Academic literature on the topic 'Linear peptides'
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Journal articles on the topic "Linear peptides"
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Lu, X., J. J. Deadman, J. A. Williams, V. V. Kakkar, and S. Rahman. "Synthetic RGD peptides derived from the adhesive domains of snake-venom proteins: evaluation as inhibitors of platelet aggregation." Biochemical Journal 296, no. 1 (November 15, 1993): 21–24. http://dx.doi.org/10.1042/bj2960021.
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Synthetic peptides based on the RGD domains of the potent platelet aggregation inhibitors kistrin and dendroaspin were generated. The 13-amino-acid peptides were synthesized as dicysteinyl linear and disulphide cyclic forms. In platelet-aggregation studies, the cyclic peptides showed 3-fold better inhibition than their linear equivalents and approx. 100-fold greater potency than synthetic linear RGDS peptides derived from fibronectin. An amino acid substitution, Asp10→Ala, in the kistrin-based peptide gave a 4-fold decrease in potency in the linear peptide, but produced a 2-fold elevation in the inhibitory activity of the cyclic form, generating a peptide of potency comparable with that of the parent protein.
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Maroto, Alicia, Ricard Boqué, Dany Jeanne Dit Fouque, and Antony Memboeuf. "Energy-Resolved Mass Spectrometry and Mid-Infrared Spectroscopy for Purity Assessment of a Synthetic Peptide Cyclised by Intramolecular Huisgen Click Chemistry." Methods and Protocols 7, no. 6 (December 2, 2024): 97. https://doi.org/10.3390/mps7060097.
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Cyclic peptides have higher stability and better properties as therapeutic agents than their linear peptide analogues. Consequently, intramolecular click chemistry is becoming an increasingly popular method for the synthesis of cyclic peptides from their isomeric linear peptides. However, assessing the purity of these cyclic peptides by mass spectrometry is a significant challenge, as the linear and cyclic peptides have identical masses. In this paper, we have evaluated the analytical capabilities of energy-resolved mass spectrometry (ER MS) and mid-infrared microscopy (IR) to address this challenge. On the one hand, mixtures of both peptides were subjected to collision-induced dissociation tandem mass spectrometry (CID MS/MS) experiments in an ion trap mass spectrometer at several excitation energies. Two different calibration models were used: a univariate model (at a single excitation voltage) and a multivariate model (using multiple excitation voltages). The multivariate model demonstrated slightly enhanced analytical performance, which can be attributed to more effective signal averaging when multiple excitation voltages are considered. On the other hand, IR microscopy was used for the quantification of the relative amount of linear peptide. This was achieved through univariate calibration, based on the absorbance of an alkyne band specific to the linear peptide, and through Partial Least Squares (PLS) multivariate calibration. The PLS calibration model demonstrated superior performance in comparison to univariate calibration, indicating that consideration of the full IR spectrum is preferable to focusing on the specific peak of the linear peptide. The advantage of IR microscopy is that it is linear across the entire working interval, from linear peptide molar ratios of 0 (equivalent to pure cyclic peptide) up to 1 (pure linear peptide). In contrast, the ER MS calibration models exhibited linearity only up to 0.3 linear peptide molar ratio. However, ER MS showed better performances in terms of the limit of detection, intermediate precision and the root-mean-square-error of calibration. Therefore, ER MS is the optimal choice for the detection and quantification of the lowest relative amounts of linear peptides.
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Ulapane, Kopec, and Siahaan. "Improving In Vivo Brain Delivery of Monoclonal Antibody Using Novel Cyclic Peptides." Pharmaceutics 11, no. 11 (October 31, 2019): 568. http://dx.doi.org/10.3390/pharmaceutics11110568.
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Many proteins can be used to treat brain diseases; however, the presence of the blood–brain barrier (BBB) creates an obstacle to delivering them into the brain. Previously, various molecules were delivered through the paracellular pathway of the BBB via its modulation, using ADTC5 and HAV6 peptides. This study goal was to design new cyclic peptides with N-to-C terminal cyclization for better plasma stability and modulation of the BBB. Cyclic HAVN1 and HAVN2 peptides were derived from a linear HAV6 peptide. Linear and N-to-C terminal cyclic ADTHAV peptides were designed by combining the sequences of ADTC5 and HAV6. These novel cyclic peptides were used to deliver an IRdye800CW-labeled IgG monoclonal antibody into the brain. Cyclic HAVN1 and HAVN2 peptides deliver IgG into the brain, while the parent linear HAV6 peptide does not. Cyclic and linear ADTHAV and ADTC5 peptides enhanced brain delivery of IgG mAb, in which cyclic ADTHAV peptide was better than linear ADTHAV (p = 0.07). Cyclic ADTHAV and ADTC5 influenced the distribution of IgG mAb in other organs while HAV6, HAVN1 and HAVN2 did not. In summary, the novel cyclic peptides are generally better BBB modulators than their linear counterparts for delivering IgG mAb into the brain.
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Amirkhanov, N. V., A. V. Bardasheva, V. N. Silnikov, and N. V. Tikunova. "Synthetic Antimicrobial Peptides. V. Histidine-containing Antifungal Peptides with a “Linear” Type of Amphipathicity." Биоорганическая химия 50, no. 4 (October 25, 2024): 538–55. http://dx.doi.org/10.31857/s0132342324040135.
