Journal articles: 'Α/β Peptide'

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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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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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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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5

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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Olsen, Christian A., Gitte Bonke, Line Vedel, Anne Adsersen, Matthias Witt, Henrik Franzyk, and Jerzy W. Jaroszewski. "α-Peptide/β-Peptoid Chimeras." Organic Letters 9, no. 8 (April 2007): 1549–52. http://dx.doi.org/10.1021/ol070316c.

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7

Yin, Hang, Hua Zhu, Gaston Vilaire, Wei Li, Rustem I. Litvinov, William F. DeGrado, and Joel S. Bennett. "Activation of Platelet α Iibβ 3 by Exogenous Peptides Corresponding to the Transmembrane Domains of α Iib and β 3." Blood 106, no. 11 (November 16, 2005): 384. http://dx.doi.org/10.1182/blood.v106.11.384.384.

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Abstract The platelet fibrinogen receptor α IIbβ 3 exists in an equilibrium between inactive and active conformations. In its inactive conformation, the transmembrane (TM) domains of α IIb and β 3 interact, but they separate when α IIbβ 3 assumes its active conformation. Peptides corresponding to the α IIb TM domain form homodimers in vitro and in bacterial membranes and the interface that mediates this interaction overlaps with the interface that mediates the heteromeric association of the α IIb TM domain with that of β 3. Because the homomeric association of α IIb TM domain is relatively strong, we expected that peptides spanning the α IIb TM domain might activate α IIbβ 3 by binding to the α IIb TM domain, thereby disrupting the α IIb/β 3 TM domain heterodimer. We synthesized a 26 residue peptide corresponding to the α IIb TM domain, flanked by pairs of lysine residues to increase its solubility in water, and assessed its ability to activate washed or gel-filtered platelets in an aggregometer. Addition of 3 μM peptide induced platelet aggregation after a short lag, but unlike aggregation stimulated by ADP, peptide-induced aggregation was not preceded by platelet shape change. Nonetheless, like ADP-induced aggregation, peptide-induced aggregation was inhibited by EDTA and the α IIbβ 3-specific monoclonal antibody A2A9. On the other hand, pre-incubating platelets with PGE1 or apyrase caused only a small decrease in the rate and extent of peptide-induced aggregation, suggesting that the peptide induced aggregation by binding directly to α IIbβ 3. A peptide corresponding the β 3 TM domain behaved in an identical manner, whereas an unrelated peptide, the model TM domain MS-1, had no effect. Similarly, there was little response to an α IIb TM peptide in which glycines 972 and 976, the first and last residues of a GxxxG motif, were changed to leucine. Confirming that the α IIb TM peptide binds to α IIbβ 3, we found that a FITC-labeled α IIb TM peptide co-eluted with purified α IIbβ 3 during size exclusion gel filtration. To determine whether the latter interaction involved the α IIb TM domain, we used the TOXCAT assay. In TOXCAT, the α IIb TM domain-mediated dimerization of a fusion protein containing the α IIb TM domain interposed between maltose binding protein and the ToxR’ transcriptional activation domain in the inner membrane of E. coli drives the activation of the chloramphenicol acetyl transferase (CAT) gene. We found that adding the α IIb TM peptide to the bacterial growth medium consistently decreased CAT synthesis, implying that its presence impaired α IIb-mediated fusion protein dimerization. These results provide evidence for the presence of an α IIb/β 3 TM domain heterodimer in unstimulated human platelets and suggest that the GxxxG motif in the α IIb TM domain is involved in its formation. Because the homomeric interaction of α IIb and β 3 TM domains is substantially stronger than their heteromeric interaction, our data are also consistent with the hypothesis that the TM peptides disrupt the heterodimer which functions to maintain α IIbβ 3 in an inactive state. Lastly, the data suggest that stabilizing the α IIb/β 3 TM heterodimer may represent a new approach for the development of novel anti-platelet agents.

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Berlicki, Łukasz, Ludwig Pilsl, Edit Wéber, István M. Mándity, Chiara Cabrele, Tamás A. Martinek, Ferenc Fülöp, and Oliver Reiser. "Unique α,β- and α,α,β,β-Peptide Foldamers Based on cis-β-Aminocyclopentanecarboxylic Acid." Angewandte Chemie International Edition 51, no. 9 (January 26, 2012): 2208–12. http://dx.doi.org/10.1002/anie.201107702.

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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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Legrand, Baptiste, and Ludovic T. Maillard. "α,β‐Unsaturated γ‐Peptide Foldamers." ChemPlusChem 86, no. 4 (April 2021): 629–45. http://dx.doi.org/10.1002/cplu.202100045.

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Vilaivan, Chotima, Choladda Srisuwannaket, Cheeraporn Ananthanawat, Chaturong Suparpprom, Junji Kawakami, Yoshie Yamaguchi, Yuko Tanaka, and Tirayut Vilaivan. "Pyrrolidinyl peptide nucleic acid with α/β-peptide backbone." Artificial DNA: PNA & XNA 2, no. 2 (April 2011): 50–59. http://dx.doi.org/10.4161/adna.2.2.16340.

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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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Price, Joshua L., W. Seth Horne, and Samuel H. Gellman. "Discrete Heterogeneous Quaternary Structure Formed by α/β-Peptide Foldamers and α-Peptides." Journal of the American Chemical Society 129, no. 20 (May 2007): 6376–77. http://dx.doi.org/10.1021/ja071203r.

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Oppegård, Camilla, Per Rogne, Per Eugen Kristiansen, and Jon Nissen-Meyer. "Structure analysis of the two-peptide bacteriocin lactococcin G by introducing d-amino acid residues." Microbiology 156, no. 6 (June 1, 2010): 1883–89. http://dx.doi.org/10.1099/mic.0.038430-0.

