Journal articles on the topic 'Peptide resonance'
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1
Martin, Aline, Valentin David, Jennifer S. Laurence, Patricia M. Schwarz, Eileen M. Lafer, Anne-Marie Hedge, and Peter S. N. Rowe. "Degradation of MEPE, DMP1, and Release of SIBLING ASARM-Peptides (Minhibins): ASARM-Peptide(s) Are Directly Responsible for Defective Mineralization in HYP." Endocrinology 149, no. 4 (December 27, 2007): 1757–72. http://dx.doi.org/10.1210/en.2007-1205.
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Mutations in PHEX (phosphate-regulating gene with homologies to endopeptidases on the X chromosome) and DMP1 (dentin matrix protein 1) result in X-linked hypophosphatemic rickets (HYP) and autosomal-recessive hypophosphatemic-rickets (ARHR), respectively. Specific binding of PHEX to matrix extracellular phosphoglycoprotein (MEPE) regulates the release of small protease-resistant MEPE peptides [acidic serine- and aspartate-rich MEPE-associated motif (ASARM) peptides]. ASARM peptides are potent inhibitors of mineralization (minhibins) that also occur in DMP1 [MEPE-related small integrin-binding ligand, N-linked glycoprotein (SIBLING) protein]. It is not known whether these peptides are directly responsible for the mineralization defect. We therefore used a bone marrow stromal cell (BMSC) coculture model, ASARM peptides, anti-ASARM antibodies, and a small synthetic PHEX peptide (SPR4; 4.2 kDa) to examine this. Surface plasmon resonance (SPR) and two-dimensional 1H/15N nuclear magnetic resonance demonstrated specific binding of SPR4 peptide to ASARM peptide. When cultured individually for 21 d, HYP BMSCs displayed reduced mineralization compared with wild type (WT) (−87%, P < 0.05). When cocultured, both HYP and WT cells failed to mineralize. However, cocultures (HYP and WT) or monocultures of HYP BMSCs treated with SPR4 peptide or anti-ASARM neutralizing antibodies mineralized normally. WT BMSCs treated with ASARM peptide also failed to mineralize properly without SPR4 peptide or anti-ASARM neutralizing antibodies. ASARM peptide treatment decreased PHEX mRNA and protein (−80%, P < 0.05) and SPR4 peptide cotreatment reversed this by binding ASARM peptide. SPR4 peptide also reversed ASARM peptide-mediated changes in expression of key osteoclast and osteoblast differentiation genes. Western blots of HYP calvariae and BMSCs revealed massive degradation of both MEPE and DMP1 protein compared with the WT. We conclude that degradation of MEPE and DMP-1 and release of ASARM peptides are chiefly responsible for the HYP mineralization defect and changes in osteoblast-osteoclast differentiation.
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Tsybin, Youri O., Per Håkansson, Magnus Wetterhall, Karin E. Markides, and Jonas Bergquist. "Capillary Electrophoresis and Electron Capture Dissociation Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Peptide Mixture and Protein Digest Analysis." European Journal of Mass Spectrometry 8, no. 5 (October 2002): 389–95. http://dx.doi.org/10.1255/ejms.514.
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Recent advances in peptide fragmentation techniques and mass spectrometry have opened up the possibility of combining peptide separation techniques, such as capillary electrophoresis (CE) and capillary liquid chromatography, with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and electron capture dissociation (ECD) in order to characterize peptide mixtures and protein digests. The results presented in this study show that CE/ECD-FT-ICR MS can be employed for peptide characterization in mixtures of standard peptides and in peptides resulting from the enzymatic digestion of proteins. Furthermore, the technique has potential for the identification and localization of post-translational modifications in peptides and proteins.
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Vernen, Felicitas, Peta J. Harvey, Susana A. Dias, Ana Salomé Veiga, Yen-Hua Huang, David J. Craik, Nicole Lawrence, and Sónia Troeira Henriques. "Characterization of Tachyplesin Peptides and Their Cyclized Analogues to Improve Antimicrobial and Anticancer Properties." International Journal of Molecular Sciences 20, no. 17 (August 26, 2019): 4184. http://dx.doi.org/10.3390/ijms20174184.
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Tachyplesin I, II and III are host defense peptides from horseshoe crab species with antimicrobial and anticancer activities. They have an amphipathic β-hairpin structure, are highly positively-charged and differ by only one or two amino acid residues. In this study, we compared the structure and activity of the three tachyplesin peptides alongside their backbone cyclized analogues. We assessed the peptide structures using nuclear magnetic resonance (NMR) spectroscopy, then compared the activity against bacteria (both in the planktonic and biofilm forms) and a panel of cancerous cells. The importance of peptide-lipid interactions was examined using surface plasmon resonance and fluorescence spectroscopy methodologies. Our studies showed that tachyplesin peptides and their cyclic analogues were most potent against Gram-negative bacteria and melanoma cell lines, and showed a preference for binding to negatively-charged lipid membranes. Backbone cyclization did not improve potency, but improved peptide stability in human serum and reduced toxicity toward human red blood cells. Peptide-lipid binding affinity, orientation within the membrane, and ability to disrupt lipid bilayers differed between the cyclized peptide and the parent counterpart. We show that tachyplesin peptides and cyclized analogues have similarly potent antimicrobial and anticancer properties, but that backbone cyclization improves their stability and therapeutic potential.
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Wilson, David, and Norelle L. Daly. "Nuclear Magnetic Resonance seq (NMRseq): A New Approach to Peptide Sequence Tags." Toxins 10, no. 11 (October 28, 2018): 437. http://dx.doi.org/10.3390/toxins10110437.
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Structural analysis of peptides with nuclear magnetic resonance (NMR) spectroscopy generally relies on knowledge of the primary sequence to enable assignment of the resonances prior to determination of the three-dimensional structure. Resonance assignment without knowledge of the sequence is complicated by redundancy in amino acid type, making complete de novo sequencing using NMR spectroscopy unlikely to be feasible. Despite this redundancy, we show here that NMR spectroscopy can be used to identify short sequence tags that can be used to elucidate full-length peptide sequences via database searching. In the current study, we have used this approach to identify conotoxins from the venom of the cone snail Conus geographus and determined the three-dimensional structure of a member of the I3 superfamily. This approach is most likely to be useful for the characterization of disulfide-rich peptides, such as those that were chosen for this study, as they generally have well-defined structures, which enhances the quality of the NMR spectra. In contrast to other sequencing methods, the lack of sample manipulation, such as protease digestion, allows for subsequent bioassays to be carried out using the native sample used for sequence identification.
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Syryamina, Victoria N., Alvaro S. Siano, Fernando Formaggio, and Marta De Zotti. "A Peptide-Based Trap for Metal Ions Studied by Electron Paramagnetic Resonance." Chemosensors 10, no. 2 (February 10, 2022): 71. http://dx.doi.org/10.3390/chemosensors10020071.
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Peptide-based materials provide a versatile platform for sensing and ion sequestration since peptides are endowed with stimuli-responsive properties. The mechanism of molecular sensing is often based on peptide structural changes (or switching), caused by the binding of the target molecule. One scope of sensing applications is the selection of a specific analyte, which may be achieved by adjusting the structure of the peptide binding site. Therefore, exact knowledge of peptide properties and 3D-structure in the ‘switched’ state is desirable for tuning the detection and for further molecular construction. Hence, here we demonstrate the performance of Electron Paramagnetic Resonance (EPR) spectroscopy in the identification of metal ion binding by the antimicrobial peptide trichogin GA IV. Na(I), Ca(II), and Cu(II) ions were probed as analytes to evaluate the impact of coordination number, ionic radii, and charge. Conclusions drawn by EPR are in line with literature data, where other spectroscopic techniques were exploited to study peptide-ion interactions for trichogin GA IV, and the structural switch from an extended helix to a hairpin structure, wrapped around the metal ion upon binding of divalent cations was proposed.
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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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Xia, Ning, Gang Liu, and Xinyao Yi. "Surface Plasmon Resonance for Protease Detection by Integration of Homogeneous Reaction." Biosensors 11, no. 10 (September 29, 2021): 362. http://dx.doi.org/10.3390/bios11100362.
