://dx.doi.org/10.1139/v99-128.
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We report the synthesis and conformational analysis of a series of cyclic and bicyclic decapeptide templates for combinatorial chemistry. The peptides were synthesized via solid phase synthesis and followed by solution cyclization. The conformation of the peptides was studied by proton NMR spectroscopy in DMSO and in TFE-water. The structure of the peptide template was calculated with the program DIANA and followed by SA from the NMR experimental constraints. The peptide adopts a fold comprising two β-strands and two type II β-turns. The design of such a restained cyclic decapeptide template will be discussed along with Template Assembled Synthetic Proteins (TASP).Key words: solid phase peptide synthesis, cyclic decapeptide, NMR, conformational analysis, β-sheet.
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Mocanu, Cosmin Stefan, Monica Jureschi, and Gabi Drochioiu. "Aluminium Binding to Modified Amyloid-β Peptides: Implications for Alzheimer’s Disease." Molecules 25, no. 19 (October 3, 2020): 4536. http://dx.doi.org/10.3390/molecules25194536.
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Aluminium (Al) is clearly neurotoxic and considerable evidence exists that Al may play a role in the aetiology or pathogenesis of Alzheimer’s disease (AD). Nevertheless, the link between AD pathology and Al is still open to debate. Therefore, we investigated here the interaction of aluminium ions with two Aβ peptide fragments and their analogues. First, we synthesised by the Fmoc/tBu solid-phase peptide synthesis (SPPS) strategy using an automated peptide synthesiser two new peptides starting from the Aβ(1–16) native peptide fragment. For this purpose, the three histidine residues (H6, H13, and H14) of the Aβ(1–16) peptide were replaced by three alanine and three serine residues to form the modified peptides Aβ(1–16)A36,13,14 and Aβ(1–16)S36,13,14 (primary structures: H-1DAEFRADSGYEVAAQK16-NH2 and H-1DAEFRSDSGYEVSSQK16-NH2). In addition, the Aβ(9–16) peptide fragment (H-9GYEVHHQK16-NH2) and its glycine analogues, namely Aβ(9–16)G110, (H-9GGEVHHQK16-NH2), Aβ(9–16)G213,14 (H-9GYEVGGQK16-NH2), and Aβ(9–16)G310,13,14 (H-9GGEVGGQK16-NH2), were manually synthesised in order to study Al binding to more specific amino acid residues. Both the peptides and the corresponding complexes with aluminium were comparatively investigated by mass spectrometry (MS), circular dichroism spectroscopy (CD), atomic force microscopy (AFM), scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FT-IR). Al–peptide molecular ions and Al-fragment ions were unambiguously identified in the MS and MS/MS spectra. AFM images showed dramatic changes in the film morphology of peptides upon Al binding. Our findings from the investigation of N-terminal 1-16 and even 9-16 normal and modified sequences of Aβ peptides suggest that they have the capability to be involved in aluminium ion binding associated with AD.
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Grewal, T. S., P. J. Lowry, and D. Savva. "Expression and partial purification of human pro-opiomelanocortin in Escherichia coli." Journal of Molecular Endocrinology 3, no. 2 (September 1989): 105–12. http://dx.doi.org/10.1677/jme.0.0030105.
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ABSTRACT A large portion of the human pro-opiomelanocortin (POMC) peptide corresponding to amino acid residues 59–241 has been cloned and expressed in Escherichia coli. A 1·0 kb DNA fragment encoding this peptide was cloned into the expression vectors pUC8 and pUR291. Plasmid pJMBG51 (a pUC8 recombinant) was found to direct the expression of a 24 kDa peptide. The recombinant pUR291 (pJMBG52) was shown to produce a β-galactosidase fusion protein of 140 kDa. Western blot analysis showed that both the 24 kDa and 140 kDa peptides are recognized by antibodies raised against POMC-derived peptides. The β-galactosidase fusion protein has been partially purified from crude E. coli cell lysates using affinity chromatography on p-aminobenzyl-1-thio-β-d-galactopyranoside agarose.
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Tomizaki, Kin-ya, Tomomi Iori, Hideyasu Fukushima, Yasuhiro Nakabayashi, Yoshiki Matsumoto, and Takahito Imai. "Tandem-Homodimer of a β-Sheet-Forming Short Peptide Inhibits Random-to-β Structural Transition of Its Original Monomer." Processes 8, no. 11 (November 8, 2020): 1421. http://dx.doi.org/10.3390/pr8111421.
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There is an increasing interest in designing fibrillogenesis modulators for treating amyloid β (Aβ)-peptide-associated diseases. The use of Aβ fragment peptides and their derivatives, as well as nonpeptidyl natural products, is one promising approach to prevent Aβ fibrillation. In this study, we demonstrate that tandem-homodimers (TDs) of a β-sheet-forming short peptide in which the amino acid sequence is duplicated in series and joined via an amino alkanoic acid linker of different chain lengths, preventing the random-to-β structural transition of the original monomer. Ape5-TD, containing 5-amino pentanoate, most potently prevented this transition for at least five days by generating disordered aggregates with reduced tryptic stability. The linkers in the TDs generated this inhibitory activity, probably due to their bent conformations and hydrophobicity, appropriate for accommodating and twisting the monomers, resulting in irregular arrangements of the peptides. The present study could allow the design of a new class of protein/peptide fibrillogenesis modulators.
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Matsuura, Kazunori, and Seiya Fujita. "A Photoresponsive Artificial Viral Capsid Self-Assembled from an Azobenzene-Containing β-Annulus Peptide." International Journal of Molecular Sciences 22, no. 8 (April 14, 2021): 4028. http://dx.doi.org/10.3390/ijms22084028.