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The importance of 3D structuring in the N- and C-terminal ends of the two peptides (39-mer LcnG-α and 35-mer LcnG-β) that constitute the two-peptide bacteriocin lactococcin G was analysed by replacing residues in the end regions with the corresponding d-isomeric residues. When assayed for antibacterial activity in combination with the complementary wild-type peptide, LcnG-α with four d-residues in its C-terminal region and LcnG-β with four d-residues in either its N- or its C-terminal region were relatively active (two- to 20-fold reduction in activity). 3D structuring of the C-terminal region in LcnG-α and the C- and N-terminal regions in LcnG-β is thus not particularly critical for retaining antibacterial activity, indicating that the 3D structure of these regions is not vital for interpeptide interactions or for interactions between the peptides and cellular components. The 3D structure of the N-terminal region in LcnG-α may be more important, as LcnG-α with four N-terminal d-residues was the least active of these four peptides (10- to 100-fold reduction in activity). The results are consistent with a proposed structural model of lactococcin G in which LcnG-α and -β form a transmembrane parallel helix–helix structure involving approximately 20 residues in each peptide, starting near the N terminus of LcnG-α and at about residue 13 in LcnG-β. Upon expressing the lactococcin G immunity protein, sensitive target cells became resistant to all of these d-residue-containing peptides. The end regions of the two lactococcin G peptides are consequently not involved in essential structure-dependent interactions with the immunity protein. The relatively high activity of most of the d-residue-containing peptides suggests that bacteriocins with increased resistance to exopeptidases may be generated by replacing their N- and C-terminal residues with d-residues.

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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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Forlano, Nicola, Raffaella Bucci, Alessandro Contini, Mariano Venanzi, Ernesto Placidi, Maria Luisa Gelmi, Raffaella Lettieri, and Emanuela Gatto. "Non-Conventional Peptide Self-Assembly into a Conductive Supramolecular Rope." Nanomaterials 13, no. 2 (January 13, 2023): 333. http://dx.doi.org/10.3390/nano13020333.

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Structures composed of alternating α and β amino acids can give rise to peculiar secondary structural motifs, which could self-assemble into complex structures of controlled geometries. This work describes the self-assembly properties of an α,β-peptide, containing three units of syn H2-(2-F-Phe)-h-PheGly-OH, able to self-organize on surfaces into a fascinating supramolecular rope. This material was characterized by AFM, electronic conduction and fluorescence measurements. Molecular dynamics simulations showed that this hexapeptide can self-assemble into an antiparallel β-sheet layer, stabilized by intermolecular H-bonds, which, in turn, can self-assemble into many side-by-side layers, due to π-π interactions. As a matter of fact, we demonstrated that in this system, the presence of aromatic residues at the intramolecular interface promoted by the alternation of α,β-amino-acids in the primary sequence, endorses the formation of a super-secondary structure where the aromatic groups are close to each other, conferring to the system good electron conduction properties. This work demonstrates the capability and future potential of designing and fabricating distinctive nanostructures and efficient bioelectronic interfaces based on an α,β-peptide, by controlling structure and interaction processes beyond those obtained with α- or β-peptides alone.

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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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Moll, Gert, Håvard Hildeng-Hauge, Jon Nissen-Meyer, Ingolf F. Nes, Wil N. Konings, and Arnold J. M. Driessen. "Mechanistic Properties of the Two-Component Bacteriocin Lactococcin G." Journal of Bacteriology 180, no. 1 (January 1, 1998): 96–99. http://dx.doi.org/10.1128/jb.180.1.96-99.1998.

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ABSTRACT Lactococcin G is a bacteriocin whose activity depends on the complementary action of two peptides, termed α and β. Biologically active, synthetic lactococcin G was used to study the mode of action on sensitive cells of Lactococcus lactis. The α and β peptides can bind independently to the target cell surface, but activity requires the complementary peptide. Once bound to the cell surface, the peptides cannot be displaced to the surfaces of other cells. A complex of α and β peptides forms a transmembrane pore that conducts monovalent cations but not protons. Efflux of potassium ions is observed only above pH 5.0, and the rate of efflux increases steeply with the pH. The consequences of cation fluxes for the viability of the target cells are discussed.

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Kitada, Sakae, Tsuneo Uchiyama, Tomoyuki Funatsu, Yumiko Kitada, Tadashi Ogishima, and Akio Ito. "A Protein from a Parasitic Microorganism, Rickettsia prowazekii, Can Cleave the Signal Sequences of Proteins Targeting Mitochondria." Journal of Bacteriology 189, no. 3 (December 8, 2006): 844–50. http://dx.doi.org/10.1128/jb.01261-06.

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ABSTRACT The obligate intracellular parasitic bacteria rickettsiae are more closely related to mitochondria than any other microbes investigated to date. A rickettsial putative peptidase (RPP) was found to resemble the α and β subunits of mitochondrial processing peptidase (MPP), which cleaves the transport signal sequences of mitochondrial preproteins. RPP showed completely conserved zinc-binding and catalytic residues compared with β-MPP but barely contained any of the glycine-rich loop region characteristic of α-MPP. When the biochemical activity of RPP purified from a recombinant source was analyzed, RPP specifically hydrolyzed basic peptides and presequence peptides with frequent cleavage at their MPP-processing sites. Moreover, RPP appeared to activate yeast β-MPP so that it processed preproteins with shorter presequences. Thus, RPP behaves as a bifunctional protein that could act as a basic peptide peptidase and a somewhat regulatory protein for other protein activities in rickettsiae. These are the first biological and enzymological studies to report that a protein from a parasitic microorganism can cleave the signal sequences of proteins targeted to mitochondria.

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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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Waku, Tomonori, Naoyuki Hirata, Masamichi Nozaki, Kanta Nogami, Shigeru Kunugi, and Naoki Tanaka. "Morphological Transformation of Peptide Nanoassemblies through Conformational Transition of Core-forming Peptides." Polymers 11, no. 1 (December 28, 2018): 39. http://dx.doi.org/10.3390/polym11010039.