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A number of histidine-containing synthetic antifungal peptides with a “linear” type of amphipathicity (SAMP LTA) (F2Hx, H10F2, H10, where x = 7, 10, 13 and 16) have been synthesized and studied. Biological screening of such histidine-containing peptides for their antifungal and hemolytic activity was carried out. It has been shown that the presented histidine-containing SAMP LTAs are capable of effectively inhibiting the growth of opportunistic fungi Candida albicans and have low hemolytic activity in most cases not exceeding 10% even at their relatively high concentration of 400 μM in a medium containing erythrocytes. The antifungal activity of the studied peptides increases with increasing histidine residues in their composition, reaching the maximum value for the histidine-containing peptide F2H16 (MIC50 = 1.0 µM). It has been shown that as the chain length of peptides increases, their hemolytic toxicity also increases. In terms of therapeutic significance, the optimal peptides in the presented series of peptides were F2H10 and F2H13, which have higher selectivity than the short or longer peptides F2H7 or F2H16. The therapeutic index (TI) for these peptides was 233, 247, 79 and 60, respectively. It has been shown that histidine-containing derivatives of peptides with phenylalanine residues at the N-terminus of the peptide (F2H10) are less effective compared to similar peptides (H10F2) containing phenylalanine residues at the C-terminus. Among all the studied peptides, the most active was the H10 peptide (MIC50 = 0.7 µM), which does not contain phenylalanine residues, which in its antifungal activity is not only more effective than all other histidine-containing peptides, including the F2H16 peptide with 16 histidine residues, but also 4-5 times more effective than the antifungal peptide P113 (MIC50 = 3.4 µM), a short active fragment of natural histatin 5, well known in the literature. Due to its relatively low hemolytic and high antifungal activity, the presented histidine-containing SAMP LTAs have relatively high TI values, more than 60. Among all the studied peptides, peptides H10 and P113 have minimal, almost zero, hemolytic activity. However, due to its higher antifungal activity, the selectivity of peptide H10 (TI 1400) exceeds that of peptide P113 (TI 340) by more than 4 times. Thus, peptide H10, due to its high antifungal activity, low hemolytic toxicity and, accordingly, high therapeutic significance, can be used as a promising antifungal peptide drug.
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Bowen, John, John Schneible, Kaitlyn Bacon, Collin Labar, Stefano Menegatti, and Balaji M. Rao. "Screening of Yeast Display Libraries of Enzymatically Treated Peptides to Discover Macrocyclic Peptide Ligands." International Journal of Molecular Sciences 22, no. 4 (February 5, 2021): 1634. http://dx.doi.org/10.3390/ijms22041634.
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We present the construction and screening of yeast display libraries of post-translationally modified peptides wherein site-selective enzymatic treatment of linear peptides is achieved using bacterial transglutaminase. To this end, we developed two alternative routes, namely (i) yeast display of linear peptides followed by treatment with recombinant transglutaminase in solution; or (ii) intracellular co-expression of linear peptides and transglutaminase to achieve peptide modification in the endoplasmic reticulum prior to yeast surface display. The efficiency of peptide modification was evaluated via orthogonal detection of epitope tags integrated in the yeast-displayed peptides by flow cytometry, and via comparative cleavage of putative cyclic vs. linear peptides by tobacco etch virus (TEV) protease. Subsequently, yeast display libraries of transglutaminase-treated peptides were screened to isolate binders to the N-terminal region of the Yes-Associated Protein (YAP) and its WW domains using magnetic selection and fluorescence activated cell sorting (FACS). The identified peptide cyclo[E-LYLAYPAH-K] featured a KD of 1.75 μM for YAP and 0.68 μM for the WW domains of YAP as well as high binding selectivity against albumin and lysozyme. These results demonstrate the usefulness of enzyme-mediated cyclization in screening combinatorial libraries to identify cyclic peptide binders.
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Appel, J. R., C. Pinilla, H. Niman, and R. Houghten. "Elucidation of discontinuous linear determinants in peptides." Journal of Immunology 144, no. 3 (February 1, 1990): 976–83. http://dx.doi.org/10.4049/jimmunol.144.3.976.
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Abstract Synthetic peptides, made by the method of simultaneous multiple peptide synthesis, were coupled to the protein carrier keyhole limpet hemocyanin and used to raise mAb. Omission and substitution analogs of the original peptides were tested by ELISA to characterize their reactivity with the respective mAb. Linear antigenic determinants were located for 18 different peptides by using omission analogs. The length of the antigenic determinants ranged from 2 to 8 residues, with an average of 6 residues. The three aromatic amino acids, phenylalanine, tryptophan, and tyrosine, the charged hydrophilic amino acids, aspartic acid and lysine, and the neutral amino acid alanine were found to occur most often in the determinant region of the peptides tested, whereas asparagine, cysteine, and histidine occurred the least often. Alanine substitution analogs provided more information than omission analogs by enabling the determination of which side chain groups of the antigenic determinant residues were not critical for binding to the mAb. Detailed, "fingerprint" information about the interaction of the peptide, GASPYPNLSNQQT, and its mAb was obtained by synthesizing a complete series of analogs with individual substitutions for each position of the antigenic determinant, PYPNLS, with the 19 other amino acids. These results suggest that, at the amino acid level, all antigenic determinants of synthetic peptides defined by mAb can be considered discontinuous linear determinants.