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Photoinduced structural changes in peptides can dynamically control the formation and dissociation of supramolecular peptide materials. However, the existence of photoresponsive viral capsids in nature remains unknown. In this study, we constructed an artificial viral capsid possessing a photochromic azobenzene moiety on the peptide backbone. An azobenzene-containing β-annulus peptide derived from the tomato bushy stunt virus was prepared through solid-phase synthesis using Fmoc-3-[(3-aminomethyl)-phenylazo]phenylacetic acid. The azobenzene-containing β-annulus (β-Annulus-Azo) peptide showed a reversible trans/cis isomerization property. The β-annulus-azo peptide self-assembled at 25 μM into capsids with the diameters of 30–50 nm before UV irradiation (trans-form rich), whereas micrometer-sized aggregates were formed after UV irradiation (cis-form rich). The artificial viral capsid possessing azobenzene facilitated the encapsulation of fluorescent-labeled dextrans and their photoinduced release from the capsid.
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Rheinschmidt, Shelby, Trason Thode, Samuel Sampson, Alexis Weston, Tithi Ghosh Halder, Serina Ng, Ryan Rodriguez del Villar, et al. "Abstract 2567: Targeting TBL1/β-catenin complex using peptides designed to competitively inhibit aberrant Wnt signaling in cancer." Cancer Research 82, no. 12_Supplement (June 15, 2022): 2567. http://dx.doi.org/10.1158/1538-7445.am2022-2567.
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Abstract Purpose: Canonical Wnt signaling is a key cascade in regulating development and stemness, however it can become dysregulated and tightly associated with oncogenesis. In human cancers, Wnt/β-catenin signaling is highly activated due to mutations of members associated with the pathway such as adenomatous polyposis coli (APC) and β-catenin. Transducin β-like protein 1 (TBL1) and highly related TBLR1, form a complex with β-catenin facilitating the translocation of β-catenin to the nucleus. The formation of this complex protects β-catenin from degradation by SIAH-1 ubiquitinase and aids β-catenin binding to TCF/LEF transcription factors to transcribe downstream Wnt target genes. We recently reported that the destruction of the TBL1/β-catenin complex using a small molecule results in ubiquitination of β-catenin and inhibition of downstream signaling. As an alternative approach, we designed a series of novel peptides to interfere with binding of β-catenin with TBL1. Methods: Homologous competitive ELISA and thermal shift assays were performed to identify potential peptides that were able to displace β-catenin from TBL1. Additionally, we evaluated the ability of the peptides to disrupt the TBL1/β-catenin complex by performing pull-down assays and monitored the levels of β-catenin ubiquitination in response to peptide treatment in colon cell lines. To assess the levels of TCF/LEF transcriptional activation downstream the Wnt/β-catenin pathway, we performed TOPFlash assays in Wnt-activated cells transfected with plasmids for peptide expression. Results: Our preliminary results identified a set of peptides that efficiently displaces β-catenin from TBL1. Homologous competitive ELISA showed that the peptides were able to displace β-catenin from TBL1 in a dose dependent manner. The top five peptide hits were then tested for their ability to inhibit Wnt signaling using the TOPFlash assay. Among these, one peptide in particular showed high efficiency in inhibiting TCF/LEF transcriptional activation downstream the Wnt/β-catenin pathway. Our study suggests that β-catenin therapeutic peptides may represent a new and exciting approach for Wnt driven cancer therapy. Citation Format: Shelby Rheinschmidt, Trason Thode, Samuel Sampson, Alexis Weston, Tithi Ghosh Halder, Serina Ng, Ryan Rodriguez del Villar, Mohan Kaadige, Anton Zernov, Marcelle Machluf, Raffaella Soldi, Sunil Sharma. Targeting TBL1/β-catenin complex using peptides designed to competitively inhibit aberrant Wnt signaling in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2567.
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Jin, Yi, Janet Hammer, Michelle Pate, Yu Zhang, Fang Zhu, Erik Zmuda, and Jack Blazyk. "Antimicrobial Activities and Structures of Two Linear Cationic Peptide Families with Various Amphipathic β-Sheet and α-Helical Potentials." Antimicrobial Agents and Chemotherapy 49, no. 12 (December 2005): 4957–64. http://dx.doi.org/10.1128/aac.49.12.4957-4964.2005.
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ABSTRACT Many naturally occurring antimicrobial peptides comprise cationic linear sequences with the potential to adopt an amphipathic α-helical conformation. We designed a linear 18-residue peptide that adopted an amphipathic β-sheet structure when it was bound to lipids. In comparison to a 21-residue amphipathic α-helical peptide of equal charge and hydrophobicity, this peptide possessed more similar antimicrobial activity and greater selectivity in binding to and inducing leakage in vesicles composed of bacterial membrane lipids than vesicles composed of mammalian membrane lipids (J. Blazyk, R. Weigand, J. Klein, J. Hammer, R. M. Epand, R. F. Epand, W. L. Maloy, and U. P. Kari, J. Biol. Chem. 276:27899-27906, 2001). Here, we compare two systematically designed families of linear cationic peptides to evaluate the importance of amphipathicity for determination of antimicrobial activity. Each peptide contains six lysine residues and is amidated at the carboxyl terminus. The first family consists of five peptides with various capacities to form amphipathic β-sheet structures. The second family consists of six peptides with various potentials to form amphipathic α helices. Only those peptides that can form a highly amphipathic structure (either a β sheet or an α helix) possessed significant antimicrobial activities. Striking differences in the abilities to bind to and induce leakage in membranes and lipid vesicles were observed for the two families. Overall, the amphipathic β-sheet peptides are less lytic than their amphipathic α-helical counterparts, particularly toward membranes containing phosphatidylcholine, a lipid commonly found in mammalian plasma membranes. Thus, it appears that antimicrobial peptides that can form an amphipathic β-sheet conformation may offer a selective advantage in targeting bacterial cells.
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Christensen, Jeffrey E., Jeffery R. Broadbent, and James L. Steele. "Hydrolysis of Casein-Derived Peptides αS1-Casein(f1-9) and β-Casein(f193-209) by Lactobacillus helveticus Peptidase Deletion Mutants Indicates the Presence of a Previously Undetected Endopeptidase." Applied and Environmental Microbiology 69, no. 2 (February 2003): 1283–86. http://dx.doi.org/10.1128/aem.69.2.1283-1286.2003.