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Morphological control of nanostructures that are composed of amphiphilic di- or tri-block molecules by external stimuli broadens their applications for molecular containers, nanoreactors, and controlled release materials. In this study, triblock amphiphiles comprising oligo(ethylene glycol), oligo(l-lysine), and tetra(l-phenylalanine) were prepared for the construction of nanostructures that can transform accompanying α-to-β transition of core-forming peptides. Circular dichroic (CD) measurements showed that the triblock amphiphiles adopted different secondary structures depending on the solvent environment: they adopt β-sheet structures in aqueous solution, while α-helix structures in 25% 2,2,2-trifluoroethanol (TFE) solution under basic pH conditions. Transmission electron microscopic (TEM) observation revealed that the triblock amphiphiles formed vesicle structures in 25% TFE aq. Solvent exchange from 25% TFE to water induced morphological transformation from vesicles to arc-shaped nanostructures accompanying α-β conformational transition. The transformable nanostructures may be useful as novel smart nanomaterials for molecular containers and micro reactors.

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Gruß, Hendrik, Rebecca C. Feiner, Ridhiwan Mseya, David C. Schröder, Michał Jewgiński, Kristian M. Müller, Rafał Latajka, Antoine Marion, and Norbert Sewald. "Peptide stapling by late-stage Suzuki–Miyaura cross-coupling." Beilstein Journal of Organic Chemistry 18 (January 3, 2022): 1–12. http://dx.doi.org/10.3762/bjoc.18.1.

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The development of peptide stapling techniques to stabilise α-helical secondary structure motifs of peptides led to the design of modulators of protein–protein interactions, which had been considered undruggable for a long time. We disclose a novel approach towards peptide stapling utilising macrocyclisation by late-stage Suzuki–Miyaura cross-coupling of bromotryptophan-containing peptides of the catenin-binding domain of axin. Optimisation of the linker length in order to find a compromise between both sufficient linker rigidity and flexibility resulted in a peptide with an increased α-helicity and enhanced binding affinity to its native binding partner β-catenin. An increased proteolytic stability against proteinase K has been demonstrated.

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23

Kindahl, Lill, Corine Sandström, A. Grey Craig, Thomas Norberg, and Lennart Kenne. "1H NMR studies on the solution conformation of contulakin-G and analogues." Canadian Journal of Chemistry 80, no. 8 (August 1, 2002): 1022–31. http://dx.doi.org/10.1139/v02-115.

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The conformation of contulakin-G, a bioactive 16 amino acid O-linked glycopeptide (ZSEEGGSNAT*KKPYIL) with the disaccharide β-D-Gal(1[Formula: see text]3)α-D-GalNAc attached to the threonine residue in position 10, has been investigated by 1H NMR spectroscopy. The 1H NMR data for the non-glycosylated peptide and for two glycopeptide analogues, one with the monosaccharide α-D-GalNAc at Thr10 and one with the disaccharide β-D-Gal(1–>3)α-D-GalNAc at Ser7, all of lower bioactivity than contulakin-G, have also been collected. The chemical shifts, NOEs, temperature coefficients of amide protons, and 3JNH,αH-values suggest that all four compounds exist mainly in random coil conformations. Some transient populations of folded conformations are also present in the glycopeptides and turns, probably induced by the sugars, are present in the peptide chain around the site of glycosylation. In the two peptides O-glycosylated at Thr10, the rotation of α-D-GalNAc around the linkage between the sugar and the peptide is restricted. There is evidence for a hydrogen bond between the amide proton of α-D-GalNAc and the peptide chain that could contribute to this torsional rigidity. An intramolecular hydrogen bond between the carbohydrate and the peptide chain does not exist in the peptide O-glycosylated at the Ser7 residue. Key words: conformation, contulakin-G, NMR, O-linked glycopeptide.

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Bandyopadhyay, Anupam, and Hosahudya N. Gopi. "Hybrid Peptides: Direct Transformation of α/α, β-Unsaturated γ-Hybrid Peptides to α/γ-Hybrid Peptide 12-Helices." Organic Letters 14, no. 11 (May 18, 2012): 2770–73. http://dx.doi.org/10.1021/ol300987d.

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25

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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Omote, Masaaki, Atsushi Tarui, Masakazu Ueo, Marino Morikawa, Masahiko Tsuta, Sumika Iwasaki, Noriko Morishita, Yukiko Karuo, Kazuyuki Sato, and Kentaro Kawai. "One-Pot Ring-Opening Peptide Synthesis Using α,α-Difluoro-β-Lactams." Synthesis 52, no. 23 (August 17, 2020): 3657–66. http://dx.doi.org/10.1055/s-0040-1707238.

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α,α-Difluoro-β-lactams successfully underwent ring-opening aminolysis with various amino acids in 2,2,2-trifluoroethanol to afford fluorine-containing peptides. In this aminolysis, it was found that 2,2,2-trifluoroethanol first attacked the α,α-difluoro-β-lactams with cleavage of lactam ring to form the corresponding open-chain 2,2,2-trifluoroethyl esters as reactive intermediates. The trifluoroethyl esters were more electrophilic compared with the corresponding methyl ester and thereby accelerated the aminolysis with various amino acids to form β-amino acid peptides with α,α-difluoromethylene unit.

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27

Aragón-Muriel, Alberto, Alessio Ausili, Kevin Sánchez, Oscar E. Rojas A., Juan Londoño Mosquera, Dorian Polo-Cerón, and Jose Oñate-Garzón. "Studies on the Interaction of Alyteserin 1c Peptide and Its Cationic Analogue with Model Membranes Imitating Mammalian and Bacterial Membranes." Biomolecules 9, no. 10 (September 25, 2019): 527. http://dx.doi.org/10.3390/biom9100527.

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Antimicrobial peptides (AMPs) are effector molecules of the innate immune system and have been isolated from multiple organisms. Their antimicrobial properties are due to the fact that they interact mainly with the anionic membrane of the microorganisms, permeabilizing it and releasing the cytoplasmic content. Alyteserin 1c (+2), an AMP isolated from Alytes obstetricans and its more cationic and hydrophilic analogue (+5) were synthesized using the solid phase method, in order to study the interaction with model membranes by calorimetric and spectroscopic assays. Differential scanning calorimetry (DSC) showed that both peptides had a strong effect when the membrane contained phosphatidylcholine (PC) alone or was mixed with phosphatidylglycerol (PG), increasing membrane fluidization. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was used to study the secondary structure of the peptide. Peptide +2 exhibited a transition from β-sheet/turns to β-sheet/α-helix structures after binding with model membranes, whereas peptide +5 had a transition from aggregation/unordered to β-sheet/α-helix structures after binding with membrane-contained PC. Interestingly, the latter showed a β-sheet structure predominantly in the presence of PG lipids. Additionally, molecular dynamics (MD) results showed that the carboxy-terminal of the peptide +5 has the ability to insert into the surface of the PC/PG membranes, resulting in the increase of the membrane fluidity.