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The heterogeneous assays of proteases usually require the immobilization of peptide substrates on the solid surface for enzymatic hydrolysis reactions. However, immobilization of peptides on the solid surface may cause a steric hindrance to prevent the interaction between the substrate and the active center of protease, thus limiting the enzymatic cleavage of the peptide. In this work, we reported a heterogeneous surface plasmon resonance (SPR) method for protease detection by integration of homogeneous reaction. The sensitivity was enhanced by the signal amplification of streptavidin (SA)-conjugated immunoglobulin G (SA-IgG). Caspase-3 (Cas-3) was determined as the model. A peptide labeled with two biotin tags at the N- and C-terminals (bio-GDEVDGK-bio) was used as the substrate. In the absence of Cas-3, the substrate peptide was captured by neutravidin (NA)-covered SPR chip to facilitate the attachment of SA-IgG by the avidin-biotin interaction. However, once the peptide substrate was digested by Cas-3 in the aqueous phase, the products of bio-GDEVD and GK-bio would compete with the substrate to bond NA on the chip surface, thus limiting the attachment of SA-IgG. The method integrated the advantages of both heterogeneous and homogeneous assays and has been used to determine Cas-3 inhibitor and evaluate cell apoptosis with satisfactory results.
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Lupaescu, Ancuta-Veronica, Cosmin Stefan Mocanu, Gabi Drochioiu, and Catalina-Ionica Ciobanu. "Zinc Binding to NAP-Type Neuroprotective Peptides: Nuclear Magnetic Resonance Studies and Molecular Modeling." Pharmaceuticals 14, no. 10 (October 1, 2021): 1011. http://dx.doi.org/10.3390/ph14101011.
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Aggregation of amyloid-β peptides (Aβ) is a hallmark of Alzheimer’s disease (AD), which is affecting an increasing number of people. Hence, there is an urgent need to develop new pharmaceutical treatments which could be used to prevent the AD symptomatology. Activity-dependent neuroprotective protein (ADNP) was found to be deficient in AD, whereas NAP, an 8-amino-acid peptide (1NAPVSIPQ8) derived from ADNP, was shown to enhance cognitive function. The higher tendency of zinc ion to induce Aβ aggregation and formation of amorphous aggregates is also well-known in the scientific literature. Although zinc binding to Aβ peptides was extensively investigated, there is a shortage of knowledge regarding the relationship between NAP peptide and zinc ions. Therefore, here, we investigated the binding of zinc ions to the native NAP peptide and its analog obtained by replacing the serine residue in the NAP sequence with tyrosine (1NAPVYIPQ8) at various molar ratios and pH values by mass spectrometry (MS) and nuclear magnetic resonancespectroscopy (NMR). Matrix-assisted laser desorption/ionization time-of-flight (MALDI ToF) mass spectrometry confirmed the binding of zinc ions to NAP peptides, while the chemical shift of Asp1, observed in 1H-NMR spectra, provided direct evidence for the coordinating role of zinc in the N-terminal region. In addition, molecular modeling has also contributed largely to our understanding of Zn binding to NAP peptides.
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Nagaraj, G., M. V. Uma, M. S. Shivayogi, and Hemalatha Balaram. "Antimalarial Activities of Peptide Antibiotics Isolated from Fungi." Antimicrobial Agents and Chemotherapy 45, no. 1 (January 1, 2001): 145–49. http://dx.doi.org/10.1128/aac.45.1.145-149.2001.
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ABSTRACT Malaria caused by Plasmodium falciparum is a major public health problem in the developing countries of the world. Clinical treatment of malaria has become complicated due to the occurrence of infections caused by drug resistant parasites. Secondary metabolites from fungi are an attractive source of chemotherapeutic agents. This work reports the isolation and in vitro antiplasmodial activities of peptide antibiotics of fungal origin. The three peptide antibiotics used in this study were efrapeptins, zervamicins, and antiamoebin. The high-performance liquid chromatography-purified peptides were characterized by nuclear magnetic resonance and mass spectral analysis. All three fungal peptides kill P. falciparum in culture with 50% inhibitory concentrations in the micromolar range. A possible mode of action of these peptide antibiotics on P. falciparum is presented.
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Kim, Minseon, and Yongae Kim. "Structural Studies of Expressed tIK, Anti-Inflammatory Peptide." International Journal of Molecular Sciences 24, no. 1 (December 30, 2022): 636. http://dx.doi.org/10.3390/ijms24010636.
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Cytokine imbalance is one of the causes of inflammation. Inflammation has yet to be adequately treated without side effects. Therefore, we tried to develop a peptide drug with minimal side effects. Peptide drugs have the advantage of being bio-friendly and bio-specific. In a previous study, three peptides with anti-inflammatory activity were derived based on a truncated IK (tIK) protein, which was a fragment of the IK protein with anti-inflammatory effects. The objective of this study was to optimize the process of expressing, isolating, and purifying the three peptides using bacterial strains and describe the process. Circular dichroism and solution state nuclear magnetic resonance spectroscopy were performed on the final purified high-purity peptide and its secondary structure was also identified.
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Gudivada, Vijaya Narasimha, Chen-Ji Huang, Yueh-Hsia Luo, and Guo-Chung Dong. "A Cyclic BMP-2 Peptide Upregulates BMP-2 Protein-Induced Cell Signaling in Myogenic Cells." Polymers 13, no. 15 (July 31, 2021): 2549. http://dx.doi.org/10.3390/polym13152549.
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In the current study, we designed four cyclic peptide analogues by incorporating two cysteine residues in a BMP-2 linear knuckle epitope in such a way that the active region of the peptide could be either inside or outside the cyclic ring. Bone morphogenetic protein receptor BMPRII was immobilized on the chip surface, and the interaction of the linear and cyclic peptide analogues was studied using surface plasmon resonance (SPR). From the affinity data, the peptides with an active region inside the cyclic ring had a higher binding affinity in comparison to the other peptides. To confirm that our affinity data are in line in vitro, we studied the expression levels of RUNX2 (runt-related transcription factor) and conducted an osteogenic marker alkaline phosphatase (ALP) assay and staining. Based on the affinity data and the in vitro experiments, peptide P-05 could be a suitable candidate for osteogenesis, with higher binding affinity and increased RUNX2 and ALP expression in comparison to the linear peptides.
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Bierzyński, A. "Methods of peptide conformation studies." Acta Biochimica Polonica 48, no. 4 (December 31, 2001): 1091–99. http://dx.doi.org/10.18388/abp.2001_3870.
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In solution most of the peptides assume multiple flexible conformations. Determination of the dominant conformers and evaluation of their populations is the aim of peptide conformation studies, in which theoretical and experimental methods play complementary roles. Molecular dynamics or Monte Carlo methods are quite effective in searching the conformational space accessible to a peptide but they are not able to estimate, precisely enough, the populations of various conformations. Therefore, they must be supplemented by experimental data. In this paper, a short review of the experimental methods, most widely used in peptide conformational studies, is presented. Among them NMR plays the leading role. Valuable information is also obtained from hydrogen exchange, fluorescence resonance energy transfer, and circular dichroism measurements. The advantages and shortcomings of these methods are discussed.
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Jaswal, JASWINDER S., and Alan S. Tracey. "Stereochemical requirements for the formation of vanadate complexes with peptides." Canadian Journal of Chemistry 69, no. 10 (October 1, 1991): 1600–1607. http://dx.doi.org/10.1139/v91-235.
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The condensation reactions occurring between vanadate and a number of amino acids and simple peptides have been studied by 51V nuclear magnetic resonance. Vanadate and ligand stoichiometry has been established for the complexes formed and their formation constants determined. The amino acids were all found to undergo rather weak interactions with vanadate and in general provided two products with 51V chemical shifts near −545 and −555 ppm. The peptides also gave minor products with NMR signals occurring with that of vanadate itself. However, in this case, the major products occur at approximately −510 ppm. These latter complexes are monovanadate, monoligand complexes which require the terminal amino, the carboxylate groups and an unsubstituted nitrogen in the peptide linkage in order for product formation to occur. Sidechains promote product formation, apparently by favouring a more readily complexed peptide conformation. Formation constants vary from about 20 to 50 M−1 depending on the sidechain. The carboxylate group can be replaced by a hydroxymethyl. This, however, leads to a significant decrease in product formation at pH 7. Hydrogen ion concentration studies showed that the complexes, when considered to be formed from VO4H2− and neutral peptide, did not require or give off protons. However, when the carboxylate was replaced by the alcohol functionality a proton was released. On the basis of this study the coordination of the vanadate/peptide complexes has been assigned. Key words: peptide, vanadate, complexes, vanadium magnetic resonance.