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Kelil, Abdellali, Emmanuel D. Levy, and Stephen W. Michnick. "Evolution of domain–peptide interactions to coadapt specificity and affinity to functional diversity." Proceedings of the National Academy of Sciences 113, no. 27 (June 17, 2016): E3862—E3871. http://dx.doi.org/10.1073/pnas.1518469113.
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Evolution of complexity in eukaryotic proteomes has arisen, in part, through emergence of modular independently folded domains mediating protein interactions via binding to short linear peptides in proteins. Over 30 years, structural properties and sequence preferences of these peptides have been extensively characterized. Less successful, however, were efforts to establish relationships between physicochemical properties and functions of domain–peptide interactions. To our knowledge, we have devised the first strategy to exhaustively explore the binding specificity of protein domain–peptide interactions. We applied the strategy to SH3 domains to determine the properties of their binding peptides starting from various experimental data. The strategy identified the majority (∼70%) of experimentally determined SH3 binding sites. We discovered mutual relationships among binding specificity, binding affinity, and structural properties and evolution of linear peptides. Remarkably, we found that these properties are also related to functional diversity, defined by depth of proteins within hierarchies of gene ontologies. Our results revealed that linear peptides evolved to coadapt specificity and affinity to functional diversity of domain–peptide interactions. Thus, domain–peptide interactions follow human-constructed gene ontologies, which suggest that our understanding of biological process hierarchies reflect the way chemical and thermodynamic properties of linear peptides and their interaction networks, in general, have evolved.
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Panayi, Tolis, Spiridoula Diavoli, Vicky Nicolaidou, Christos Papaneophytou, Christos Petrou, and Yiannis Sarigiannis. "Short-Chained Linear Scorpion Peptides: A Pool for Novel Antimicrobials." Antibiotics 13, no. 5 (May 5, 2024): 422. http://dx.doi.org/10.3390/antibiotics13050422.
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Scorpion venom peptides are generally classified into two main groups: the disulfide bridged peptides (DBPs), which usually target membrane-associated ion channels, and the non-disulfide bridged peptides (NDBPs), a smaller group with multifunctional properties. In the past decade, these peptides have gained interest because most of them display functions that include antimicrobial, anticancer, haemolytic, and anti-inflammatory activities. Our current study focuses on the short (9–19 amino acids) antimicrobial linear scorpion peptides. Most of these peptides display a net positive charge of 1 or 2, an isoelectric point at pH 9–10, a broad range of hydrophobicity, and a Grand Average of Hydropathy (GRAVY) Value ranging between −0.05 and 1.7. These features allow these peptides to be attracted toward the negatively charged phospholipid head groups of the lipid membranes of target cells, a force driven by electrostatic interactions. This review outlines the antimicrobial potential of short-chained linear scorpion venom peptides. Additionally, short linear scorpion peptides are in general more attractive for large-scale synthesis from a manufacturing point of view. The structural and functional diversity of these peptides represents a good starting point for the development of new peptide-based therapeutics.
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New, Roger R. C., Tam T. T. Bui, and Michal Bogus. "Binding Interactions of Peptide Aptamers." Molecules 25, no. 24 (December 21, 2020): 6055. http://dx.doi.org/10.3390/molecules25246055.
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Peptide aptamers are short amino acid chains that are capable of binding specifically to ligands in the same way as their much larger counterparts, antibodies. Ligands of therapeutic interest that can be targeted are other peptide chains or loops located on the surface of protein receptors (e.g., GCPR), which take part in cell-to-cell communications either directly or via the intermediary of hormones or signalling molecules. To confer on aptamers the same sort of conformational rigidity that characterises an antibody binding site, aptamers are often constructed in the form of cyclic peptides, on the assumption that this will encourage stronger binding interactions than would occur if the aptamers were simply linear chains. However, no formal studies have been conducted to confirm the hypothesis that linear peptides will engage in stronger binding interactions with cyclic peptides than with other linear peptides. In this study, the interaction of a model cyclic decamer with a series of linear peptide constructs was compared with that of a linear peptide with the same sequence, showing that the cyclic configuration does confer benefits by increasing the strength of binding.
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Pullen, Jeffrey K., George W. Anderson, Susan L. Welkos, and Arthur M. Friedlander. "Analysis of the Yersinia pestis V Protein for the Presence of Linear Antibody Epitopes." Infection and Immunity 66, no. 2 (February 1, 1998): 521–27. http://dx.doi.org/10.1128/iai.66.2.521-527.1998.
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ABSTRACT The V protein expressed by pathogenic Yersinia pestisis an important virulence factor and protective immunogen. The presence of linear B-cell epitopes in the V protein was investigated by using a series of 17 overlapping linear peptides. Groups of 10 mice were immunized intraperitoneally with 30 μg of each peptide on days 0, 30, and 60. Although the V protein-specific antibody response to the peptides varied, most of the peptides elicited high antibody titers. The immunized mice were challenged subcutaneously with 60 50% lethal doses (LD50) (1 LD50 = 1.9 CFU) of a virulent Y. pestis strain, CO92. None of the peptide-immunized mice survived challenge. The animals immunized with the V protein were completely protected against challenge. The immunogenicity of some of the V peptides was increased by conjugating them to keyhole limpet hemocyanin. Only one peptide (encompassing amino acids 1 to 30) conjugate demonstrated some protection; the others were not protective. In additional experiments, V peptides that reacted well with sera from mice surviving Y. pestis infection were combined and used to immunize mice. Although the combined peptides appeared to be very immunogenic, they were not protective. Therefore, the protective B-lymphocyte epitope(s) in the V protein is most likely to be conformational.