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Tollersrud, O. K., T. Heiskanen, and L. Peltonen. "Human leucocyte glycosylasparaginase is an α/β-heterodimer of 19 kDa α-subunit and 17 and 18 kDa β-subunit." Biochemical Journal 300, no. 2 (June 1, 1994): 541–44. http://dx.doi.org/10.1042/bj3000541.

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Human lysosomal glycosylasparaginase (AGA; EC 3.5.1.26) consists of two glycosylated subunits, alpha and beta. Treatment with 3% SDS at 45 degrees C as part of a new purification scheme did not affect enzyme activity, but the alpha-subunit migrated an apparent 19 kDa peptide on SDS/PAGE instead of as a 24 kDa peptide, as observed without this SDS treatment. The N-terminal sequence was similar to that of the 24 kDa form, and, after reversed-phase h.p.l.c., the 19 kDa form was transformed to an apparent 24 kDa peptide on SDS/PAGE, indicating that their primary structures were identical. As the molecular mass of the alpha-subunit deduced from its cDNA was 19.5 kDa, the variation might be due to incomplete SDS coating of the 24 kDa form. This was confirmed by the tendency of the 24 kDa variant to polymerize even in the presence of SDS. The molecular mass of the beta-subunit was 17 and 18 kDa in accordance with previous reports. Chemical cross-linking with 1-ethyl-3-(3-dimethylaminopropyl)carbodi-imide resulted in the appearance of a 38 kDa peptide on SDS/PAGE which reacted with both the subunit-specific antisera on Western-blot analysis. On SDS/PAGE at pH 10.2 the active enzyme migrated as an apparent 43 kDa peptide. These results indicate that native human glycosylasparaginase is a heterodimer.

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GREEN, Daniel, Suzi PACE, Suzanne M. CURTIS, Magdalena SAKOWSKA, Graham D. LAMB, Angela F. DULHUNTY, and Marco G. CASAROTTO. "The three-dimensional structural surface of two beta-sheet scorpion toxins mimics that of an alpha-helical dihydropyridine receptor segment." Biochemical Journal 370, no. 2 (March 1, 2003): 517–27. http://dx.doi.org/10.1042/bj20021488.

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An α-helical II—III loop segment of the dihydropyridine receptor activates the ryanodine receptor calcium-release channel. We describe a novel manipulation in which this agonist's activity is increased by modifying its surface structure to resemble that of a toxin molecule. In a unique system, native β-sheet scorpion toxins have been reported to activate skeletal muscle ryanodine receptor calcium channels with high affinity by binding to the same site as the lower-affinity α-helical dihydropyridine receptor segment. We increased the alignment of basic residues in the α-helical peptide to mimic the spatial orientation of active residues in the scorpion toxin, with a consequent 2—20-fold increase in the activity of the α-helical peptide. We hypothesized that, like the native peptide, the modified peptide and the scorpion toxin may bind to a common site. This was supported by (i) similar changes in ryanodine receptor channel gating induced by the native or modified α-helical peptide and the β-sheet toxin, a 10—100-fold reduction in channel closed time, with a ≤2-fold increase in open dwell time and (ii) a failure of the toxin to further activate channels activated by the peptides. These results suggest that diverse structural scaffolds can present similar conformational surface properties to target common receptor sites.

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30

Maruyama, Nobuyuki, Tomohiro Goshi, Shigeru Sugiyama, Mayumi Niiyama, Hiroaki Adachi, Kazufumi Takano, Satoshi Murakami, et al. "Preliminary X-ray analysis of the binding domain of the soybean vacuolar sorting receptor complexed with a sorting determinant of a seed storage protein." Acta Crystallographica Section F Structural Biology Communications 71, no. 2 (January 28, 2015): 132–35. http://dx.doi.org/10.1107/s2053230x14027484.

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β-Conglycinin is a major seed storage protein in soybeans, which are an important source of protein. The major subunits (α, α′ and β) of β-conglycinin are sorted to protein-storage vacuoles in seed cells. Vacuolar sorting receptor (VSR) is an integral membrane protein that recognizes the sorting determinant of vacuolar proteins, including β-conglycinin, and regulates their sorting process. Vacuolar sorting determinants of the α′ and β subunits of β-conglycinin exist in their C-terminal peptides. Here, the preliminary X-ray diffraction analysis of the binding domain of soybean VSR crystallized with the peptide responsible for the sorting determinant in β-conglycinin is reported. X-ray diffraction data were collected to a resolution of 3.5 Å. The crystals belonged to space groupP3121, with unit-cell parametersa=b= 116.4,c= 86.1 Å.

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John-White, Marietta, Geoff J. Dumsday, Priscilla Johanesen, Dena Lyras, Nyssa Drinkwater, and Sheena McGowan. "Crystal structure of a β-aminopeptidase from an AustralianBurkholderiasp." Acta Crystallographica Section F Structural Biology Communications 73, no. 7 (June 17, 2017): 386–92. http://dx.doi.org/10.1107/s2053230x17007737.

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β-Aminopeptidases are a unique group of enzymes that have the unusual capability to hydrolyze N-terminal β-amino acids from synthetic β-peptides. β-Peptides can form secondary structures mimicking α-peptide-like structures that are resistant to degradation by most known proteases and peptidases. These characteristics of β-peptides give them great potential as peptidomimetics. Here, the X-ray crystal structure of BcA5-BapA, a β-aminopeptidase from a Gram-negativeBurkholderiasp. that was isolated from activated sludge from a wastewater-treatment plant in Australia, is reported. The crystal structure of BcA5-BapA was determined to a resolution of 2.0 Å and showed a tetrameric assembly typical of the β-aminopeptidases. Each monomer consists of an α-subunit (residues 1–238) and a β-subunit (residues 239–367). Comparison of the structure of BcA5-BapA with those of other known β-aminopeptidases shows a highly conserved structure and suggests a similar proteolytic mechanism of action.