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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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Mishra, Vinod K., and Gattadahalli M. Anantharamaiah. "High-Resolution Structural Studies Elucidate Antiatherogenic and Anti-Inflammatory Properties of Peptides Designed to Mimic Amphipathic α-Helical Domains of Apolipoprotein A-I." Natural Product Communications 14, no. 5 (May 2019): 1934578X1984913. http://dx.doi.org/10.1177/1934578x19849131.
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Peptides designed to mimic the antiatherogenic and anti-inflammatory properties of apolipoprotein A-I show that although lipid association is required, not all lipid-associating peptides exhibit these properties. Our studies of a series of peptides showed that peptides with aromatic residues at the center of the nonpolar face were able to interact with inflammatory lipids and inhibited inflammation, which resulted in the amelioration of several lipid-mediated disorders such as lesion development, tumor formation, and Alzheimer’s plaque formation. The p K a values determined using 13C nuclear magnetic resonance (NMR) spectroscopy of K residues located at the polar-nonpolar interface provided the first clue to the relative orientations of the peptide helices with respect to each other and around the edge of the lipid discoidal complexes. High-resolution 1H-NMR studies of peptide-lipid discoidal complex confirmed the amphipathic α-helical structure of the peptide, location of aromatic residues of the peptide closer to the polar-nonpolar interface, and head-to-tail arrangement of the peptide helices around the edge of the disc. Amphipathic α-helical structure and the location of aromatic residues (F, W, Y) closer to the polar-nonpolar interface in a lipid environment allow the peptide to strongly bind oxidized lipids resulting in its anti-inflammatory properties.
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Natarajan, Kannan, Giora Morozov, Jiansheng Jiang, Lisa F. Boyd, Michael G. Mage, and David H. Margulies. "TAPBPR, a Peptide Editor – interactions with MHC complexes and SAXS structural studies." Journal of Immunology 196, no. 1_Supplement (May 1, 2016): 116.5. http://dx.doi.org/10.4049/jimmunol.196.supp.116.5.
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Abstract TAPBPR (TAP Binding Protein-Related), a tapasin homolog, functions as a peptide editor independent of the classical peptide loading complex (PLC) that consists of tapasin, transporter associated with antigen processing (TAP), ERp57, and calreticulin. Using insect-cell expressed recombinant luminal human TAPBPR, we previously reported interaction with HLA-A*02:01 molecules freed of peptide following photolysis of HLA-A2/beta2m complexes prepared with photolabile peptides. Here, we extend our analysis of the TABPBPR/MHC interaction by examining the binding of a set of MHC/peptide complexes prepared with different MHC-I molecules refolded with a variety of peptides. Using surface plasmon resonance, we show that a variety of refolded complexes, with or without photolysis of the bound peptide, bind to TAPBPR, raising the possibility that TAPBPR may interact either with a small proportion of peptide free molecules found in some MHC/peptide preparations, or with molecular conformations containing peptide in dynamic equilibrium with the lowest energy state. We extend our analysis of TAPBPR by determination of the low resolution small angle X-ray scattering structures of both TAPBPR and tapasin luminal domains, revealing expected structural similarities.
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Young, John K., Donghui Li, Matthew C. Abramowitz, and Trudy G. Morrison. "Interaction of Peptides with Sequences from the Newcastle Disease Virus Fusion Protein Heptad Repeat Regions." Journal of Virology 73, no. 7 (July 1, 1999): 5945–56. http://dx.doi.org/10.1128/jvi.73.7.5945-5956.1999.
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ABSTRACT Typical of many viral fusion proteins, the sequence of the Newcastle disease virus (NDV) fusion protein has several heptad repeat regions. One, HR1, is located just carboxyl terminal to the fusion peptide, while the other, HR2, is located adjacent to the transmembrane domain. The structure and function of a synthetic peptide with a sequence from the region of the NDV HR1 region (amino acids 150 to 173) were characterized. The peptide inhibited fusion with a half-maximal concentration of approximately 2 μM; however, inhibition was observed only if the peptide was added prior to protease activation of the fusion protein. This inhibition was virus specific since the peptide had minimal effect on fusion directed by the Sendai virus glycoproteins. To explore the mechanism of action, the potential HR1 peptide interaction with a previously characterized fusion inhibitory peptide with a sequence from the HR2 domain (J. K. Young, R. P. Hicks, G. E. Wright, and T. G. Morrison, Virology 238:291–304, 1997) was characterized. The results demonstrated an interaction between the two peptides both functionally and directly. First, while the individual peptides each inhibit fusion, equimolar mixtures of the two peptides had minimal effect on fusion, suggesting that the two peptides form a complex preventing their interaction with a target protein. Second, an HR2 peptide covalently linked with biotin was found to bind specifically to HR1 peptide in a Western blot. The structure of the HR1 peptide was analyzed by nuclear magnetic resonance spectroscopy and found to be an α helix.
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Kim, Young Soo, and Hyung Joon Cha. "High-Throughput and Facile Assay of Antimicrobial Peptides Using pH-Controlled Fluorescence Resonance Energy Transfer." Antimicrobial Agents and Chemotherapy 50, no. 10 (October 2006): 3330–35. http://dx.doi.org/10.1128/aac.00455-06.
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ABSTRACT Amphipathic antimicrobial peptides can destroy bacteria cells by inducing membrane permeabilization, forming one strategy for innate defense by various organisms. However, although the antimicrobial peptides are considered a promising alternative for use against multidrug-resistant bacteria, large-scale screening of potential candidate antimicrobial peptides will require a simple, rapid assay for antimicrobial activity. Here, we describe a novel fluorescence resonance energy transfer (FRET)-based assay system for antimicrobial peptides which takes advantage of pH-related changes in FRET efficiency due to the instability of enhanced yellow fluorescent protein versus the stability of enhanced cyan fluorescent protein in a reduced-pH environment. We successfully showed that quantification of antimicrobial activity is possible through a difference of FRET efficiency between ECFP-EYFP fusion molecules released from disrupted Escherichia coli in an extracellular environment (pH 6) and those retained in an intracellular environment (pH ∼7). Thus, we herein suggest a new simple, effective, and efficient pH-controlled FRET-based antimicrobial peptide screening method applicable to high-throughput screening of candidate peptide libraries.
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Morozov, Giora, Huaying Zhao, Michael Mage, Lisa Boyd, Ramesh Venna, Michael Norcross, Curtis McMurtrey, et al. "Direct interaction of recombinant TAPBPR with MHC-I molecules: stabilization of peptide-free MHC-I promotes high affinity peptide loading (APP5P.102)." Journal of Immunology 194, no. 1_Supplement (May 1, 2015): 183.4. http://dx.doi.org/10.4049/jimmunol.194.supp.183.4.
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Abstract The loading of MHC-I molecules with peptides for cell surface display is a crucial step in self-tolerance and activation of CD8 T cells. We studied TAPBPR (TAP binding protein-related) protein, a tapasin homolog, which is widely expressed and IFN-γ inducible, but is not part of the classical MHC-I peptide-loading complex. We produced recombinant soluble TAPBPR and evaluated its interactions with several recombinant MHC-I molecules in vitro, by gel-shift, size exclusion chromatography, ultracentrifugation, and surface plasmon resonance. We show that TAPBPR binds MHC-I after photolysis of a bound peptide, and that the TAPBPR/MHC-I complex is dissociated by exposure to peptides that bind the MHC-I molecule, indicating a role of TAPBPR in stabilizing a peptide-receptive form of the MHC-I/β2m complex. Peptide-dependent release of MHC-I from TAPBPR is directly proportional to the peptide’s affinity for MHC-I. Peptide binding experiments indicate a role for TAPBPR in selection of high affinity peptides. Mutagenesis of TAPBPR and MHC-I confirm the importance of amino acid residues conserved with the putative tapasin/MHC-I binding site and reveal additional residues important for the TAPBPR/MHC-I interaction. Molecular docking simulations suggest a detailed mechanism for the interaction of TAPBPR with peptide free MHC-I. These studies are consistent with the view that TAPBPR functions as a chaperone that stabilizes peptide-free MHC-I to permit binding of high affinity peptides.
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Kakizuka, Taishi, Akira Takai, Keiko Yoshizawa, Yasushi Okada, and Tomonobu M. Watanabe. "An improved fluorescent protein-based expression reporter system that utilizes bioluminescence resonance energy transfer and peptide-assisted complementation." Chemical Communications 56, no. 25 (2020): 3625–28. http://dx.doi.org/10.1039/c9cc08664a.