Dissertations / Theses on the topic "Linear peptides"
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Ng, Choi I.-teng Montserrat. "Solid-phase synthesis of 5-arylhistidine-containing peptides: from linear antimicrobial peptides to cyclic peptides derived from arylomycins and aciculitins." Doctoral thesis, Universitat de Girona, 2015. http://hdl.handle.net/10803/380739.
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The incorporation of unsymmetrical biaryl systems into peptide sequences is a strategy that can improve their biological activity. Due to the difficulty of arylating the 4(5}-position of the imidazole ring, this doctoral thesis was focused on the development of efficient methodologies for the solid-phase synthesis of 5-arylhistidine-containing antimicrobial undecapeptides through a Suzuki-Miyaura reaction under microwave irradiation. The extension of this protocol allowed the preparation of biaryl cyclic peptides of different ring sizes bearing a His-Phe or His-Tyr biaryl linkage. Then, it was developed a procedure for the total solid-phase synthesis of biaryl cyclic lipopeptides derived from arylomycins. These strategies were extended to the preparation of biaryl cyclic analogues of the marine bicyclic pptides aciculitins. In particular, it was achieved the synthesis of analogues of the northern and the southern hemispheres of aciculitins as well as biaryl bicyclic peptides incorporating a Phe-Phe, a Phe-Tyr, a His-Tyr or a Tyr-Tyr biaryl bridgeLa incorporació de sistemes biarílics asimiètrics en seqüències peptídiques es considera un enfocament útil per a millorar l'activitat biològica de pèptids. Tenint en compte la dificultat d'arilar la posició 4 (5) de l'anell d'imidazole, aquesta tesi doctoral es centra en el desenvolupament de noves estratègies eficients per a la preparació en fase sòlida d'undecapèptids antimicrobians contenint una 5-arilhistidina a través d'una reacció de Suzuki-Miyaura sota irradiació microones. L'extensió d'aquesta metodologia ha permès la síntesi de pèptids biarílics cíclics de diferents mides que incorporen un enllaç His-Phe 0 His-Tyr. Posteriorment, s'ha desenvolupat un procediment per la síntesi total en fase sòlida de lipopèptids biarílics cíclics derivats de les arilomicines. Les estratègies anteriors s'han estès a la preparació de compostos biarílics anàlegs dels pèptids bicíclics marins aciculitines. Concretament, s'ha preparat anàlegs dels hemisferis nord i sud de las aciculitines així com pèptids biarílics bicíclics que incorporen un pont Phe-Phe, Phe-Tyr, Tyr-His 0 Tyr-Tyr.
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Oglęcka, Kamila. "Biophysical studies of membrane interacting peptides derived from viral and Prion proteins." Doctoral thesis, Stockholm University, Department of Biochemistry and Biophysics, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-7109.
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This thesis focuses on peptides derived from the Prion, Doppel and Influenza haemagglutinin proteins in the context of bilayer interactions with model membranes and live cells. The studies involve spectroscopic techniques like fluorescence, fluorescence correlation spectroscopy (FCS), circular and linear dichroism (CD and LD), confocal fluorescence microscopy and NMR.
The peptides derived from the Prion and Doppel proteins combined with their subsequent nuclear localization-like sequences, makes them resemble cell-penetrating peptides (CPPs). mPrPp(1-28), corresponding to the first 28 amino acids of the mouse PrP, was shown to translocate across cell membranes, concomitantly causing cell toxicity. Its bovine counterpart bPrPp(1-30) was demonstrated to enter live cells, with and without cargo, mainly via macropinocytosis. The mPrPp(23-50) peptide sequence overlaps with mPrPp(1-28) sharing the KKRPKP sequence believed to encompass the driving force behind translocation. mPrPp(23-50) was however found unable to cross over cell membranes and had virtually no perturbing effects on membranes.
mDplp(1-30), corresponding of the first 30 N-terminal amino acids of the Doppel protein, was demonstrated to be almost as membrane perturbing as melittin. NMR experiments in bicelles implied a transmembrane configuration of its alpha-helix, which was corroborated by LD in vesicle bilayers. The positioning of the induced alpha-helix in transportan was found to be more parallel to the bilayer surface in the same model system.
Positioning of the native Influenza derived fusion peptide in bilayers showed no pH dependence. The glutamic acid enriched variant however, changed its insertion angle from 70 deg to a magic angle alignment relative the membrane normal upon a pH drop from 7.4 to 5.0. Concomitantly, the alpha-helical content dramatically rose from 18% to 52% in partly anionic membranes, while the native peptide’s helicity increased only from 39% to 44% in the same conditions.
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Mozaffari, Saghar. "Amphiphilic Cell-Penetrating Hybrid Cyclic-Linear Peptides as a Drug Delivery System." Chapman University Digital Commons, 2019. https://digitalcommons.chapman.edu/pharmaceutical_sciences_dissertations/2.