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UEKI, M., J. S. CHIOU, and H. KAMAYA. "BARBITURATES TRANSFORM α-HELIX PEPTIDE TO β-SHEET." Anesthesiology 77, Supplement (September 1992): A753. http://dx.doi.org/10.1097/00000542-199209001-00753.

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33

Pilsl, Ludwig K. A., and Oliver Reiser. "α/β-Peptide foldamers: state of the art." Amino Acids 41, no. 3 (April 5, 2011): 709–18. http://dx.doi.org/10.1007/s00726-011-0894-2.

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34

Alonso, Eduardo, Carlos del Pozo, and Javier González. "Synthesis of α,α-Disubstituted β-Amino Esters and Peptide Derivatives." Synlett 2002, no. 01 (2002): 0069–72. http://dx.doi.org/10.1055/s-2002-19326.

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35

Rinker, Sherri D., Michael P. Trombley, Xiaoping Gu, Kate R. Fortney, and Margaret E. Bauer. "Deletion ofmtrCin Haemophilus ducreyi Increases Sensitivity to Human Antimicrobial Peptides and Activates the CpxRA Regulon." Infection and Immunity 79, no. 6 (March 28, 2011): 2324–34. http://dx.doi.org/10.1128/iai.01316-10.

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ABSTRACTHaemophilus ducreyiresists killing by antimicrobial peptides encountered during human infection, including cathelicidin LL-37, α-defensins, and β-defensins. In this study, we examined the role of the proton motive force-dependent multiple transferable resistance (MTR) transporter in antimicrobial peptide resistance inH. ducreyi. We found a proton motive force-dependent effect onH. ducreyi's resistance to LL-37 and β-defensin HBD-3, but not α-defensin HNP-2. Deletion of the membrane fusion protein MtrC renderedH. ducreyimore sensitive to LL-37 and human β-defensins but had relatively little effect on α-defensin resistance. ThemtrCmutant 35000HPmtrCexhibited phenotypic changes in outer membrane protein profiles, colony morphology, and serum sensitivity, which were restored to wild type bytrans-complementation withmtrC. Similar phenotypes were reported in acpxAmutant; activation of the two-component CpxRA regulator was confirmed by showing transcriptional effects on CpxRA-regulated genes in 35000HPmtrC. AcpxRmutant had wild-type levels of antimicrobial peptide resistance; acpxAmutation had little effect on defensin resistance but led to increased sensitivity to LL-37. 35000HPmtrCwas more sensitive than thecpxAmutant to LL-37, indicating that MTR contributed to LL-37 resistance independent of the CpxRA regulon. The CpxRA regulon did not affect proton motive force-dependent antimicrobial peptide resistance; however, 35000HPmtrChad lost proton motive force-dependent peptide resistance, suggesting that the MTR transporter promotes proton motive force-dependent resistance to LL-37 and human β-defensins. This is the first report of a β-defensin resistance mechanism inH. ducreyiand shows that LL-37 resistance inH. ducreyiis multifactorial.

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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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Shea, Dylan, Cheng-Chieh Hsu, Timothy M. Bi, Natasha Paranjapye, Matthew Carter Childers, Joshua Cochran, Colson P. Tomberlin, et al. "α-Sheet secondary structure in amyloid β-peptide drives aggregation and toxicity in Alzheimer’s disease." Proceedings of the National Academy of Sciences 116, no. 18 (April 19, 2019): 8895–900. http://dx.doi.org/10.1073/pnas.1820585116.

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Alzheimer’s disease (AD) is characterized by the deposition of β-sheet–rich, insoluble amyloid β-peptide (Aβ) plaques; however, plaque burden is not correlated with cognitive impairment in AD patients; instead, it is correlated with the presence of toxic soluble oligomers. Here, we show, by a variety of different techniques, that these Aβ oligomers adopt a nonstandard secondary structure, termed “α-sheet.” These oligomers form in the lag phase of aggregation, when Aβ-associated cytotoxicity peaks, en route to forming nontoxic β-sheet fibrils. De novo-designed α-sheet peptides specifically and tightly bind the toxic oligomers over monomeric and fibrillar forms of Aβ, leading to inhibition of aggregation in vitro and neurotoxicity in neuroblastoma cells. Based on this specific binding, a soluble oligomer-binding assay (SOBA) was developed as an indirect probe of α-sheet content. Combined SOBA and toxicity experiments demonstrate a strong correlation between α-sheet content and toxicity. The designed α-sheet peptides are also active in vivo where they inhibit Aβ-induced paralysis in a transgenic Aβ Caenorhabditis elegans model and specifically target and clear soluble, toxic oligomers in a transgenic APPsw mouse model. The α-sheet hypothesis has profound implications for further understanding the mechanism behind AD pathogenesis.

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38

PIMENTA, Daniel C., Iseli L. NANTES, Eduardo S. de SOUZA, Bernard Le BONNIEC, Amando S. ITO, Ivarne L. S. TERSARIOL, Vitor OLIVEIRA, Maria A. JULIANO, and Luiz JULIANO. "Interaction of heparin with internally quenched fluorogenic peptides derived from heparin-binding consensus sequences, kallistatin and anti-thrombin III." Biochemical Journal 366, no. 2 (September 1, 2002): 435–46. http://dx.doi.org/10.1042/bj20020023.