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Lau, Tong-Lay, Kevin J. Barnham, Cyril C. Curtain, Colin L. Masters, and Frances Separovic. "Magnetic Resonance Studies of β-Amyloid Peptides." Australian Journal of Chemistry 56, no. 5 (2003): 349. http://dx.doi.org/10.1071/ch02268.
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The deposition of senile plaques is a characteristic event in the progression of Alzheimer's disease (AD). Associated with the progression of the disease, the main component of the deposited material, the β-amyloid peptide (Aβ), undergoes a structural transition and a toxic gain of function. For this reason, extensive structural studies of Aβ and Aβ fragments have been carried out in order to determine the relationship between neurotoxicity and conformational changes of the peptide that lead to fibril formation. NMR studies in aqueous solution and in membrane-mimicking environments are reviewed, and include the effects of temperature, pH, and metal ions on Aβ structure. In addition, electron paramagnetic resonance (EPR) studies of Aβ in model membranes and the effect of metals of Aβ are discussed and demonstrate the pleiomorphic nature of the peptide. The contradictory results obtained from the various experiments are a result of studying different fragments of Aβ and illustrate the importance of studying the full-length peptide.
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Galzitskaya, O. V., O. M. Selivanova, U. F. Dzhus, V. V. Marchenkov, M. Yu Suvorina, and A. K. Surin. "Influence of Chaperones on Amyloid Formation of Аβ Peptide." Current Protein & Peptide Science 23, no. 1 (January 2022): 44–51. http://dx.doi.org/10.2174/1389203723666220127152545.
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Background: An extensive study of the folding and stability of proteins and their complexes has revealed a number of problems and questions that need to be answered. One of them is the effect of chaperones on the process of fibrillation of various proteins and peptides. Methods: We studied the effect of molecular chaperones, such as GroEL and α-crystallin, on the fibrillogenesis of the Aβ(1-42) peptide using electron microscopy and surface plasmon resonance. Results: Recombinant GroEL and Aβ(1-42) were isolated and purified. It was shown that the assembly of GroEL occurs without the addition of magnesium and potassium ions, as is commonly believed. According to the electron microscopy results, GroEL insignificantly affects the fibrillogenesis of the Aβ(1-42) peptide, while α-crystallin prevents the elongation of the Aβ(1-42) peptide fibrils. We have demonstrated that GroEL interacts nonspecifically with Aβ(1-42), while α-crystallin does not interact with Aβ(1-42) at all using surface plasmon resonance. Conclusion: The data obtained will help us understand the process of amyloid formation and the effect of various components on it.
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Yin, Liusong, Peter Trenh, and Lawrence Stern. "MHC II-peptide complex conformation constrained by interactions throughout the peptide binding groove determines HLA-DM susceptibility (P5014)." Journal of Immunology 190, no. 1_Supplement (May 1, 2013): 41.8. http://dx.doi.org/10.4049/jimmunol.190.supp.41.8.
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Abstract HLA-DM (DM) mediates the exchange of peptides loaded onto MHC II. However, the determinants of DM-mediated peptide release remain unclear and controversial. In this study, we synthesized a series of peptides derived from HLA-A2104-117 and measured their kinetic stabilities when bound to HLA-DR1 (DR1) in the absence or presence of DM. As expected from previous work, we found that peptides with non-optimal pocket 1 residues were highly DM susceptible. Surprisingly we found that substitution of the pocket 9 residue can counteract the low binding affinity, low kinetic stability and high DM-susceptibility of peptides containing non-optimal pocket 1 residues. Surface Plasmon Resonance demonstrated that DM bound well to DR1 loaded with a peptide variant with pocket 1 alanine (A1), while no binding was observed for a rescue variant with leucine at pocket 9 (A1L9) or for the wild-type peptide (W1Q9). We determined the crystal structure of DR1-A1L9 to 2.3Å resolution, confirming the expected binding frame with alanine at pocket 1. DR1-A1 appeared to adopt a different conformation which can be better detected and edited by DM, as evidenced by the sodium dodecyl sulfate-resistance and recognition by a conformation-specific monoclonal antibody UL-5A1. Together with the results that multiple substitutions influence DM-susceptibility, our data suggest that conformation of MHC II-peptide complex constrained by interactions throughout the peptide binding site determines DM-susceptibility.
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Kurepa, Zoran, Charles A. Hasemann, and James Forman. "Qa-1b Binds Conserved Class I Leader Peptides Derived from Several Mammalian Species." Journal of Experimental Medicine 188, no. 5 (September 7, 1998): 973–78. http://dx.doi.org/10.1084/jem.188.5.973.
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Qa-1b binds a peptide (AMAPRTLLL), referred to as Qdm (for Qa-1 determinant modifier), derived from the signal sequence of murine class Ia molecules. This peptide binds with high affinity and accounts for almost all of the peptides associated with this molecule. Human histocompatibility leukocyte antigen (HLA)-E, a homologue of Qa-1b, binds similar peptides derived from human class Ia molecules and interacts with CD94/NKG2 receptors on natural killer cells. We used surface plasmon resonance to determine the ability of Qa-1b to bind related ligands representing peptides derived from the leaders of class I molecules from several mammalian species. All of the peptides reported to bind HLA-E bound readily to Qa-1b. In addition, peptides derived from leader segments of different mammals also bound to Qa-1b, indicating a conservation of this “Qdm-like” epitope throughout mammalian evolution. We have attempted to define a minimal peptide on a polyglycine backbone that binds Qa-1b. Our previous findings showed that P2 and P9 are important but not sufficient for binding to Qa-1b. Although a minimum peptide (GMGGGGLLL) bound Qa-1b, its interaction was relatively weak, as were peptides sharing five or six residues with Qdm, indicating that multiple native residues are required for a strong interaction. This finding is consistent with the observation that this molecule preferentially binds this single ligand.
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Ribeiro, Ana R. M., Helena P. Felgueiras, Susana P. G. Costa, and Sílvia M. M. A. Pereira-Lima. "Synthesis of Peptaibolin, an Antimicrobial Peptide." Proceedings 78, no. 1 (December 1, 2020): 47. http://dx.doi.org/10.3390/iecp2020-08654.
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To tackle one of the biggest global health problems, the resistance of microorganisms to antibiotics, a collective effort in the search for more effective agents against bacteria was required. Peptides with antimicrobial activity have been raising much attention as a promising alternative for antibiotics. Peptaibols, for instance, are a family of antimicrobial peptides (AMPs) with great biomedical potential, in which the Peptaibolin can be highlighted. This peptide has gained relevance due to its small amino acids content, only four, and its acetyl group and a phenylalaninol residue (Phol) at the N-terminal and C-terminal, respectively. Here, we report the synthesis of Peptaibolin through Solid Phase Peptide Synthesis assisted by Microwave heating (MW-SPPS) in a pre-loaded Phe-Wang resin. Starting from a loading of 0.51 mmol/g, two syntheses were made, using two different combinations of coupling reagents. The best option was DIC/Oxima, achieving a yield of 50.0%. Proton Nuclear Magnetic Resonance (1H-NMR) studies confirmed the peptide structure, while High Performance Liquid Chromatography (HPLC) verified the peptide purity. The peptide solubility was examined against several combinations of solvents. Peptaibolin was not soluble in water, only in organic solvents or in the combination of both. Antimicrobial testing was conducted using Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, and Pseudomonas aeruginosa. Minimum inhibitory concentration studies demonstrated the resistance of bacteria to the peptide action and the peptide instability in bacterial growth conditions.
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Sgourakis, Nikolaos, Andrew C. McShan, Kannan Natarajan, Vlad K. Kumirov, David Flores-Solis, Jiansheng Jiang, Mareike Badstuebner, Evgenii L. Kovrigin, and David H. Margulies. "Chaperone-assisted peptide exchange on MHC-I is driven by a negative allostery release cycle: Implications for a role of peptide-editing Molecular Chaperones in scrutinizing the peptide repertoire." Journal of Immunology 200, no. 1_Supplement (May 1, 2018): 99.23. http://dx.doi.org/10.4049/jimmunol.200.supp.99.23.