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ABSTRACT Peptides derived from hydrolysis of αS1-casein(f1-9) [αS1-CN(f1-9)] and β-CN(f193-209) with cell extracts of Lactobacillus helveticus CNRZ32 and single-peptidase mutants (ΔpepC, ΔpepE, ΔpepN, ΔpepO, and ΔpepX) were isolated by using reverse-phase high-performance liquid chromatography and were characterized by mass spectrometry. The peptides identified suggest that there was activity of an endopeptidase, distinct from previously identified endopeptidases (PepE and PepO), with specificity for peptide bonds C terminal to Pro residues. Identification of hydrolysis products derived from a carboxyl-blocked form of β-CN(f193-209) confirmed that the peptides were derived from the activity of an endopeptidase.
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Bąchor, Urszula, Agnieszka Lizak, Remigiusz Bąchor, and Marcin Mączyński. "5-Amino-3-methyl-Isoxazole-4-carboxylic Acid as a Novel Unnatural Amino Acid in the Solid Phase Synthesis of α/β-Mixed Peptides." Molecules 27, no. 17 (August 31, 2022): 5612. http://dx.doi.org/10.3390/molecules27175612.
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The hybrid peptides consisting of α and β-amino acids show great promise as peptidomimetics that can be used as therapeutic agents. Therefore, the development of new unnatural amino acids and the methods of their incorporation into the peptide chain is an important task. Here, we described our investigation of the possibility of 5-amino-3-methyl-isoxazole-4-carboxylic acid (AMIA) application in the solid phase peptide synthesis. This new unnatural β-amino acid, presenting various biological activities, was successfully coupled to a resin-bound peptide using different reaction conditions, including classical and ultrasonic agitated solid-phase synthesis. All the synthesized compounds were characterized by tandem mass spectrometry. The obtained results present the possibility of the application of this β-amino acid in the synthesis of a new class of bioactive peptides.
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Ningrum, Andriati, Dian Wahyu Wardani, Nurul Vanidia, Achmat Sarifudin, Rima Kumalasari, Riyanti Ekafitri, Dita Kristanti, Woro Setiaboma, and Heli Siti Halimatul Munawaroh. "In Silico Approach of Glycinin and Conglycinin Chains of Soybean By-Product (Okara) Using Papain and Bromelain." Molecules 27, no. 20 (October 13, 2022): 6855. http://dx.doi.org/10.3390/molecules27206855.
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This study explores utilization of a sustainable soybean by-product (okara) based on in silico approach. In silico approaches, as well as the BIOPEP database, PeptideRanker database, Peptide Calculator database (Pepcalc), ToxinPred database, and AllerTop database, were employed to evaluate the potential of glycinin and conglycinin derived peptides as a potential source of bioactive peptides. These major protein precursors have been found as protein in okara as a soybean by-product. Furthermore, primary structure, biological potential, and physicochemical, sensory, and allergenic characteristics of the theoretically released antioxidant peptides were predicted in this research. Glycinin and α subunits of β-conglycinin were selected as potential precursors of bioactive peptides based on in silico analysis. The most notable among these are antioxidant peptides. First, the potential of protein precursors for releasing bioactive peptides was evaluated by determining the frequency of occurrence of fragments with a given activity. Through the BIOPEP database analysis, there are several antioxidant bioactive peptides in glycinin and β and α subunits of β-conglycinin sequences. Then, an in silico proteolysis using selected enzymes (papain, bromelain) to obtain antioxidant peptides was investigated and then analyzed using PeptideRanker and Pepcalc. Allergenic analysis using the AllerTop revealed that all in silico proteolysis-derived antioxidant peptides are probably nonallergenic peptides. We also performed molecular docking against MPO (myeloperoxidases) for this peptide. Overall, the present study highlights that glycinin and β and α subunits of β-conglycinin could be promising precursors of bioactive peptides that have an antioxidant peptide for developing several applications.
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Shao, Qing, Kong M. Wong, Dillon T. Seroski, Yiming Wang, Renjie Liu, Anant K. Paravastu, Gregory A. Hudalla, and Carol K. Hall. "Anatomy of a selectively coassembled β-sheet peptide nanofiber." Proceedings of the National Academy of Sciences 117, no. 9 (February 18, 2020): 4710–17. http://dx.doi.org/10.1073/pnas.1912810117.
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Peptide self-assembly, wherein molecule A associates with other A molecules to form fibrillar β-sheet structures, is common in nature and widely used to fabricate synthetic biomaterials. Selective coassembly of peptide pairs A and B with complementary partial charges is gaining interest due to its potential for expanding the form and function of biomaterials that can be realized. It has been hypothesized that charge-complementary peptides organize into alternating ABAB-type arrangements within assembled β-sheets, but no direct molecular-level evidence exists to support this interpretation. We report a computational and experimental approach to characterize molecular-level organization of the established peptide pair, CATCH. Discontinuous molecular dynamics simulations predict that CATCH(+) and CATCH(−) peptides coassemble but do not self-assemble. Two-layer β-sheet amyloid structures predominate, but off-pathway β-barrel oligomers are also predicted. At low concentration, transmission electron microscopy and dynamic light scattering identified nonfibrillar ∼20-nm oligomers, while at high concentrations elongated fibers predominated. Thioflavin T fluorimetry estimates rapid and near-stoichiometric coassembly of CATCH(+) and CATCH(−) at concentrations ≥100 μM. Natural abundance13C NMR and isotope-edited Fourier transform infrared spectroscopy indicate that CATCH(+) and CATCH(−) coassemble into two-component nanofibers instead of self-sorting. However,13C–13C dipolar recoupling solid-state NMR measurements also identify nonnegligible AA and BB interactions among a majority of AB pairs. Collectively, these results demonstrate that strictly alternating arrangements of β-strands predominate in coassembled CATCH structures, but deviations from perfect alternation occur. Off-pathway β-barrel oligomers are also suggested to occur in coassembled β-strand peptide systems.
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Terada, Tomohiro, Kyoko Sawada, Hideyuki Saito, Yukiya Hashimoto, and Ken-Ichi Inui. "Functional characteristics of basolateral peptide transporter in the human intestinal cell line Caco-2." American Journal of Physiology-Gastrointestinal and Liver Physiology 276, no. 6 (June 1, 1999): G1435—G1441. http://dx.doi.org/10.1152/ajpgi.1999.276.6.g1435.