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Internally quenched fluorogenic (IQF) peptides bearing the fluorescence donor/acceptor pair o-aminobenzoic acid (Abz)/N-(2,4-dinitrophenyl)ethylenediamine (EDDnp) at N- and C-terminal ends were synthesized containing heparin-binding sites from the human serpins kallistatin and antithrombin, as well as consensus heparin-binding sequences (Cardin clusters). The dissociation constant (Kd), as well as the stoichiometry for the heparin–peptide complexes, was determined directly by measuring the decrease in fluorescence of the peptide solution. Experimental procedures were as sensitive as those used to follow the fluorescence change of tryptophan in heparin-binding proteins. The conformation of the peptides and the heparin–peptide complexes were obtained from measurements of time-resolved fluorescence decay and CD spectra. Kallistatin (Arg300–Pro319)-derived peptide (HC2) and one derived from antithrombin III helix D [(AT3D), corresponding to Ser112–Lys139], which are the heparin-binding sites in these serpins, showed significant affinity for 4500Da heparin, for which Kd values were 17nM and 100nM respectively. The CD spectra of the heparin–HC2 peptide complex did not show any significant α-helix content, different from the situation with peptide AT3D, for which complex-formation with heparin resulted in 24% α-helix content. The end-to-end distance distribution and the time-resolved fluorescence-decay measurements agree with the CD spectra and Kd values. The synthetic α-methyl glycoside pentasaccharide AGA∗IAM (where A represents N,6-O-sulphated α-d-glucosamine; G, β-d-glucuronic acid; A∗, N,3,6-O-sulphated α-d-glucosamine; I, 2-O-sulphated α-l-iduronic acid; and AM, α-methyl glycoside of A) also binds to AT3D and other consensus heparin-binding sequences, although with lower affinity. The interaction of IQF peptides with 4500Da heparin was displaced by protamine. In conclusion, IQF peptides containing Abz/EDDnp as the donor/acceptor fluorescence pair are very promising tools for structure–activity relationship studies on heparin–peptide complexes, as well as for the development of new peptides as heparin reversal-effect compounds.

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39

Paul, Ashim, Krishna Chaitanya Nadimpally, Tanmay Mondal, Kishore Thalluri, and Bhubaneswar Mandal. "Inhibition of Alzheimer's amyloid-β peptide aggregation and its disruption by a conformationally restricted α/β hybrid peptide." Chemical Communications 51, no. 12 (2015): 2245–48. http://dx.doi.org/10.1039/c4cc09063b.

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40

Matsuzaki, K. "Why and how are peptide-lipid interactions utilized for self defence?" Biochemical Society Transactions 29, no. 4 (August 1, 2001): 598–601. http://dx.doi.org/10.1042/bst0290598.

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Animals defend themselves against invading pathogenic micro-organisms by utilizing cationic anti-microbial peptides, which rapidly kill various micro-organisms without exerting toxicity against the host. Physicochemical peptide-lipid interactions provide attractive mechanisms for innate immunity. Many of these peptides form amphipathic secondary structures (α-helices and β-sheets) which can selectively interact with anionic bacterial membranes by electrostatic interaction. Rapid, peptide-induced membrane permeabilization is an effective mechanism of anti-microbial action. Magainin 2 from frog skin forms a dynamic peptide-lipid supramolecular-complex pore that allows mutually coupled transmembrane transport of ions and lipids. The peptide molecule is internalized upon the disintegration of the pore. Several anti-microbial peptides are known to work synergistically.

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Rago, James V., Gregory M. Vath, Timothy J. Tripp, Gregory A. Bohach, Douglas H. Ohlendorf, and Patrick M. Schlievert. "Staphylococcal Exfoliative Toxins Cleave α- and β-Melanocyte-Stimulating Hormones." Infection and Immunity 68, no. 4 (April 1, 2000): 2366–68. http://dx.doi.org/10.1128/iai.68.4.2366-2368.2000.

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ABSTRACT The staphylococcal exfoliative toxins (ETs) A and B (ETA and ETB) are 27-kDa exotoxins produced by certain strains ofStaphylococcus aureus and are the causative agents of staphylococcal scalded-skin syndrome. The crystal structures of the ETs strongly indicate that the proteins are members of the serine protease family of enzymes, although protease activity until now has not yet been conclusively demonstrated. Here, we show that the peptide β-melanocyte-stimulating hormone (β-MSH) is cleaved by ETA and that both ETA and ETB are capable of cleaving α-MSH. Both toxins exhibit cleavage at specific glutamic acid residues in MSH peptides. Moreover, biologically inactive mutants of ETA were incapable of cleaving β-MSH.

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42

Busch, Robert, Robert C. Doebele, Emily von Scheven, Jimothy Fahrni, and Elizabeth D. Mellins. "Aberrant Intermolecular Disulfide Bonding in a Mutant HLA-DM Molecule: Implications for Assembly, Maturation, and Function." Journal of Immunology 160, no. 2 (January 15, 1998): 734–43. http://dx.doi.org/10.4049/jimmunol.160.2.734.

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Abstract HLA-DM (abbreviated DM) is an MHC-encoded glycoprotein that catalyzes the selective release of peptides, including class II-associated invariant chain peptides, from MHC class II molecules. To perform its function, DM must assemble in the endoplasmic reticulum (ER), travel to endosomes, and interact productively with class II molecules. We have described previously an EBV-transformed B cell line, 7.12.6, which displays a partial Ag presentation defect and expresses a mutated DM β-chain with Cys79 replaced by Tyr. In this study, we show that HLA-DR molecules in 7.12.6 have a defect in peptide loading and accumulate class II-associated invariant chain peptides (CLIP). Peptide loading is restored by transfection of wild-type DMB. The mutant DM molecules exit the ER slowly and are degraded rapidly, resulting in greatly reduced levels of mutant DM in post-Golgi compartments. Whereas wild-type DM forms noncovalent αβ dimers, such dimers form inefficiently in 7.12.6; many mutant DM β-chains instead form a disulfide-bonded dimer with DM α. Homodimers of DM β are also detected in 7.12.6 and in the α-chain defective mutant, 2.2.93. We conclude that during folding of wild-type DM, the native conformation is stabilized by a conserved disulfide bond involving Cys79β and by noncovalent contacts with DM α. Without these interactions, DM β can form malfolded structures containing interchain disulfide bonds; malfolding is correlated with ER retention and accelerated degradation.