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Abstract Molecular chaperones TAPBPR (TAP-binding protein related) and tapasin associate with major histocompatibility complex class I (MHC-I) to promote the loading of antigenic peptides through a poorly understood mechanism. Here, we use solution Nuclear Magnetic Resonance (NMR) spectroscopy to probe TAPBPR-induced changes on MHC-I. Dynamic motions present in the empty MHC groove become progressively dampened with increasing peptide occupancy, while allosteric communication between the A- and F-pockets regulates a conformational switch located near the TAPBPR binding site, which is crucial for chaperone release from the complex. Our analysis of NMR data recorded for a range of TAPBPR complexes prepared with both murine H2 and human HLA alleles complements the recent X-ray structures to provide atomic-resolution mechanistic insights into the selection of optimal peptide sequences for the displayed antigen repertoire. In particular, our results show that negative allosteric coupling between the MHC groove and chaperone binding sites allows TAPBPR to proofread MHC molecules containing a range of different peptides. Since the affinity of incoming peptides for the empty groove is greatly reduced in the chaperone complex, (micromolar range, relative to nanomolar for the free MHC), these interactions can provide a mechanism for optimizing the peptide repertoire, where only the highest-affinity peptides can drive chaperone release. Finally, our results suggest that TAPBPR may promote the dissociation of tightly bound peptides from MHC molecules, thereby further scrutinizing the displayed repertoire. These findings imply a similar mechanism for the specificity and editing function of tapasin in the peptide-loading complex.
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Tan, Ying, Ling Jiang, Manli Wang, Feifei Yin, Fei Deng, Maili Liu, Zhihong Hu, and Hualin Wang. "Mutagenesis and Nuclear Magnetic Resonance Analyses of the Fusion Peptide of Helicoverpa armigera Single Nucleocapsid Nucleopolyhedrovirus F Protein." Journal of Virology 82, no. 16 (June 4, 2008): 8138–48. http://dx.doi.org/10.1128/jvi.00368-08.
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ABSTRACT The entry of enveloped viruses into cells is normally mediated by fusion between viral and cellular membranes, in which the fusion peptide plays a crucial role. The fusion peptides of group II nucleopolyhedrovirus (NPV) F proteins are quite conserved, with a hydrophobic region located at the N terminal of the F1 fragment. For this report, we used mutagenesis and nuclear magnetic resonance (NMR) to study the structure and function of the fusion peptide of the Helicoverpa armigera single-nucleocapsid NPV (HearNPV) F protein (HaF). Five mutations in the fusion peptide of HaF, N1G, N1L, I2N, G3L, and D11L, were generated separately, and the mutated f genes were transformed into the f-null HearNPV bacmid. The mutations N1L, I2N, and D11L were found to completely abolish the ability of the recombinant bacmids to produce infectious budded virus, while the mutations N1G and G3L did not. The low-pH-induced envelope fusion assay demonstrated that the N1G substitution increased the fusogenicity of HaF, while the G3L substitution reduced its fusogenicity. NMR spectroscopy was used to determine the structure of a synthetic fusion peptide of HaF in the presence of sodium dodecyl sulfate micelles at pH 5.0. The fusion peptide appeared to be an amphiphilic structure composed of a flexible coil in the N terminus from N1 to N5, a 310-helix from F6 to G8, a turn at S9, and a regular α-helix from V10 to D19. The data provide the first NMR structure of a baculovirus fusion peptide and allow us to further understand the relationship of structure and function of the fusion peptide.
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Kim, Seongsoo, Sang-Myung Lee, Je Pil Yoon, Namhun Lee, Jinhyo Chung, Woo-Jae Chung, and Dong-Sik Shin. "Robust Magnetized Graphene Oxide Platform for In Situ Peptide Synthesis and FRET-Based Protease Detection." Sensors 20, no. 18 (September 15, 2020): 5275. http://dx.doi.org/10.3390/s20185275.
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Graphene oxide (GO)/peptide complexes as a promising disease biomarker analysis platform have been used to detect proteolytic activity by observing the turn-on signal of the quenched fluorescence upon the release of peptide fragments. However, the purification steps are often cumbersome during surface modification of nano-/micro-sized GO. In addition, it is still challenging to incorporate the specific peptides into GO with proper orientation using conventional immobilization methods based on pre-synthesized peptides. Here, we demonstrate a robust magnetic GO (MGO) fluorescence resonance energy transfer (FRET) platform based on in situ sequence-specific peptide synthesis of MGO. The magnetization of GO was achieved by co-precipitation of an iron precursor solution. Magnetic purification/isolation enabled efficient incorporation of amino-polyethylene glycol spacers and subsequent solid-phase peptide synthesis of MGO to ensure the oriented immobilization of the peptide, which was evaluated by mass spectrometry after photocleavage. The FRET peptide MGO responded to proteases such as trypsin, thrombin, and β-secretase in a concentration-dependent manner. Particularly, β-secretase, as an important Alzheimer’s disease marker, was assayed down to 0.125 ng/mL. Overall, the MGO platform is applicable to the detection of other proteases by using various peptide substrates, with a potential to be used in an automated synthesis system operating in a high throughput configuration.
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Poluektov, Yuri, AeRyon Kim, and Scheherazade Sadegh-Nasseri. "HLA-DO and its effect on peptide binding to MHC Class II (106.29)." Journal of Immunology 188, no. 1_Supplement (May 1, 2012): 106.29. http://dx.doi.org/10.4049/jimmunol.188.supp.106.29.
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Abstract True function of HLA-DO (DO), an MHC Class II accessory molecule remains a mystery. The leading model on it function proposes that DO inhibits the effects of DM. Most of those studies were have used in vivo mouse models, looking at the endpoint of peptide presentation, not taking into account the individual steps in the process. To directly study DO function, we designed a recombinant soluble DO that included leucine zipper for better dimerization of the DOα- and β- chains and expressed it in insect cells. Kinetic experiments involving DR1 and the peptide with or without DM and DO revealed unexpected results. We found that; a) DO diminishes the binding of two peptides that are DM-sensitive, b)DO has positive effects on binding of peptides that form DM-resistant complexes, c) DO only has an effect on peptide association and virtually no effect on peptide dissociation, and d) DO functionsdirectly on DR molecules.We propose that DO binds to the peptide-receptive MHC II molecules that DM generates either by dissociating the bound peptides, or opening of the empty groove. The role for DO then is to enforce another layer of control on peptide selection. In support of this hypothesis, using BIACore Surface Plasmon Resonance, we have measured direct binding of DO to an open conformation of HLA-DR1 in real time, while no binding to a closed DR1 conformation wasdetected.
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Brunel, Florence M., Michael B. Zwick, Rosa M. F. Cardoso, Josh D. Nelson, Ian A. Wilson, Dennis R. Burton, and Philip E. Dawson. "Structure-Function Analysis of the Epitope for 4E10, a Broadly Neutralizing Human Immunodeficiency Virus Type 1 Antibody." Journal of Virology 80, no. 4 (February 15, 2006): 1680–87. http://dx.doi.org/10.1128/jvi.80.4.1680-1687.2006.
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ABSTRACT The human immunodeficiency virus type 1 (HIV-1) neutralizing antibody 4E10 binds to a linear, highly conserved epitope within the membrane-proximal external region of the HIV-1 envelope glycoprotein gp41. We have delineated the peptide epitope of the broadly neutralizing 4E10 antibody to gp41 residues 671 to 683, using peptides with different lengths encompassing the previously suggested core epitope (NWFDIT). Peptide binding to the 4E10 antibody was assessed by competition enzyme-linked immunosorbent assay, and the Kd values of selected peptides were determined using surface plasmon resonance. An Ala scan of the epitope indicated that several residues, W672, F673, and T676, are essential (>1,000-fold decrease in binding upon replacement with alanine) for 4E10 recognition. In addition, five other residues, N671, D674, I675, W680, and L679, make significant contributions to 4E10 binding. In general, the Ala scan results agree well with the recently reported crystal structure of 4E10 in complex with a 13-mer peptide and with our circular dichroism analyses. Neutralization competition assays confirmed that the peptide NWFDITNWLWYIKKKK-NH2 could effectively inhibit 4E10 neutralization. Finally, to limit the conformational flexibility of the peptides, helix-promoting 2-aminoisobutyric acid residues and helix-inducing tethers were incorporated. Several peptides have significantly improved affinity (>1,000-fold) over the starting peptide and, when used as immunogens, may be more likely to elicit 4E10-like neutralizing antibodies. Hence, this study represents the first stage toward iterative development of a vaccine based on the 4E10 epitope.
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Carmona, Adriana K., Maria Aparecida Juliano, and Luiz Juliano. "The use of Fluorescence Resonance Energy Transfer (FRET) peptidesfor measurement of clinically important proteolytic enzymes." Anais da Academia Brasileira de Ciências 81, no. 3 (September 2009): 381–92. http://dx.doi.org/10.1590/s0001-37652009000300005.