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The apical H+-coupled peptide transporter (PEPT1) and basolateral peptide transporter in human intestinal Caco-2 cells were functionally compared by the characterization of [14C]glycylsarcosine transport. The glycylsarcosine uptake via the basolateral peptide transporter was less sensitive to medium pH than uptake via PEPT1 and was not transported against the concentration gradient. Kinetic analysis indicated that glycylsarcosine uptake across the basolateral membranes was apparently mediated by a single peptide transporter. Small peptides and β-lactam antibiotics inhibited glycylsarcosine uptake by the basolateral peptide transporter, and these inhibitions were revealed to be competitive. Comparison of the inhibition constant values of various β-lactam antibiotics between PEPT1 and the basolateral peptide transporter suggested that the former had a higher affinity than the latter. A histidine residue modifier, diethyl pyrocarbonate, inhibited glycylsarcosine uptake by both transporters, although the inhibitory effect was greater on PEPT1. These findings suggest that a single facilitative peptide transporter is expressed at the basolateral membranes of Caco-2 cells and that PEPT1 and the basolateral peptide transporter cooperate in the efficient transepithelial transport of small peptides and peptidelike drugs.
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Fukui, Yoshinori, Osamu Hashimoto, Ayumi Inayoshi, Takahiro Gyotoku, Tetsuro Sano, Takahiro Koga, Toshifumi Gushima, and Takehiko Sasazuki. "Highly Restricted T Cell Repertoire Shaped by a Single Major Histocompatibility Complex–Peptide Ligand in the Presence of a Single Rearranged T Cell Receptor β Chain." Journal of Experimental Medicine 188, no. 5 (September 7, 1998): 897–907. http://dx.doi.org/10.1084/jem.188.5.897.
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The T cell repertoire is shaped by positive and negative selection of thymocytes through the interaction of α/β-T cell receptors (TCR) with self-peptides bound to self-major histocompatibility complex (MHC) molecules. However, the involvement of specific TCR-peptide contacts in positive selection remains unclear. By fixing TCR-β chains with a single rearranged TCR-β irrelevant to the selecting ligand, we show here that T cells selected to mature on a single MHC–peptide complex express highly restricted TCR-α chains in terms of Vα usage and amino acid residue of their CDR3 loops, whereas such restriction was not observed with those selected by the same MHC with diverse sets of self-peptides including this peptide. Thus, we visualized the TCR structure required to survive positive selection directed by this single ligand. Our findings provide definitive evidence that specific recognition of self-peptides by TCR could be involved in positive selection of thymocytes.
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McFarland, Benjamin J., Craig Beeson, and Andrea J. Sant. "Cutting Edge: A Single, Essential Hydrogen Bond Controls the Stability of Peptide-MHC Class II Complexes." Journal of Immunology 163, no. 7 (October 1, 1999): 3567–71. http://dx.doi.org/10.4049/jimmunol.163.7.3567.
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Abstract The binding of peptides to MHC class II molecules is mediated in part by a conserved array of intermolecular hydrogen bonds. We have evaluated the consequences of disrupting the hydrogen bond between β-His-81 of the class II molecule and bound peptide. These studies revealed that peptide dissociation rates were accelerated by factors ranging to 200-fold. The sensitivity of a peptide to loss of the hydrogen bond is inversely correlated with the inherent kinetic stability of the peptide-MHC complex. The same relationship has been observed between inherent kinetic stability and the susceptibility to DM. Given that the rate enhancement observed for MHC class II I-Ad protein mutated at position 81 in the β-chain is comparable with DM-catalyzed rates for other class II molecules, we suggest that DM could function by stabilizing a peptide-MHC intermediate in which one or more hydrogen bonds between the peptide and MHC, such as that contributed by the β-His-81 hydrogen bond, are disrupted.
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El-Agnaf, Omar M. A., G. Brent Irvine, David J. S. Guthrie, and Dominic M. Walsh. "Properties of some peptides related to amyloid β-peptide." Biochemical Society Transactions 24, no. 1 (February 1, 1996): 59S. http://dx.doi.org/10.1042/bst024059s.
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Pimont-Farge, Mathilde, Amélie Bérubé, Véronique Perreault, Guillaume Brisson, Shyam Suwal, Yves Pouliot, and Alain Doyen. "Occurrence of Peptide-Peptide Interactions during the Purification of Self-Assembling Peptide f1-8 from a β-Lactoglobulin Tryptic Hydrolysate." Molecules 26, no. 5 (March 6, 2021): 1432. http://dx.doi.org/10.3390/molecules26051432.
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Self-assembling peptides have gained attention because of their nanotechnological applications. Previous work demonstrated that the self-assembling peptide f1-8 (Pf1-8) that is generated from the tryptic hydrolysis of β-lactoglobulin can form a hydrogel after several purification steps, including membrane filtration and consecutive washes. This study evaluates the impact of each processing step on peptide profile, purity, and gelation capacity of each fraction to understand the purification process of Pf1-8 and the peptide-peptide interactions involved. We showed that peptide-peptide interactions mainly occurred through electrostatic and hydrophobic interactions, influencing the fraction compositions. Indeed, the purity of Pf1-8 did not correlate with the number of wash steps. In addition to Pf1-8, two other hydrophobic peptides were identified, peptide f15-20, and peptide f41-60. The gelation observed could be induced either through peptide-peptide interactions or through self-assembling, both being driven by non-covalent bond and more specifically hydrophobic interactions.
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Kalergis, Alexis M., Toshiro Ono, Fuming Wang, Teresa P. DiLorenzo, Shinichiro Honda, and Stanley G. Nathenson. "Single Amino Acid Replacements in an Antigenic Peptide Are Sufficient to Alter the TCR Vβ Repertoire of the Responding CD8+ Cytotoxic Lymphocyte Population." Journal of Immunology 162, no. 12 (June 15, 1999): 7263–70. http://dx.doi.org/10.4049/jimmunol.162.12.7263.