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A number of cyclic peptides containing a positively charged ring composed of arginine residues attached to hydrophobic tail made of tryptophan residues through a lysine linker namely [R5K]W5, [R6K]W5, [R5K]W6, [R7K]W5, [R5K]W7, [R6K]W6, and [R7K]W7 were synthesized and evaluated as molecular transporters. The peptides were evaluated for their ability to deliver, fluorescence-labeled cell-impermeable negatively charged phosphopeptide (F′-GpYEEI), and fluorescent labeled anti-HIV drugs (F′-FTC and F′-d4T). The results indicated that the presence of positively charged arginine residues on the ring and hydrophobic tryptophan residues in a sequential linear outside the ring was an optimal approach to improve the intracellular uptake of cargo molecules through non-covalent interactions. Some of these peptides were also evaluated for their efficiency for intracellular delivery of siRNA to triple-negative breast cancer cell lines in the presence and absence of 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE). [R6K]W6 and [R5K]W5 were found to be very efficient in the delivery of siRNA. Furthermore, co-formulation of peptides with lipid DOPE significantly enhanced the efficiency of siRNA delivery compared to peptide alone. Silencing of kinesin spindle protein (KSP) and Janus kinase 2 (JAK2) was evaluated in MDA-MB-231 cells in the presence of the peptides. The addition of DOPE significantly enhanced the silencing efficiency for all selected peptides.
A chemotherapeutic drug, doxorubicin (Dox) was covalently conjugated to the cyclic peptide [R5K]W7A and linear peptide R5KW7A, and the biological activity was evaluated in cell-based assays. Comparative antiproliferative assays between covalently conjugated peptide-Dox and the corresponding noncovalent physical mixtures of the peptides and Dox were performed. The conjugation of Dox with cyclic [R5K]W7A-Dox exhibited similar antiproliferative activity compared to Dox alone after 72 h incubation time in all cancer cell lines, such as leukemia, ovarian and gastric cancer cells. However, [R5K]W7A-Dox significantly reduced the cell cytotoxicity in normal cell lines such as normal heart muscle and normal kidney cells after 72 h when compared with Dox alone. These results revealed that this cyclic peptide prodrug can be used as a potential candidate for the treatment of cancer cells with reduced side effects against normal cells in the body.
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Ye, Guofeng. "Applications of linear and cyclic peptides as enzyme inhibitors and molecular transporters /." View online ; access limited to URI, 2008. http://0-digitalcommons.uri.edu.helin.uri.edu/dissertations/AAI3346862.
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Eißmann, Frank. "Linear und tetragonal strukturierte Tektone mit peripheren Aminosäure- und Peptidhaftgruppen." Doctoral thesis, Technische Universitaet Bergakademie Freiberg Universitaetsbibliothek "Georgius Agricola", 2011. http://nbn-resolving.de/urn:nbn:de:bsz:105-qucosa-76997.
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Im Rahmen der vorliegenden Arbeit gelang die Synthese einer Reihe von neuartigen linear oder tetragonal präorganisierten tektonischen Verbindungen mit peripheren Haftgruppen, bestehend aus den natürlich vorkommenden Aminosäuren Glycin und L-Alanin oder kurzen Peptiden. Neben der Synthese stand die strukturelle Charakterisierung der Zielsubstanzen und Vorstufen im Vordergrund, wobei die Aufklärung der Kristallstrukturen einer Zielverbindung und elf relevanter Vorstufen gelang, deren Packungsstrukturen überwiegend durch N–H•••O-Interaktionen determiniert sind. Ergänzend konnten Informationen bezüglich der von den Haftgruppen gebildeten Strukturmotive im Festkörper mittels FT-IR-Spektroskopie abgeleitet werden. Die Auswertung konformationssensitiver 1H- und 13C-NMR-Signale zeigt, dass Aminosäurereste innerhalb identischer Haftgruppen in Lösung jeweils in derselben Konformation vorliegen. Fluoreszenzspektroskopische Untersuchungen der hergestellten Zielverbindungen lassen interessante Anwendungen auf dem Gebiet der Sensorik erwarten.
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Lao, Ying. "Chromatographic Behavior of Peptides Containing Oxidized Methionine in Reversed-phase Chromatography: Application to Cyclolinopeptides in Flaxseed Oil and Linear Tryptic Peptides." Elsevier, 2012. http://hdl.handle.net/1993/30202.
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The thesis consists of two parts targeting the characterization of chromatographic behavior of linear tryptic and cyclic peptides containing oxidized methionine (Met) in reversed-phased chromatography. The retention order of methionine-containing peptide analogues was observed to be the same in both studies: Met oxide < Met dioxide < Met. For linear tryptic peptides, the magnitude of the retention time shift may vary dramatically: from –9 % to +0.36 % acetonitrile. Particularly, large negative retention time shifts are found mostly associated with methionine being in the hydrophobic face of an amphipathic helix. Contrary to previously reported observations, I demonstrate for the first time that methionine oxidation may increase peptide hydrophobicity, this occurs only when methionine is in the N3 position of the N-capping stabilization motif preceding an amphipathic helix. In the second study, the effect of peak splitting was observed for some Met oxide-containing cyclolinopeptides, which most likely appear due to diastereomerization.
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Welsh, Daniel J. "Dendritic and self-assembling linear RGD peptides : from integrin binding to responsive hydrogels." Thesis, University of York, 2011. http://etheses.whiterose.ac.uk/2350/.