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Proteolytic enzymes have a fundamental role in many biological processes and are associated with multiple pathological conditions. Therefore, targeting these enzymes may be important for a better understanding of their function and development of therapeutic inhibitors. Fluorescence Resonance Energy Transfer (FRET) peptides are convenient tools for the study of peptidases specificity as they allow monitoring of the reaction on a continuous basis, providing a rapid method for the determination of enzymatic activity. Hydrolysis of a peptide bond between the donor/acceptor pair generates fluorescence that permits the measurement of the activity of nanomolar concentrations of the enzyme. The assays can be performed directly in a cuvette of the fluorimeter or adapted for determinations in a 96-well fluorescence plate reader. The synthesis of FRET peptides containing ortho-aminobenzoic acid (Abz) as fluorescent group and 2, 4-dinitrophenyl (Dnp) or N-(2, 4-dinitrophenyl)ethylenediamine (EDDnp) as quencher was optimized by our group and became an important line of research at the Department of Biophysics of the Federal University of São Paulo. Recently, Abz/Dnp FRET peptide libraries were developed allowing high-throughput screening of peptidases substrate specificity. This review presents the consolidation of our research activities undertaken between 1993 and 2008 on the synthesis of peptides and study of peptidases specificities.
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Marsh, D. "Application of electron spin resonance for investigating peptide-lipid interactions, and correlation with thermodynamics." Biochemical Society Transactions 29, no. 4 (August 1, 2001): 582–89. http://dx.doi.org/10.1042/bst0290582.
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Peptide-lipid interactions can be investigated with spin-labelled lipid probes by using electron spin resonance (ESR) methods that have been developed for studying lipid-protein interactions with both integral and peripheral membrane proteins and also with surface-binding proteins that additionally penetrate the membrane. This approach has the advantage that a direct comparison can be made with the databank of ESR results from the various types of membrane protein. The appropriateness of the peptides as models for membrane proteins, or for their specific segments, can then be assessed. Further, differences in behaviour can be readily identified, as for example in the case of surface-active cytolytic or fusogenic peptides. Comparison with thermodynamic predictions for membrane insertion provides a useful adjunct to the spin-label method.
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Fischer, Sebastian Nils, and Armin Geyer. "Assembly of synthetic Aβ miniamyloids on polyol templates." Beilstein Journal of Organic Chemistry 11 (December 17, 2015): 2646–53. http://dx.doi.org/10.3762/bjoc.11.284.
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Covalent dynamic chemistry is used to mimic the first steps of the highly cooperative fibril formation of Aβ peptides. For that purpose, Aβ peptide pentapeptide boronic acids 1 and 2 were synthesized by solid-phase peptide synthesis and studied in esterification experiments with polyhydroxylated templates. The bis-hydroxylated dipeptide Hot=Tap serves as a template of adjustable degree of oligomerization which spontaneously forms boronic esters with peptides of type 1 and 2. Nuclear magnetic resonance can differentiate between regioisomeric boronic esters and identifies preferred sites of esterification on the dimeric template 9. 2-Formylphenylboronic acid (14) is used to link the parent pentapeptide Leu-Val-Phe-Phe-Ala to the template 16 to obtain threefold boronic ester 17. The miniamyloid 17 assembles from seven components by imine and boronic ester bonds between the peptides and the template. The relative orientation and spacing of the peptides mimic the assembly of peptides in Alzheimer β-amyloids.
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SHE, Wenchuan, Kui LUO, Bin HE, Hua AI, and ZHongwei GU. "FUNCTIONAL PEPTIDE DENDRIMERS AS MAGNETIC RESONANCE IMAGING PROBES." Acta Polymerica Sinica 011, no. 2 (February 18, 2011): 157–65. http://dx.doi.org/10.3724/sp.j.1105.2011.10027.
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JiJi, Renee D., Jian Xiong, and Mingjuan Wang. "Ultraviolet Resonance Raman Studies of a Disordered Peptide." Biophysical Journal 100, no. 3 (February 2011): 202a. http://dx.doi.org/10.1016/j.bpj.2010.12.1316.
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Gorbenko, Galyna, Hiroyuki Saito, Julian Molotkovsky, Masafumi Tanaka, Masashi Egashira, Minoru Nakano, and Tetsurou Handa. "Resonance energy transfer study of peptide–lipid complexes." Biophysical Chemistry 92, no. 3 (September 2001): 155–68. http://dx.doi.org/10.1016/s0301-4622(01)00195-8.
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Karas, John A., David W. Keizer, and Marc-Antoine Sani. "Nuclear Magnetic Resonance Study of the Peptide FRANCESSEPAROVIC." Australian Journal of Chemistry 73, no. 3 (2020): 158. http://dx.doi.org/10.1071/ch19357.
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As an eminent ambassador of STEM and renowned NMR spectroscopist, Frances Separovic is an internationally famous name, but could it also be a valuable membrane-active peptide sequence? Her name has been used as an amino acid sequence (FS), successfully synthesised, oxidised, and put into contact with membrane models to investigate any serendipitous activity. The 3D structure of the cyclic FS was determined in dodecylphosphocholine (DPC) micelles by solution NMR spectroscopy. FS displayed a twisted bend separating a helical stretch and an unstructured segment. Using solid-state NMR spectroscopy, the effect of FS on 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dimyristoyl-sn-glycero-3-phosphoserine (DMPS) lipid bilayers was studied. FS did not strongly disturb the neutral membrane surface but likely inserted into their hydrophobic core without a strong effect on the lipid dynamics, while perturbation of the negatively charged membranes remained at the headgroup interface with a strong effect on the lipid dynamics. This study demonstrated that FS is a candidate for discovering potential future therapeutic activities.
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Kota, S., C. Coito, G. Mousseau, J. P. Lavergne, and A. D. Strosberg. "Peptide inhibitors of hepatitis C virus core oligomerization and virus production." Journal of General Virology 90, no. 6 (June 1, 2009): 1319–28. http://dx.doi.org/10.1099/vir.0.008565-0.
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Hepatitis C virus (HCV) nucleocapsid assembly requires dimerization of the core protein, an essential step in the formation of the virus particle. We developed a novel quantitative assay for monitoring this protein–protein interaction, with the goal of identifying inhibitors of core dimerization that might block HCV production in infected Huh-7.5 hepatoma cells. Two core-derived, 18-residue peptides were found that inhibited the dimerization of a fragment of core comprising residues 1–106 (core106) by 68 and 63 %, respectively. A third, related 15-residue peptide displayed 50 % inhibition, with an IC50 of 21.9 μM. This peptide was shown, by fluorescence polarization, to bind directly to core106 with a K d of 1.9 μM and was displaced by the unlabelled peptide with an IC50 of 18.7 μM. When measured by surface plasmon resonance, the same peptide bound core169 with a K d of 7.2 μM. When added to HCV-infected cells, each of the three peptides blocked release, but not replication, of infectious virus. When measured by real-time RT-PCR, the RNA levels were reduced by 7-fold. The 15-residue peptide had no effect on HIV propagation. Such inhibitors may constitute useful tools to investigate the role of core dimerization in the virus cycle.
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Hunter, Howard N., A. Ross Demcoe, Håvard Jenssen, Tore J. Gutteberg, and Hans J. Vogel. "Human Lactoferricin Is Partially Folded in Aqueous Solution and Is Better Stabilized in a Membrane Mimetic Solvent." Antimicrobial Agents and Chemotherapy 49, no. 8 (August 2005): 3387–95. http://dx.doi.org/10.1128/aac.49.8.3387-3395.2005.
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ABSTRACT Lactoferricins are highly basic bioactive peptides that are released in the stomach through proteolytic cleavage of various lactoferrin proteins. Here we have determined the solution structure of human lactoferricin (LfcinH) by conventional two-dimensional nuclear magnetic resonance methods in both aqueous solution and a membrane mimetic solvent. Unlike the 25-residue bovine lactoferricin (LfcinB), which adopts a somewhat distorted antiparallel β sheet, the longer LfcinH peptide shows a helical content from Gln14 to Lys29 in the membrane mimetic solvent but a nonexistent β-sheet character in either the N- or C-terminal regions of the peptide. The helical characteristic of the LfcinH peptide resembles the conformation that this region adopts in the crystal structure of the intact protein. The LfcinH structure determined in aqueous solution displays a nascent helix in the form of a coiled conformation in the region from Gln14 to Lys29. Numerous hydrophobic interactions create the basis for the better-defined overall structure observed in the membrane mimetic solvent. The 49-residue LfcinH peptide isolated for these studies was found to be slightly longer than previously reported peptide preparations and was found to have an intact peptide bond between residues Ala11 and Val12. The distinct solution structures of LfcinH and LfcinB represent a novel difference in the physical properties of these two peptides, which contributes to their unique physiological activities.