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Abstract Cytotoxic CD8+ T lymphocytes are activated upon the engagement of their Ag-specific receptors by MHC class I molecules loaded with peptides 8–11 amino acids long. T cell responses triggered by certain antigenic peptides are restricted to a limited number of TCR Vβ elements. The precise role of the peptide in causing this restricted TCR Vβ expansion in vivo remains unclear. To address this issue, we immunized C57BL/6 mice with the immunodominant peptide of the vesicular stomatitis virus (VSV) and several peptide variants carrying single substitutions at TCR-contact residues. We observed the expansion of a limited set of TCR Vβ elements responding to each peptide variant. To focus our analysis solely on the TCR β-chain, we created a transgenic mouse expressing exclusively the TCR α-chain from a VSV peptide-specific CD8+ T cell clone. These mice showed an even more restricted TCR Vβ usage consequent to peptide immunization. However, in both C57BL/6 and TCRα transgenic mice, single amino acid replacements in TCR-contact residues of the VSV peptide could alter the TCR Vβ usage of the responding CD8+ T lymphocytes. These results provide in vivo evidence for an interaction between the antigenic peptide and the germline-encoded complementarity-determining region-β loops that can influence the selection of the responding TCR repertoire. Furthermore, only replacements at residues near the C terminus of the peptide were able to alter the TCR Vβ usage, which is consistent with the notion that the TCR β-chain interacts in vivo preferentially with this region of the MHC/peptide complex.
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Bag, Subhendu Sekhar, Subhashis Jana, Afsana Yashmeen, and Suranjan De. "Triazolo-β-aza-ε-amino acid and its aromatic analogue as novel scaffolds for β-turn peptidomimetics." Chemical Communications 51, no. 25 (2015): 5242–45. http://dx.doi.org/10.1039/c4cc08414d.
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Triazolo-β-aza-ε-amino acid and its aromatic analogue (AlTAA/ArTAA) in the peptide backbone mark a novel class of conformationally constrained molecular scaffolds to induce β-turn conformations. This was demonstrated in a Leu-enkephalin analogue and in other designed peptides.
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Hill, Susan H. A., and Michael J. Gasson. "A qualitative screening procedure for the detection of casein hydrolysis by bacteria, using sodium dodecyl sulphate polyacrylamide gel electrophoresis." Journal of Dairy Research 53, no. 4 (November 1986): 625–29. http://dx.doi.org/10.1017/s0022029900033148.
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SummaryIncubation of bacteria with casein at 30 °C (pH 7·2) resulted in the formation of a number of peptide fragments. The peptides were separable when subjected to electrophoresis. A proteinase-positive strain ofStreptococcus lactispreferentially hydrolysed the β-casein moiety of whole casein, and after incubation for 5 min produced a characteristic pattern of four peptides on sodium dodecyl sulphate (SDS) polyacrylamide gels. After 30 min incubation only one peptide remained. This single polypeptide was then further hydrolysed to produce one (60 min) and eventually two (120 min) lower molecular weight peptides. Hydrolysis was generally complete after about 480 min. Two proteinase-negative variants of this strain did not hydrolyse casein. Crude proteinase preparations gave the same characteristic peptide patterns. SDS-polyacrylamide gel electrophoresis was used to screen more proteinase-positive strains ofStr. Lactisfor casein hydrolysing activity. Of those so far tested all produced the same peptide patterns from β-casein. Proteinase negative variants of all these strains did not hydrolyse casein.
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Hayes, M., C. Stanton, H. Slattery, O. O'Sullivan, C. Hill, G. F. Fitzgerald, and R. P. Ross. "Casein Fermentate of Lactobacillus animalis DPC6134 Contains a Range of Novel Propeptide Angiotensin-Converting Enzyme Inhibitors." Applied and Environmental Microbiology 73, no. 14 (May 4, 2007): 4658–67. http://dx.doi.org/10.1128/aem.00096-07.
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ABSTRACT This work evaluated the angiotensin-converting-enzyme (ACE)-inhibitory activities of a bovine sodium caseinate fermentate generated using the proteolytic capabilities of the porcine small intestinal isolate Lactobacillus animalis DPC6134 (NCIMB deposit 41355). The crude 10-kDa L. animalis DPC6134 fermentate exhibited ACE-inhibitory activity of 85.51% (±15%) and had a 50% inhibitory concentration (IC50) of 0.8 mg protein/ml compared to captopril, which had an IC50 value of 0.005 mg/ml. Fractionation of the crude L. animalis DPC6134 fermentate by membrane filtration and reversed-phase high-performance liquid chromatography (HPLC) generated three bioactive fractions from a total of 72 fractions. Fractions 10, 19, and 43 displayed ACE-inhibitory activity percentages of 67.53 (±15), 83.71 (±19), and 42.36 (±11), respectively, where ACE inhibition was determined with 80 μl of the fractions with protein concentrations of 0.5 mg/ml. HPLC and mass spectrometry analysis identified 25 distinct peptide sequences derived from α-, β-, and κ-caseins. In silico predictions, based on the C-terminal tetrapeptide sequences, suggested that peptide NIPPLTQTPVVVPPFIQ, corresponding to β-casein f(73-89); peptide IGSENSEKTTMP, corresponding to αs1-casein f(201212); peptide SQSKVLPVPQ, corresponding to β-casein f(166-175); peptide MPFPKYPVEP, corresponding to β-casein f(124133); and peptide EPVLGPVRGPFP, corresponding to β-casein f(210-221), contained ACE-inhibitory activities. These peptides were chosen for chemical synthesis to confirm the ACE-inhibitory activity of the fractions. Chemically synthesized peptides displayed IC50 values in the range of 92 μM to 790 μM. Additionally, a simulated gastrointestinal digestion confirmed that the ACE-inhibitory 10-kDa L. animalis DPC6134 fermentation was resistant to a cocktail of digestive enzymes found in the gastrointestinal tract.
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Sridhar, Vidya R., Joanne E. Hughes, Dennis L. Welker, Jeffery R. Broadbent, and James L. Steele. "Identification of Endopeptidase Genes from the Genomic Sequence of Lactobacillus helveticus CNRZ32 and the Role of These Genes in Hydrolysis of Model Bitter Peptides." Applied and Environmental Microbiology 71, no. 6 (June 2005): 3025–32. http://dx.doi.org/10.1128/aem.71.6.3025-3032.2005.