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Several studies exist in the literature which utilise either dendritic (covalent) or self-assembling (non-covalent) strategies to achieve multivalent binding to a biological target, but rarely are the two explored together. Herein, we compare and contrast dendritic and self-assembling approaches to organise a multivalent array of ligands to bind the protein, integrin αvβ3. In the first instance, linear RGD (Arg-Gly-Asp) peptides were covalently attached to first and second generation dendritic frameworks, and a positive (monovalent) and negative control were synthesised. A fluorescence polarisation (FP) competition assay was used to quantify the binding. The first generation dendron (2.16) was the most effective binder, with an EC50 of 125 μM (375 μM per peptide unit); significantly better than the monovalent ligand (2.19), the binding of which could not be quantified in our assay, even at 1 mM concentration; whilst the second generation dendron (2.17) was somewhat less effective, indicating that there is an optimum number of ligands that can be displayed before the multiple ligand array becomes disadvantageous to the binding. To explore the non-covalent approach, the linear RGD peptide was conjugated to either a single hydrophobic C12 aliphatic chain (3.2), an aromatic pyrene (3.4), a C22 aliphatic chain (3.6), or two C12 aliphatic chains (3.18), which gave rise to amphiphilic peptides which were able to self-assemble to differing degrees and into markedly different morphologies, as shown by a Nile Red encapsulation study and TEM imaging. Spherical micelles were formed by amphiphiles 3.2 and 3.4, whereas 3.6 and 3.18 produced cylindrical, rod-like micelles. Compounds 3.2 and 3.4 were the most effective integrin binders at concentrations of 200 μM and 110 μM, respectively, whilst 3.6 and 3.18 failed to produce a quantifiable binding concentration. The results therefore show that not only does the micellar self-assembly approach yield multivalent ligand displays with improved efficiency of binding compared with the dendritic method, but the morphology of the self-assembled system can also be detrimental to the recognition of the protein, at least in our FP assay and using purified integrin in solution. Finally, we report on a family of linear RGD peptide conjugate hydrogelators. Of particular interest was the novel bolaamphiphile C12-[urea-RGD]2 (4.4), comprised of linear RGD peptide head groups connected to either end of a hydrophobic C12 aliphatic chain via urea linkages. The molecule undergoes thermoreversible chiral self-assembly in water and generates a sample-spanning nanofibrous gel network, as determined by circular dichroism spectroscopy and TEM/SEM imaging, respectively. Gels were formed at a minimum gel concentration (MGC) of 0.06 wt % (0.6 mg/ml, 0.5 mM), one of the lowest MGCs reported and represents a “super” hydrogel. We report on its responsiveness (breakdown) towards charge dense basic anions such as phosphate and acetate, but its stability in the presence of more charge diffuse halide and nitrate anions. Furthermore, we demonstrate the passive diffusion of encapsulated low MW additives out of the gel phase, whereas high MW, protein-sized molecules remain trapped within the fibrous network.
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Rella, Maria Rosaria. "Dioxiranes and bioactive molecules : selective oxyfunctionalization of vitamin D synthons, linear peptides, and cyclosporins." View abstract/electronic edition; access limited to Brown University users, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3318352.
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Lizio, Maria Giovanna. "Exploring peptide foldamer-membrane interactions using optical spectroscopic techniques." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/exploring-peptide-foldamermembrane-interactions-using-optical-spectroscopic-techniques(694db937-1fb6-430d-98af-ba147c857e6e).html.
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The evolution of drug resistant pathogens creates the need for the introduction of new antimicrobial drugs. Peptaibols, a class of naturally occurring peptides, contain large amounts of alpha aminoisobutyric acid (Aib). They are known to exhibit their antimicrobial activity by perturbing the membranes of pathogens. However, a comprehensive model of action for these peptides has not yet been identified. Aib residues support the formation of 310-helix conformation and it is thought that this secondary structure is important for their antimicrobial activity. It is possible to design small synthetic peptides, known as foldamers, endowed with specific properties; in particular, Aib-rich foldamers are used as a model for the understanding of the folding and membrane interaction of the naturally occurring species. The aim of this thesis is to investigate the conformational preference of monodisperse Aib-oligomers as well as understanding their interaction with bilayer membranes. A large set of spectroscopic techniques have been used to establish the conformation of Aib-rich foldamers both in solution and when bound to membranes. In particular: Raman, Raman Optical Activity (ROA), Infrared (IR), Vibrational Circular Dichroism (VCD), Linear Dichroism (LD) and Neutron Scattering (NR) were employed to provide new structural insights. These vibrational analysis (VA) and vibrational optical analysis (VOA) investigations in solution were focused on the identification of spectral features for 310-helix conformation, particularly with Raman and Raman Optical Activity spectroscopies. Spectroscopic markers for this conformation in the amide I region were successfully identified. Moreover, it is known that chiral Aib-rich peptides can show a right or left handed screw-preference based on the primary sequence. VOA studies successfully distinguished between peptides with opposite helicity. VCD, ROA, LD and NR of Aib-foldamers bound to membranes were shown to be useful for identification of conformational preferences of the peptides within the membrane as well as for determining their orientation in the bilayer, and ultimately the effect of the peptides on the membrane structure.
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Cao, Yichen. "APPLICATION OF LINEAR FREE ENERGY RELATIONSHIPS IN THE PREDICTION OF TRIGLYCERIDE/WATER PARTITION COEFFICIENTS AND LIPID BILAYER PERMEABILITY COEFFICIENTS OF SMALL ORGANIC MOLECULES AND PEPTIDES." UKnowledge, 2008. http://uknowledge.uky.edu/gradschool_diss/655.