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Kim, Minseon, Jinyoung Son, and Yongae Kim. "Structural and Mechanismic Studies of Lactophoricin Analog, Novel Antibacterial Peptide." International Journal of Molecular Sciences 22, no. 7 (April 2, 2021): 3734. http://dx.doi.org/10.3390/ijms22073734.
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Naturally derived antibacterial peptides exhibit excellent pharmacological action without the risk of resistance, suggesting a potential role as biologicals. Lactophoricin-I (LPcin-I), found in the proteose peptone component-3 (PP3; lactophorin) of bovine milk, is known to exhibit antibiotic activity against Gram-positive and Gram-negative bacteria. Accordingly, we derived a new antibacterial peptide and investigated its structure–function relationship. This study was initiated by designing antibacterial peptide analogs with better antibacterial activity, less cytotoxicity, and shorter amino acid sequences based on LPcin-I. The structural properties of antibacterial peptide analogs were investigated via spectroscopic analysis, and the antibacterial activity was confirmed by measurement of the minimal inhibitory concentration (MIC). The structure and mechanism of the antibacterial peptide analog in the cell membrane were also studied via solution-state nuclear magnetic resonance (NMR) and solid-state NMR spectroscopy. Through 15N one-dimensional and two-dimensional NMR experiments and 31P NMR experiments, we suggest the 3D morphology and antibacterial mechanism in the phospholipid bilayer of the LPcin analog. This study is expected to establish a system for the development of novel antibacterial peptides and to establish a theoretical basis for research into antibiotic substitutes.
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Cantisani, Marco, Marilisa Leone, Eleonora Mignogna, Katerina Kampanaraki, Annarita Falanga, Giancarlo Morelli, Massimiliano Galdiero, and Stefania Galdiero. "Structure-Activity Relations of Myxinidin, an Antibacterial Peptide Derived from the Epidermal Mucus of Hagfish." Antimicrobial Agents and Chemotherapy 57, no. 11 (September 3, 2013): 5665–73. http://dx.doi.org/10.1128/aac.01341-13.
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ABSTRACTThe structure-activity relations of myxinidin, a peptide derived from epidermal mucus of hagfish,Myxine glutinosaL., were investigated. Analysis of key residues allowed us to design new peptides with increased efficiency. Antimicrobial activity of native and modified peptides demonstrated the key role of uncharged residues in the sequence; the loss of these residues reduces almost entirely myxinidin antimicrobial activity, while insertion of arginine at charged and uncharged position increases antimicrobial activity compared with that of native myxinidin. Particularly, we designed a peptide capable of achieving a high inhibitory effect on bacterial growth. Experiments were conducted using both Gram-negative and Gram-positive bacteria. Nuclear magnetic resonance (NMR) studies showed that myxinidin is able to form an amphipathic α-helical structure at the N terminus and a random coil region at the C terminus.
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Pastori, Claudia, Alberto Clivio, Lorenzo Diomede, Roberto Consonni, Giacomo M. S. De Mori, Renato Longhi, Giorgio Colombo, and Lucia Lopalco. "Two Amino Acid Substitutions within the First External Loop of CCR5 Induce Human Immunodeficiency Virus-Blocking Antibodies in Mice and Chickens." Journal of Virology 82, no. 8 (February 6, 2008): 4125–34. http://dx.doi.org/10.1128/jvi.02232-07.
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ABSTRACT Antibodies to the first loop (ECL1) of CCR5 have been identified in human immunodeficiency virus (HIV)-exposed uninfected individuals (ESN) and in HIV-positive nonprogressing subjects. Thus, these antibodies may confer resistance against HIV infection. To define which amino acids are involved in antibody binding to CCR5, we performed a peptide-scanning assay and studied the immunogenicity of peptides in animal models. A panel of synthetic peptides spanning the CCR5-ECL1 region and displaying glycine or alanine substitutions was assayed for antibody binding with a pool of natural anti-CCR5 antibodies. We used mice and chickens to study the immunogenicity of mutagenized peptide. Structural characterization by nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations were performed to better understand the structural and conformational features of the mutagenized peptide. Amino acid substitutions in positions Ala95 and Ala96 (A95-A96) increased antibody-peptide binding compared to that of the wild-type peptide (Asp95-Phe96). The Ala95-96 peptide was shown to induce, in mice and chickens, antibodies displaying biological activity at very low concentrations. Strikingly, chicken antibodies to the Ala95-96 peptide specifically recognize human CCR5 molecules, downregulate receptors from lymphocytes, inhibit CCR5-dependent chemotaxis, and prevent infection by several R5 viruses, displaying 50% inhibitory concentrations of less than 3 ng/ml. NMR spectroscopy and molecular dynamics simulations proved the high flexibility of isolated epitopes and suggested that A95-A96 substitutions determine a slightly higher tendency to generate helical conformations combined with a lower steric hindrance of the side chains in the peptides. These findings may be relevant to the induction of strong and efficient HIV-blocking antibodies.
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Hosseinzadeh, Parisa, Gaurav Bhardwaj, Vikram Khipple Mulligan, Matthew D. Shortridge, Timothy W. Craven, Fátima Pardo-Avila, Stephen A. Rettie, et al. "Comprehensive computational design of ordered peptide macrocycles." Science 358, no. 6369 (December 14, 2017): 1461–66. http://dx.doi.org/10.1126/science.aap7577.
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Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with l-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of l- and d-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods.
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Tkach, Igor, Ulf Diederichsen, and Marina Bennati. "Studies of transmembrane peptides by pulse dipolar spectroscopy with semi-rigid TOPP spin labels." European Biophysics Journal 50, no. 2 (February 28, 2021): 143–57. http://dx.doi.org/10.1007/s00249-021-01508-6.
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AbstractElectron paramagnetic resonance (EPR)-based pulsed dipolar spectroscopy measures the dipolar interaction between paramagnetic centers that are separated by distances in the range of about 1.5–10 nm. Its application to transmembrane (TM) peptides in combination with modern spin labelling techniques provides a valuable tool to study peptide-to-lipid interactions at a molecular level, which permits access to key parameters characterizing the structural adaptation of model peptides incorporated in natural membranes. In this mini-review, we summarize our approach for distance and orientation measurements in lipid environment using novel semi-rigid TOPP [4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazin-1-yl)-L-phenylglycine] labels specifically designed for incorporation in TM peptides. TOPP labels can report single peak distance distributions with sub-angstrom resolution, thus offering new capabilities for a variety of TM peptide investigations, such as monitoring of various helix conformations or measuring of tilt angles in membranes. Graphical Abstract
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Wentink, Madelon Q., Tilman M. Hackeng, Sebastien P. Tabruyn, Wouter C. Puijk, Klaus Schwamborn, Daniele Altschuh, Rob H. Meloen, Teun Schuurman, Arjan W. Griffioen, and Peter Timmerman. "Targeted vaccination against the bevacizumab binding site on VEGF using 3D-structured peptides elicits efficient antitumor activity." Proceedings of the National Academy of Sciences 113, no. 44 (October 17, 2016): 12532–37. http://dx.doi.org/10.1073/pnas.1610258113.
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Therapeutic targeting of the VEGF signaling axis by the VEGF-neutralizing monoclonal antibody bevacizumab has clearly demonstrated clinical benefit in cancer patients. To improve this strategy using a polyclonal approach, we developed a vaccine targeting VEGF using 3D-structured peptides that mimic the bevacizumab binding site. An in-depth study on peptide optimization showed that the antigen’s 3D structure is essential to achieve neutralizing antibody responses. Peptide 1 adopts a clear secondary, native-like structure, including the typical cysteine-knot fold, as evidenced by CD spectroscopy. Binding and competition studies with bevacizumab in ELISA and surface plasmon resonance analysis revealed that peptide 1 represents the complete bevacizumab binding site, including the hairpin loop (β5–turn–β6) and the structure-supporting β2–α2–β3 loop. Vaccination with peptide 1 elicited high titers of cross-reactive antibodies to VEGF, with potent neutralizing activity. Moreover, vaccination-induced antisera displayed strong angiostatic and tumor-growth-inhibiting properties in a preclinical mouse model for colorectal carcinoma, whereas antibodies raised with peptides exclusively encompassing the β5–turn–β6 loop (peptides 15 and 20) did not. Immunization with peptide 1 or 7 (murine analog of 1) in combination with the potent adjuvant raffinose fatty acid sulfate ester (RFASE) showed significant inhibition of tumor growth in the B16F10 murine melanoma model. Based on these data, we conclude that this vaccination technology, which is currently being investigated in a phase I clinical trial (NCT02237638), can potentially outperform currently applied anti-VEGF therapeutics.