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43

Serrano, Griselda N., George G. Zhanel, and Frank Schweizer. "Antibacterial Activity of Ultrashort Cationic Lipo-β-Peptides." Antimicrobial Agents and Chemotherapy 53, no. 5 (February 23, 2009): 2215–17. http://dx.doi.org/10.1128/aac.01100-08.

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ABSTRACT Previously reported d,l-lipo-α-peptides and their lipo-β-peptide counterparts (C16-KGGK, C16-KAAK, C16-KKKK, and C12-KLLK) were studied, and the lipo-β-peptides were found to retain antimicrobial activity. Likewise, no significant changes in antimicrobial activity were found upon activity comparisons with d,l-amino acid-based lipopeptides or any l-amino acid lipopeptides. As a defined amphipathic structure is unlikely to form with such short molecules and as similar activities were obtained from all lipopeptides, we suspect that the action of membrane permeation is retained.

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Breloer, Minka, Bernhard Fleischer, and Arne von Bonin. "In Vivo and In Vitro Activation of T Cells After Administration of Ag-Negative Heat Shock Proteins." Journal of Immunology 162, no. 6 (March 15, 1999): 3141–47. http://dx.doi.org/10.4049/jimmunol.162.6.3141.

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Abstract Heat shock proteins (HSP) Hsp70 and gp96 prime class I-restricted cytotoxic T cells against Ags present in the cells from which they were isolated. The immunization capacity of HSPs is believed to rely on their ability to bind antigenic peptides. In this study, we employed the well-established OVA and β-galactosidase (β-gal) antigenic model systems. We show that in vitro long-term established OVA and β-gal-specific CTL clones release TNF-α and IFN-γ when incubated with Ag-negative Hsp70 and gp96. In the absence of antigenic peptides, HSP-mediated secretion of TNF-α and IFN-γ requires cell contact of the APC with the T cell but is not MHC-I restricted. Moreover, Hsp70 molecules purified from Ag-negative tissue, e.g., negative for antigenic peptide, are able to activate T cells in vivo, leading to significant higher frequencies in OVA-specific CD8+ T cells. In unprimed animals, these T cells lyse OVA-transfected cell lines and produce TNF-α and IFN-γ after Ag stimulus. Taken together our data show that, besides the well-established HSP/peptide-specific CTL induction and activation, a second mechanism exists by which Hsp70 and gp96 molecules activate T cells in vivo and in vitro.

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EI-Agnaf, O. M. A., and G. B. Irvine. "Aggregation and neurotoxicity of α-synuclein and related peptides." Biochemical Society Transactions 30, no. 4 (August 1, 2002): 559–65. http://dx.doi.org/10.1042/bst0300559.

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Fibrillar deposits of α-synuclein occur in several neurodegenerative diseases. Two mutant forms of α-synuclein have been associated with early-onset Parkinson's disease, and a fragment has been identified as the non-amyloid-β peptide component of Alzheimer's disease amyloid (NAC). Upon aging, solutions of α-synuclein and NAC change conformation to β-sheet, detectable by CD spectroscopy, and form oligomers that deposit as amyloid-like fibrils, detectable by electron microscopy. These aged peptides are also neurotoxic. Experiments on fragments of NAC have enabled the region of NAC responsible for its aggregation and toxicity to be identified. NAC(8–18) is the smallest fragment that aggregates, as indicated by the concentration of peptide remaining in solution after 3 days, and forms fibrils, as determined by electron microscopy. Fragments NAC(8–18) and NAC(8–16) are toxic, whereas NAC(12–18), NAC(9–16) and NAC(8–15) are not. Hence residues 8–16 of NAC comprise the region crucial for toxicity. Toxicity induced by α-synuclein, NAC and NAC(1–18) oligomers occurs via an apoptotic mechanism, possibly initiated by oxidative damage, since these peptides liberate hydroxyl radicals in the presence of iron. Molecules with anti-aggregational and/or antioxidant properties may therefore be potential therapeutic agents.

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Kojima, Suzuka, Hitomi Nakamura, Sungho Lee, Fukue Nagata, and Katsuya Kato. "Hydroxyapatite Formation on Self-Assembling Peptides with Differing Secondary Structures and Their Selective Adsorption for Proteins." International Journal of Molecular Sciences 20, no. 18 (September 19, 2019): 4650. http://dx.doi.org/10.3390/ijms20184650.

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Self-assembling peptides have been employed as biotemplates for biomineralization, as the morphologies and sizes of the inorganic materials can be easily controlled. We synthesized two types of highly ordered self-assembling peptides with different secondary structures and investigated the effects of secondary structures on hydroxyapatite (HAp) biomineralization of peptide templates. All as-synthesized HAp-peptides have a selective protein adsorption capacity for basic protein (e.g., cytochrome c and lysozyme). Moreover, the selectivity was improved as peptide amounts increased. In particular, peptide–HAp templated on β-sheet peptides adsorbed more cytochrome c than peptide–HAp with α-helix structures, due to the greater than 2-times carboxyl group density at their surfaces. It can be expected that self-assembled peptide-templated HAp may be used as carriers for protein immobilization in biosensing and bioseparation applications and as enzyme-stabilizing agents.

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Lu, Yating, Peng Lu, Yu Wang, Xiaodong Fang, Jianming Wu, and Xiaochang Wang. "A Novel Dipeptidyl Peptidase IV Inhibitory Tea Peptide Improves Pancreatic β-Cell Function and Reduces α-Cell Proliferation in Streptozotocin-Induced Diabetic Mice." International Journal of Molecular Sciences 20, no. 2 (January 14, 2019): 322. http://dx.doi.org/10.3390/ijms20020322.