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Computational methods such as linear free energy relationships (LFERs) offer a useful high-throughput solution to quickly evaluate drug developability, e.g. membrane permeability, organic solvent/water partition coefficients, and solubility. LFERs typically assume the contribution of structural components/functional groups to the overall properties of a given molecule to be constant and independent. This dissertation describes a series of studies in which linear free energy relationships were developed to predict solvation of small organic molecules in lipid formulations, specifically, triglyceride containing solvents and phospholipid-based liposomes. The formation of intermolecular HBs in triglyceride solvents (homogenous with H-bond accepting ability) and intramolecular HBs within the bilayer barrier domain (hydrocarbon-like) proved to be the major factors to consider in developing LFERs to account for the increased oil/water partition coefficients and enhanced bilayer permeability of small organic molecules.
The triglyceride solvent/water partition coefficients of a series of model compounds varying in polarity and H-bond donating/accepting capability were used to establish a correlation between the solvent descriptors and the ester concentration in these solvents using the Abraham LFER approach. The LFER analyses showed that the descriptors representing the polarizability and H-bond basicity of the solvents vary systematically with the ester concentration.
A fragment-based LFER to predict membrane permeability or 1,9- decadiene/water partition coefficients of small organic molecules including small peptides was systematically constructed using a total of 47 compounds. Significant nonadditivity was observed in peptides in that the contribution of the peptide backbone amide to the apparent transfer free energy from water into the bilayer barrier domain is considerably smaller than that of a “well-isolated” amide and greatly affected by adjacent polar substituents on the C-termini.
In order to explain the phenomenon of nonadditivity, the formation of intramolecular HBs and inductive effects of neighboring polar groups on backbone amide, were investigated using FTIR and MD simulations. Both spectroscopic and computational results provided supportive evidence for the hypothesis that the formation of intramolecular HBs in peptides is the main reason for the observed nonadditivity of Δ(ΔG°)-CONH-. The MD simulation results showed that the inductive effect of neighboring groups is not as important as the effect of intramolecular HBs.
Books on the topic "Linear peptides"
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Chan, W., and Peter White, eds. Fmoc Solid Phase Peptide Synthesis. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780199637256.001.0001.
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In the years since the publication of Atherton and Sheppard's volume, the technique of Fmoc solid-phase peptide synthesis has matured considerably and is now the standard approach for the routine production of peptides. The basic problems outstanding at the time of publication of this earlier work have now been, for the most part, solved. As a result, innovators in the field have focussed their efforts to develop methodologies and chemistry for the synthesis of more complex structures. The focus of this new volume is much broader, and covers not only the essential procedures for the production of linear peptides but also more advanced techniques for preparing cyclic, side-chain modified, phospho- and glycopeptides. Many other methods also deserving attention have been included: convergent peptide synthesis; peptide-protein conjugation; chemoselective ligation; and chemoselective purification. The difficult preparation of cysteine and methionine-containing peptides is also covered, as well as methods for overcoming aggregation during peptide chain assembly and a survey of available automated instrumentation.
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Leelasvatanakij, Leena. Comparison and optimization of chromatographic conditions for separation of cyclic dynorphin A analogues from linear byproducts. 1993.
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Burton, Derek, and Margaret Burton. Food procurement and processing. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198785552.003.0004.
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Fish display a wide range of adaptations of the mouth and pharynx for specific feeding patterns including planktivory, fin-biting, picking and scraping. Appetite control is complex, involving stimulatory and inhibitory hormones. The gut has a linear plan similar to other vertebrates but with considerable variation between taxa, and a stomach may be absent. Many bony fish possess pyloric caeca, containing digestive enzymes, and may increase surface area for digestion. In chondrichthyes (sharks, etc.), a ‘spiral valve’ increases surface area of the intestine. Smooth muscle contractions in the gut wall pass food along the tract under control of food pressure, the autonomic nervous system and specific peptides. Digestion by hydrolytic enzymes, and absorption occur in the intestine, monomers produced being absorbed mainly through transcellular routes, involving enterocytes, into the blood of the hepatic portal vein to the liver. Dietary requirements and nutrition are discussed.
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Voll, Reinhard E., and Barbara M. Bröker. Innate vs acquired immunity. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0048.
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The innate and the adaptive immune system efficiently cooperate to protect us from infections. The ancient innate immune system, dating back to the first multicellular organisms, utilizes phagocytic cells, soluble antimicrobial peptides, and the complement system for an immediate line of defence against pathogens. Using a limited number of germline-encoded pattern recognition receptors including the Toll-like, RIG-1-like, and NOD-like receptors, the innate immune system recognizes so-called pathogen-associated molecular patterns (PAMPs). PAMPs are specific for groups of related microorganisms and represent highly conserved, mostly non-protein molecules essential for the pathogens' life cycles. Hence, escape mutants strongly reduce the pathogen's fitness. An important task of the innate immune system is to distinguish between harmless antigens and potentially dangerous pathogens. Ideally, innate immune cells should activate the adaptive immune cells only in the case of invading pathogens. The evolutionarily rather new adaptive immune system, which can be found in jawed fish and higher vertebrates, needs several days to mount an efficient response upon its first encounter with a certain pathogen. As soon as antigen-specific lymphocyte clones have been expanded, they powerfully fight the pathogen. Importantly, memory lymphocytes can often protect us from reinfections. During the development of T and B lymphocytes, many millions of different receptors are generated by somatic recombination and hypermutation of gene segments making up the antigen receptors. This process carries the inherent risk of autoimmunity, causing most inflammatory rheumatic diseases. In contrast, inadequate activation of the innate immune system, especially activation of the inflammasomes, may cause autoinflammatory syndromes.