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ABSTRACT Genes encoding three putative endopeptidases were identified from a draft-quality genome sequence of Lactobacillus helveticus CNRZ32 and designated pepO3, pepF, and pepE2. The ability of cell extracts from Escherichia coli DH5α derivatives expressing CNRZ32 endopeptidases PepE, PepE2, PepF, PepO, PepO2, and PepO3 to hydrolyze the model bitter peptides, β-casein (β-CN) (f193-209) and αS1-casein (αS1-CN) (f1-9), under cheese-ripening conditions (pH 5.1, 4% NaCl, and 10°C) was examined. CNRZ32 PepO3 was determined to be a functional paralog of PepO2 and hydrolyzed both peptides, while PepE and PepF had unique specificities towards αS1-CN (f1-9) and β-CN (f193-209), respectively. CNRZ32 PepE2 and PepO did not hydrolyze either peptide under these conditions. To demonstrate the utility of these peptidases in cheese, PepE, PepO2, and PepO3 were expressed in Lactococcus lactis, a common cheese starter, using a high-copy vector pTRKH2 and under the control of the pepO3 promoter. Cell extracts of L. lactis derivatives expressing these peptidases were used to hydrolyze β-CN (f193-209) and αS1-CN (f1-9) under cheese-ripening conditions in single-peptide reactions, in a defined peptide mix, and in Cheddar cheese serum. Peptides αS1-CN (f1-9), αS1-CN (f1-13), and αS1-CN (f1-16) were identified from Cheddar cheese serum and included in the defined peptide mix. Our results demonstrate that in all systems examined, PepO2 and PepO3 had the highest activity with β-CN (f193-209) and αS1-CN (f1-9). Cheese-derived peptides were observed to affect the activity of some of the enzymes examined, underscoring the importance of incorporating such peptides in model systems. These data indicate that L. helveticus CNRZ32 endopeptidases PepO2 and PepO3 are likely to play a key role in this strain's ability to reduce bitterness in cheese.
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Findeis, Mark A., Gary M. Musso, Christopher C. Arico-Muendel, Howard W. Benjamin, Arvind M. Hundal, Jung-Ja Lee, Joseph Chin, et al. "Modified-Peptide Inhibitors of Amyloid β-Peptide Polymerization." Biochemistry 38, no. 21 (May 1999): 6791–800. http://dx.doi.org/10.1021/bi982824n.
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MORI, TAKESHI, YOICHI FUKAWA, KENJI SHIMOYAMA, KEIJI MINAGAWA, and MASAMI TANAKA. "POLYMERIZATION OF DIACETYLENE USING β-SHEET AS A TEMPLATE." International Journal of Modern Physics B 20, no. 25n27 (October 30, 2006): 3872–77. http://dx.doi.org/10.1142/s0217979206040519.
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In the parallel and anti-parallel β-sheet structures, hydrogen bonding arises between the amide bonds of the peptide chains to arrange them with a distance of ca. 5 Å. That distance matched with the repeating unit distance of polydiacetylene. In this study, the effectiveness of the β-sheet as a template for the polymerization of diacetylene was examined by using diacetylene-introduced oligopeptides. The diacetylene-introduced amino acid (Thr(DA)) was synthesized from L-threonine. Though peptides Ac-Thr(DA)-NHMe and Ac -[ Thr(DA) ]2- NHMe formed anti-parallel β-sheet, they showed slight or no polymerization in both of the solid and the solution states. On the other hand, Ac -[ Thr(DA) ]5- NHMe and 11mer peptide with a Thr(DA) in the center of the sequence contained anti-parallel β-sheet structure and formed polydiacetylene of high degree of polymerization with high conversion during the cleavage process of the peptide from resin in the solution. This result indicated that the preorganization of the peptide through the β-sheet formation was necessary for the polymerization of diacetylene group. Thus, the β-sheet motif was effective template for the polymerization of diacetylene.
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Luder, Kerstin, Ketav Kulkarni, Huey Wen Lee, Robert E. Widdop, Mark P. Del Borgo, and Marie-Isabel Aguilar. "Decorated self-assembling β3-tripeptide foldamers form cell adhesive scaffolds." Chemical Communications 52, no. 24 (2016): 4549–52. http://dx.doi.org/10.1039/c6cc00247a.
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β-Peptide foldamers were functionalised with the cell recognition motifs RGD or IKVAV, self-assembled into fibres, and co-assembled with non-functionalised β-peptides to yield tunable bioscaffolds with cell adhering properties.
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Schön, István, and Attila Rill. "Ammonolysis mediated side reactions of β-tert-butyl aspartyl peptides." Collection of Czechoslovak Chemical Communications 54, no. 12 (1989): 3360–73. http://dx.doi.org/10.1135/cccc19893360.
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Ammonolysis of Z-Asp(OBut)-Phe-NH2 and Boc-Leu-Asp(OBut)-Phe-NH2, as well as their diastereomers, resulted not only in transpeptidated, but also in epimerized peptides through a complex mechanism. Key compounds of these transformations are presumably very reactive cyclic aminosuccinyl derivatives. In some cases, the amount of α-peptide formed approached that of the β-peptide, in one case it exceeded this amount.
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Dingess, Kelly A., Inge Gazi, Henk W. P. van den Toorn, Marko Mank, Bernd Stahl, Karli R. Reiding, and Albert J. R. Heck. "Monitoring Human Milk β-Casein Phosphorylation and O-Glycosylation Over Lactation Reveals Distinct Differences between the Proteome and Endogenous Peptidome." International Journal of Molecular Sciences 22, no. 15 (July 29, 2021): 8140. http://dx.doi.org/10.3390/ijms22158140.