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Dipeptidyl peptidase IV (DPP-IV) inhibitors occupy a growing place in the drugs used for the management of type 2 diabetes. Recently, food components, including food-derived bioactive peptides, have been suggested as sources of DPP-IV inhibitors without side effects. Chinese black tea is a traditional health beverage, and it was used for finding DPP-IV inhibitory peptides in this study. The ultra-filtrated fractions isolated from the aqueous extracts of black tea revealed DPP-IV inhibitory activity in vitro. Four peptides under 1 kDa were identified by SDS-PAGE and LC-MS/MS (Liquid Chromatography-Mass Spectrometry-Mass Spectrometry) from the ultra-filtrate. The peptide II (sequence: AGFAGDDAPR), with a molecular mass of 976 Da, showed the greatest DPP-IV inhibitory activity (in vitro) among the four peptides. After administration of peptide II (400 mg/day) for 57 days to streptozotocin (STZ)-induced hyperglycemic mice, the concentration of glucagon-like peptide-1 (GLP-1) in the blood increased from 9.85 ± 1.96 pmol/L to 19.22 ± 6.79 pmol/L, and the insulin level was increased 4.3-fold compared to that in STZ control mice. Immunohistochemistry revealed the improved function of pancreatic beta-cells and suppressed proliferation of pancreatic alpha-cells. This study provides new insight into the use of black tea as a potential resource of food-derived DPP-IV inhibitory peptides for the management of type 2 diabetes.

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YAŞAR, FATİH. "THE EQUILIBRIUM THERMODYNAMICS OF VARIOUS PEPTIDE SEQUENCES." International Journal of Modern Physics C 15, no. 04 (May 2004): 583–93. http://dx.doi.org/10.1142/s0129183104006066.

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The equilibrium thermodynamic properties of two peptide sequences of β-casein in the α-helix regions were studied by three-dimensional molecular modeling in vacuum. All the three-dimensional conformations of each peptide sequences were obtained by multicanonical simulations using ECEPP/2 force field and each simulation was started from completely random initial conformation. No a-priori information about ground-state is used in the simulations. In the present study, we calculated the average values of total energy, specific heat, fourth-order cumulant for two peptide sequences of β-casein as a function of temperature. We observed that the specific heat shows two peaks as a function of temperature for both peptides. Because our sequences have highly helical structure and two peaks in the specific heat, we have also studied the helix–coil transitions to determine these peaks. Our data indeed show these peptides have highly helical structure and better agreement with the results of spectroscopic techniques and other prediction methods.

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BRADY, Jeffrey D., Julia JU, and Simon P. ROBINS. "Isoaspartyl bond formation within N-terminal sequences of collagen type I: implications for their use as markers of collagen degradation." Clinical Science 96, no. 2 (February 1, 1999): 209–15. http://dx.doi.org/10.1042/cs0960209.

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An ELISA was developed for the measurement of N-telopeptides of the α2(I) collagen chain containing an isomerized Asp-Gly bond (β-peptide) using polyclonal antibodies raised against the synthetic peptide. The presence of this isomerized form in bone was confirmed by positive immunostaining of sections from human femoral head. The ELISA was used to measure isomerized peptide in both human bone digests and urine samples, showing that an isoaspartyl rearrangement occurs in the Asp-Gly sequence at the N-terminus of the α2(I) chain in an analogous fashion to that found in the C-terminal telopeptide of the α1(I) chain of collagen. Using this assay in conjunction with a monoclonal antibody ELISA to the non-isomerized α2(I) N-telopeptide (α-peptide), ratios of isomerized to normal peptides were estimated in the bone and urine samples. Urinary α2(I) N-telopeptides showed a higher degree of isomerization than the peptides derived from a human bone digest. This is possibly due to relative enrichment of the isoaspartyl-bonded peptide during metabolic processing due to the proximity of the isoaspartyl bond to a cross-link site. Urinary concentrations of isomerized and normal peptides were determined in normal adults, children, post-menopausal control subjects and subjects with osteoporosis. A lower ratio of β-peptide to α-peptide was observed in children's urine, indicative of a higher rate of bone metabolism allowing less time for the isomerization to occur. No significant differences were found between the post-menopausal control and osteoporotic populations although the trends observed supported the hypothesis that a lower degree of isomerization may be associated with faster bone turnover.

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Rosenman, G., and B. Apter. "Bioinspired materials: Physical properties governed by biological refolding." Applied Physics Reviews 9, no. 2 (June 2022): 021303. http://dx.doi.org/10.1063/5.0079866.

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Peptide and protein biomolecules folded into two fundamentally different conformations, either α-helical or β-sheet, carry out dissimilar biological functions. In living organisms, an α-helical secondary structure is adopted by different types of proteins such as myoglobin, keratin, collagen, and more. They can be found in diverse biological tissues of muscle, bone, cartilage, etc.. Biological functions of β-sheet peptide/protein structures are different and associated with a wide range of human mental amyloid diseases such as Alzheimer and Parkinson. The fundamental basis of these diseases is misfolding or refolding of natively soluble α-helical amyloid proteins into solid-state β-sheet fibrillary structures. Bioinspired chemically synthesized biomolecules mimic their biological counterparts. Although these artificial and biological peptides/proteins molecules are completely dissimilar in origin and environment, they demonstrate the common properties of folding and refolding into identical secondary architectures. In this review, we show that these two structural conformations, native (helix-like) and β-sheet, exhibit exclusive and different sets of fold-sensitive physical properties that are surprisingly similar in both biological and bioinspired materials. A native (helix-like) self-assembled fold having asymmetric structure demonstrates ferroelectric-like pyroelectric, piezoelectric, nonlinear optical, and electro-optical effects. β-sheet peptide/protein structures acquire unique visible fluorescence (FL) and reveal a new property of lossless FL photonic transport followed by a long-range FL waveguiding in amyloidogenic fibers. An applied thermally mediated refolding native-to-β-sheet allows us to observe adoption, disappearance, and switching of the revealed physical properties in detail in each fold and study dynamics of all critical stages of refolding from the metastable (native) helix-like conformation via intermediate disordered state to stable β-sheet fibrillary ordering. In the intermediate state, the appearance of the visible FL provides imaging, monitoring, and direct observation of the early stages of seeding and nucleation of β-sheet fibrils. The diverse fold-sensitive physical properties found, give a new insight into biological refolding processes and pave the way for the development of advanced physical methods of fold recognition, bioimaging, light theranostics at nanoscale, and peptide/protein nanophotonics from new visible FL bionanodots to bioinspired multifunctional peptide photonic chips.

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Journal articles on the topic 'Α/β Peptide'

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