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Wohlhueter, R. M., K. Parekh, V. Udhayakumar, S. Fang, and A. A. Lal. "Analysis of binding of monoclonal antibody to a malarial peptide by surface plasmon resonance biosensor and integrated rate equations." Journal of Immunology 153, no. 1 (July 1, 1994): 181–89. http://dx.doi.org/10.4049/jimmunol.153.1.181.
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Abstract Using biosensor technology and integrated rate equations, we have developed procedures to determine the kinetic parameters and equilibrium affinity constant of Ag-Ab interactions. The Ag used in these studies was a peptide that represents the major B cell epitope of the circumsporozoite protein of Plasmodium falciparum, a promising malaria vaccine candidate Ag. Measurements of association and dissociation rate constants of this peptide with the mAb 2A10 were determined by fitting integrated rate equations to binding data obtained with a BIAcore surface plasmon-resonance biosensor. We examined whether accurate estimates of initial velocity and final equilibrium levels of binding of Ab to peptides can be obtained using these methods, and whether kinetic rates and equilibrium constants obtained with systematic variation of the experimental parameters conform to a simple bimolecular model of binding. We found that initial velocity was approximately first order with respect to Ab concentration. When we used a series of four sensor cells with different peptides loads, however, we found that the initial velocity of binding appeared to be nearly independent of peptide concentration. Equilibrium analyses yielded dissociation constants of approximately 3 x 10(-7) M. Integrated rate treatment of biosensor data supports a critical examination of the assumptions on which the binding models are based and suggests a need to refine such models. Nevertheless, it provides a powerful quantitative tool for assessing the Ag-Ab binding reaction.
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Lu, Hongyan, Li Fang, Xiyan Wang, Dan Wu, Chunlei Liu, Xiaoting Liu, Ji Wang, Yawen Gao, and Weihong Min. "Structure-Activity Relationship of Pine Nut-Derived Peptides and Their Protective Effect on Nerve-Cell Mitochondria." Foods 11, no. 10 (May 15, 2022): 1428. http://dx.doi.org/10.3390/foods11101428.
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This study aimed to investigate the structure-activity relationship of the pine nut antioxidant peptide WYPGK and its derivative peptides, and to evaluate the protective effect of the latter on oxidative damage to mitochondrial structure and function in PC12 cells. Molecular docking revealed the derivative peptides WYFGK and WYSGK to have higher affinity to the active region of sirtuin 3 (SIRT3) (−6.08 kcal/mol and −5.87 kcal/mol, respectively), hence indicating that they are promising SIRT3 inducers and antioxidant factors. The derivative peptide WYSGK presented the highest ORAC value (5457.70 µmol TE/g), ABTS scavenging activity (70.05%), and Fe2+-chelating activity (81.70%), followed by WYPGK and WYFGK. Circular dichroism and nuclear magnetic resonance data suggested that the presence of 3-Ser in WYSGK increased its β-sheet content, and that the active hydrogen atoms produced chemical shifts. In H2O2-induced PC12 cells, WYSGK substantially reduced ROS and MDA levels, and increased ATP levels. Transmission electron microscopy and Seahorse Analyze assay proved the peptide WYSGK to significantly alleviate mitochondrial damage and respiratory dysfunction (p < 0.05), thereby implying that a study of structure-activity relationships of the peptides can possibly be an effective approach for the development of functional factors.
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Yoo, Jingon, Soobin Han, Bumjun Park, Sonam Sonwal, Munirah Alhammadi, Eunsu Kim, Sheik Aliya, et al. "Highly Specific Peptide-Mediated Cuvette-Form Localized Surface Plasmon Resonance (LSPR)-Based Fipronil Detection in Egg." Biosensors 12, no. 11 (October 23, 2022): 914. http://dx.doi.org/10.3390/bios12110914.
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Herein, we have developed peptide-coated gold nanoparticles (AuNPs) based on localized surface plasmon resonance (LSPR) sensor chips that can detect fipronil with high sensitivity and selectivity. The phage display technique has been exploited for the screening of highly specific fipronil-binding peptides for the selective detection of the molecule. LSPR sensor chips are fabricated initially by attaching uniformly synthesized AuNPs on the glass substrate, followed by the addition of screened peptides. The parameters, such as the peptide concentration of 20 µg mL−1 and the reaction time of 30 min, are further optimized to maximize the efficacy of the fabricated LSPR sensor chips. The sensing analysis is performed systematically under standard fipronil solutions and spike samples from eggs. The developed sensor has shown excellent sensitivity towards both standard solutions and spike samples with limit of detection (LOD) values of 0.01 ppb, respectively. Significantly, the developed LSPR sensor chips offer distinct features, such as a facile fabrication approach, on-site sensing, rapid analysis, cost-effectiveness, and the possibility of mass production, in which the chips can be effectively used as a promising and potential on-site detection tool for the estimation of fipronil.
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Son, Woo-Sung, Ji-Sun Kim, Hyung-Eun Kim, Sang-Ho Park, and Bong-Jin Lee. "Structural studies on the antimicrobial peptide Brevinin 1E by spectroscopic methods." Spectroscopy 17, no. 2-3 (2003): 127–38. http://dx.doi.org/10.1155/2003/650369.
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Skin extracts of frogs are a rich source of pharmacologically active peptides such as caeruleins, tachykinins, bradykinins, thyrotropin-releasing hormone, bombesin-like and opioid peptides. A large variety of antimicrobial peptides has been isolated fromRanaspecies. These peptides, grouped in several families on the basis of differing length and distinct activity, were found to have one structural motif in common: an intramolecular disulfide bridge located at the C-terminal end, forming a seven-member ring, which was designated ‘Rana box’. Brevinin 1E is a 24-residue antimicrobial peptide isolated from the skin of a frog,Rana brevipoda. This peptide shows a broad range of antimicrobial activity against prokaryotic cells but shows very much hemolytic activity against human red blood cells. The solution structure of Brevinin 1E was studied by using CD (circular dichroism) and NMR (nuclear magnetic resonance) spectroscopy. CD investigation revealed that Brevinin 1E adopts random structure in aqueous solution but adopts mainlyα-helical structure in TFE/water (6 : 4, v/v) solution. The three-dimensional structure of Brevinin 1E was determined in 60% TFE/water solution using homonuclear NMR spectroscopy. This peptide showed mainly anα-helical structure with amphipathic property. Its three-dimensional structure is similar to those of other peptides such as magainin, nigrocin and ranalexin. Therefore, Brevinin 1E can be classified into the family of antimicrobial peptides containing a single linearα-helix that interact with target microbial membrane, leading to cell death through disruption of membrane integrity.
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Larive, Cynthia K., Dimuthu Jayawickrama, and Laszlo Orfi. "Quantitative Analysis of Peptides with NMR Spectroscopy." Applied Spectroscopy 51, no. 10 (October 1997): 1531–36. http://dx.doi.org/10.1366/0003702971939055.
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The determination of peptide concentration with 1H nuclear magnetic resonance (NMR) spectroscopy using an internal standard or an external standard in a sealed glass capillary was investigated for three tyrosine-containing tripeptides. Trimethylsilylpropionic acid (TSP) and maleic acid were tested as external standards for quantitation by proton NMR. Although comparable results were obtained for either standard, the performance of maleic acid was found to be superior because of its better long-term stability in the sealed capillary. Loss of TSP from solution occurred over time due to adsorption onto the walls of the capillary, necessitating frequent recalibration against the primary standard, potassium acid phthalate (KHP). The peptide contents of solid peptides determined with 1H NMR are compared with those obtained from ultraviolet (UV) absorbance measurements of the tyrosine chromophore. The versatility of NMR for the quantitative analysis of peptides that do not contain an appropriate UV chromophore make it well-suited for the determination of peptide concentration in aggregation studies or for the preparation of solutions for high-throughput screening of biological activity.