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Human milk is a vital biofluid containing a myriad of molecular components to ensure an infant’s best start at a healthy life. One key component of human milk is β-casein, a protein which is not only a structural constituent of casein micelles but also a source of bioactive, often antimicrobial, peptides contributing to milk’s endogenous peptidome. Importantly, post-translational modifications (PTMs) like phosphorylation and glycosylation typically affect the function of proteins and peptides; however, here our understanding of β-casein is critically limited. To uncover the scope of proteoforms and endogenous peptidoforms we utilized mass spectrometry (LC-MS/MS) to achieve in-depth longitudinal profiling of β-casein from human milk, studying two donors across 16 weeks of lactation. We not only observed changes in β-casein’s known protein and endogenous peptide phosphorylation, but also in previously unexplored O-glycosylation. This newly discovered PTM of β-casein may be important as it resides on known β-casein-derived antimicrobial peptide sequences.
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Akagi, Keiko, Taku Nagao, and Tetsuro Urushidani. "Responsiveness of β-escin-permeabilized rabbit gastric gland model: effects of functional peptide fragments." American Journal of Physiology-Gastrointestinal and Liver Physiology 277, no. 3 (September 1, 1999): G736—G744. http://dx.doi.org/10.1152/ajpgi.1999.277.3.g736.
Full textAbstract:
We established a β-escin-permeabilized gland model with the use of rabbit isolated gastric glands. The glands retained an ability to secrete acid, monitored by [14C]aminopyrine accumulation, in response to cAMP, forskolin, and histamine. These responses were all inhibited by cAMP-dependent protein kinase inhibitory peptide. Myosin light-chain kinase inhibitory peptide also suppressed aminopyrine accumulation, whereas the inhibitory peptide of protein kinase C or that of calmodulin kinase II was without effect. Guanosine-5′- O-(3-thiotriphosphate) (GTPγS) abolished cAMP-stimulated acid secretion concomitantly, interfering with the redistribution of H+-K+-ATPase from tubulovesicles to the apical membrane. To identify the targets of GTPγS, effects of peptide fragments of certain GTP-binding proteins were examined. Although none of the peptides related to Rab proteins showed any effect, the inhibitory peptide of Arf protein inhibited cAMP-stimulated secretion. These results demonstrate that our new model, the β-escin-permeabilized gland, allows the introduction of relatively large molecules, e.g., peptides, into the cell, and will be quite useful for analyzing signal transduction of parietal cell function.
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CROSS, Keith J., N. Laila HUQ, Wendy BICKNELL, and Eric C. REYNOLDS. "Cation-dependent structural features of β-casein-(1–25)." Biochemical Journal 356, no. 1 (May 8, 2001): 277–86. http://dx.doi.org/10.1042/bj3560277.
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Complete sequence-specific, proton-resonance assignments have been determined for the calcium phosphate-stabilizing tryptic peptide β-casein-(1–25) containing the phosphorylated sequence motif Ser(P)17-Ser(P)-Ser(P)-Glu-Glu21. Spectra of the peptide have been recorded, in separate experiments, in the presence of excess ammonium ions, sodium ions and calcium ions, and of the dephosphorylated peptide in the presence of excess sodium ions. We observed significant changes to chemical shifts for backbone and side-chain resonances that were dependent upon the nature of the cation present. Medium-range nuclear Overhauser effect (nOe) enhancements, characteristic of small structured regions in the peptide, were observed and also found to be cation dependent. The secondary structure of the peptide was characterized by sequential and medium-range (i, i+2/3/4, which denotes an interaction between residue i and residue i+2, i+3 or i+4 in the peptide) nOe connectivities, and Hα chemical shifts. Four structured regions were identified in the calcium-bound peptide: residues Arg1 to Glu4 were involved in a loop-type structure, and residues Val8 to Glu11, Ser(P)17 to Glu20 and Glu21 to Thr24 were implicated in β-turn conformations. Comparison of the patterns of medium-range nOe connectivities in β-casein-(1–25) with those in αS1-casein-(59–79) suggest that the two peptides have distinctly different conformations in the presence of calcium ions, despite having a high degree of sequential and functional similarity.
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Waku, Tomonori, Ayane Kasai, Akio Kobori, and Naoki Tanaka. "Investigation on the Interactions between Self-Assembled β-Sheet Peptide Nanofibers and Model Cell Membranes." International Journal of Molecular Sciences 21, no. 24 (December 14, 2020): 9518. http://dx.doi.org/10.3390/ijms21249518.
Full textAbstract:
Self-assembled peptide nanofibers (NFs) obtained from β-sheet peptides conjugated with drugs, including antigenic peptides, have recently attracted significant attention. However, extensive studies on the interactions of β-sheet peptide NFs with model cell membranes have not been reported. In this study, we investigated the interactions between three types of NFs, composed of PEG-peptide conjugates with different ethylene glycol (EG) lengths (6-, 12- and 24-mer), and dipalmitoylphosphatidylcholine (DPPC) Langmuir membranes. When increasing the EG chain length, those interactions significantly decreased considering measurements in the presence of the NFs of: (i) changes in surface pressure of the DPPC Langmuir monolayers and (ii) surface pressure–area (π–A) compression isotherms of DPPC. Because the observed trend was similar to the EG length dependency with regard to cellular association and cytotoxicity of the NFs that was reported previously, the interaction of NFs with phospholipid membranes represented a crucial factor to determine the cellular association and toxicity of the NFs. In contrast to NFs, no changes were observed with varying EG chain length on the interaction of the building block peptide with the DPPC membrane. The results obtained herein can provide a design guideline on the formulation of β-sheet peptide NFs, which may broaden its potential.
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Park, Sunghyouk, Michael E. Johnson, and Leslie W. M. Fung. "Nuclear magnetic resonance studies of mutations at the tetramerization region of human alpha spectrin." Blood 100, no. 1 (July 1, 2002): 283–88. http://dx.doi.org/10.1182/blood.v100.1.283.
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Abstract Many spectrin mutations that destabilize tetramer formation and lead to hereditary hemolytic anemias are located at the N-terminal region of α-spectrin, with the Arg28 position considered to be a mutation hot spot. We have introduced mutations at positions 28 and 45 into a model peptide, Spα1-156, consisting of the first 156 residues in the N-terminal region of α-spectrin (αN). The association of these α-spectrin peptides that have single amino acid replacements with a β-spectrin model peptide, consisting of the C-terminal region of β-spectrin (βC), was determined, and structural changes due to amino acid replacements were monitored by nuclear magnetic resonance (NMR). We found evidence for similar and very localized structural changes in Spα1-156Arg45Thr and Spα1-156Arg45Ser, although these 2 mutant peptides associated with β-spectrin peptide with significantly differing affinities. The Spα1-156Arg28Ser peptide showed an affinity for the β-spectrin peptide comparable to that of Spα1-156Arg45Ser, but it exhibited substantial and widespread spectral changes. Our results suggest that both Arg45 replacements induce only minor structural perturbations in the first helix of Spα1-156, but the Arg28Ser replacement affects both the first helix and the following structural domain. Our results also indicate that the mechanism for reduced spectrin tetramerization is through mutation-induced changes in molecular recognition at the αβ-tetramerization site, rather than through conformational disruption, as has been suggested in prior literature.
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Rheinschmidt, Shelby, Trason Thode, Samuel Sampson, Alexis Weston, Tithi Ghosh Halder, Serina Ng, Sydney Adamson, et al. "Abstract 1666: Novel peptides target the β-catenin/TBL1 complex to competitively inhibit dysregulated Wnt signaling in cancer." Cancer Research 83, no. 7_Supplement (April 4, 2023): 1666. http://dx.doi.org/10.1158/1538-7445.am2023-1666.
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Abstract Purpose: The canonical Wnt pathway is a stem cell pathway essential during embryogenesis, and functions to direct stem cell fate, renewal, and proliferation. Mutations in this pathway induce overexpression of Wnt genes resulting in a variety of human cancers including breast, colorectal, and ovarian. Canonical Wnt signaling is β-catenin-dependent and when active, β-catenin forms a complex with transducin β-like protein 1 (TBL1) and transducin β-like related protein 1 (TBLR1) to promote gene TCF/LEF-dependent expression downstream the Wnt pathway. Previously we developed a small-molecule inhibitor that disrupts this protein complex to inhibit Wnt signaling and promote a cytotoxic effect in tumor cells. While this approach is effective, our current efforts are focused to develop a peptide-based therapy that targets the β-catenin/TBL1 complex which will result in increased target specificity and less overall toxicity compared to small-molecule counterparts. We have generated a library of peptides corresponding to the binding interface of β-catenin and TBL1 with the aim of developing a specific drug that disrupts the complex. Methods: Selected peptides were tested for their ability to affect the aberrant Wnt pathway on the Wnt-activated colon cancer cell line SW480. Displacement of β-catenin from TBL1 was assessed using a heterologous competition ELISA screen in cell lysate. Hit peptides were identified then tested for specific binding to recombinant TBL1 using an additional ELISA. Further validation to determine associated levels of β-catenin with and without peptide treatment was performed with a co-immunoprecipitation. In situ detection of β-catenin/TBL1 complex dissociation in response to peptide treatment was investigated with a proximity ligation assay (PLA). A ubiquitin enrichment kit was used to measure induced β-catenin degradation. Hit peptides were tested with a viability assay for efficacy in their ability to promote a cytotoxic effect on tumor cells. Transcriptional TCF/LEF activation, which is promoted by β-catenin, was evaluated with TOPFlash in the Wnt activated TCF/LEF reporter HEK293 cell line. Results: We identified a series of peptides that selectively bind TBL1 and displace β-catenin from the complex in Wnt-driven colon cancer cell line SW480 in a dose-dependent manner. Further, we found that treatment with 5 μM peptides in TCF/LEF reporter cells significantly blocks the activity of TCF/LEF, inhibiting downstream transcription of Wnt genes. The disruption of the β-catenin/TBL1 complex results in the ubiquitination of β-catenin. Our findings confirmed this data showing that peptide treatment depletes ubiquitinated β-catenin over time. When these peptides are used to treat Wnt-driven tumor cells, they display strong on-target cytotoxic effects indicating a potential clinical application for the use of these specific peptides as a novel therapeutic. Citation Format: Shelby Rheinschmidt, Trason Thode, Samuel Sampson, Alexis Weston, Tithi Ghosh Halder, Serina Ng, Sydney Adamson, Kate Gutowsky, Mohan Kaadige, Raffaella Soldi, Sunil Sharma. Novel peptides target the β-catenin/TBL1 complex to competitively inhibit dysregulated Wnt signaling in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1666.
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Panteleev, Pavel V., Andrey V. Tsarev, Victoria N. Safronova, Olesia V. Reznikova, Ilia A. Bolosov, Sergei V. Sychev, Zakhar O. Shenkarev, and Tatiana V. Ovchinnikova. "Structure Elucidation and Functional Studies of a Novel β-hairpin Antimicrobial Peptide from the Marine Polychaeta Capitella teleta." Marine Drugs 18, no. 12 (December 4, 2020): 620. http://dx.doi.org/10.3390/md18120620.
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Endogenous antimicrobial peptides (AMPs) are evolutionary ancient molecular factors of innate immunity that play a key role in host defense. Among the most active and stable under physiological conditions AMPs are the peptides of animal origin that adopt a β-hairpin conformation stabilized by disulfide bridges. In this study, a novel BRICHOS-domain related AMP from the marine polychaeta Capitella teleta, named capitellacin, was produced as the recombinant analogue and investigated. The mature capitellacin exhibits high homology with the known β-hairpin AMP family—tachyplesins and polyphemusins from the horseshoe crabs. The β-hairpin structure of the recombinant capitellacin was proved by CD and NMR spectroscopy. In aqueous solution the peptide exists as monomeric right-handed twisted β-hairpin and its structure does not reveal significant amphipathicity. Moreover, the peptide retains this conformation in membrane environment and incorporates into lipid bilayer. Capitellacin exhibits a strong antimicrobial activity in vitro against a wide panel of bacteria including extensively drug-resistant strains. In contrast to other known β-hairpin AMPs, this peptide acts apparently via non-lytic mechanism at concentrations inhibiting bacterial growth. The molecular mechanism of the peptide antimicrobial action does not seem to be related to the inhibition of bacterial translation therefore other molecular targets may be assumed. The reduced cytotoxicity against human cells and high antibacterial cell selectivity as compared to tachyplesin-1 make it an attractive candidate compound for an anti-infective drug design.