Book chapters on the topic "Linear peptides"
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Calmes, Monique, Jacques Daunis, Dominique David, René Lazaro, Driss Benamar, and Frédéric Heitz. "New linear gramicidin A analogue." In Peptides 1992, 587–88. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1470-7_265.
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Jaspers, H., P. Verheyden, and G. Van Binst. "Low temperature conformation of linear and cyclic peptide analogs." In Peptides, 305–6. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2264-1_110.
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Lehrman, S. R., M. E. Lund, K. A. Farley, and W. M. Moseley. "Stable helicity in linear growth hormone releasing factor analogs." In Peptides, 802–3. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-0683-2_267.
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Reissmann, S. "New potent selective linear and cyclic bradykinin agonists and antagonists." In Peptides, 550–52. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-0683-2_182.
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Felix, Arthur M., Ching-Tso Wang, Edgar Heimer, Alain Fournier, David R. Bolin, Mushtaq Ahmad, Theodore Lambros, Thomas Mowles, and Lindy Miller. "Synthesis and biological activity of novel linear and cyclic GRF analogs." In Peptides, 465–67. Dordrecht: Springer Netherlands, 1988. http://dx.doi.org/10.1007/978-94-010-9595-2_137.
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Stura, E. A., D. C. Kaslow, and A. C. Satterthwait. "Crystallization of a neutralizing malaria immunoglobulin with linear and cyclic peptides." In Peptides, 817–19. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-0683-2_274.
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Vosekalna, I., B. Gyurcsik, and E. Larsen. "Copper(II) complexes of linear and cyclic hexapeptides." In Peptides 1994, 539–40. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-1468-4_244.
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Reissmann, S., L. F. Pineda, L. Seyfarth, G. Greiner, B. Schölkens, G. Vietinghoff, and I. Paegelow. "New linear and cyclic bradykinin agonists and antagonists." In Peptides 1994, 619–20. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-1468-4_282.
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Ben Ayad, Ahmed, Driss Ben Amar, Nicole Van Mau, and Frédéric Heitz. "Interactions between lipids and linear gramicidins: Influence of the chemical structure of the peptide." In Peptides, 165–67. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2264-1_58.
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Ye, Yun-Hua, Hai-Bo Xie, Gui-Ling Tian, Chong-Xu Fan, Ying Liu, Yong-Jun Lu, and Gui-Yang Xie. "Application of DEPBT for synthesis of linear and cyclic heptapeptide from a Caryophyllaceae plant." In Peptides, 68–70. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-010-9069-8_18.
Full textConference papers on the topic "Linear peptides"
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Demadis, Konstantinos D. "Bioinspired “Green” Scale Inhibitors for Mitigation of Silica Scales." In CORROSION 2016, 1–10. NACE International, 2016. https://doi.org/10.5006/c2016-07332.
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Abstract Marine biological systems annually process 6.7 gigatons of “Si”. Diatoms and other marine organisms stabilize high concentrations of “soluble silica” (~ 19-340 mM, depending on the diatom species) prior to biosilica formation. It is believed that Nature can achieve that by the intervention of, unknown as of yet, biopolymers that act as stabilizers of silicic acid. We have been active in devising chemical approaches to mimic the above phenomenon. Thus, in a bioinspired approach, we have used several non-toxic, “green” polyelectrolytes that possess “active” chemical moieties, capable of stabilizing silicic acid, for a prolonged time period. These additives include either neutral (uncharged or zwitterionic) or charged (cationic) polymers that stabilize two soluble forms of “Si”, silicic and disilicic acids. These polymers include amine-terminated dendrimers, amine-containing linear polymers, polyethylene glycol (PEG) neutral polymers, co-polymers, phosphonium end-grafted PEG polymers, histidine-grafted polyacrylates and carefully designed peptides. These polymers not only reduce the rate of silicic acid condensation, but also influence silica particle growth. Possible mechanisms for silicic acid stabilization by certain examples are discussed.
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Obeyesekere, Nihal, and Thusitha Wickramarachchi. "Transition from Combinatorial Chemistry to Present Day Robotics in Product Development for Oil Field Chemicals." In MECC 2023, 1–15. AMPP, 2023. https://doi.org/10.5006/mecc2023-20245.
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Abstract In this paper, the slow evolution of combinatorial chemistry from its dawn in 1980’s to today’s oil field product development is discussed. Combinatorial chemistry comprises chemical synthetic methods that make it possible to prepare a vast number of compounds in a single process. These compound libraries can be made as mixtures, sets of individual compounds or chemical structures generated by computer software. This phenomenon was first invented by Arpad Furka (Lorand University, Budapest) in 1982. He described the principle of it, the combinatorial synthesis and a deconvolution procedure. The methodology was first used in drug discovery using a wide range of linear or wide range of macrocyclic chemical molecules: peptides, non-peptide oligomers, peptidomimetics, small-molecules, and natural product-like organic molecules. However, handling vast amounts of data and extremely small chemical recovery were a very difficult endeavor. To avoid this problem and help to refine the size of the chemical libraries, various software programs were utilized. This was achieved by utilizing a tool known as Design of Experiment (DoE). In this paper, the high throughput product screening to identify corrosion inhibitors was performed by utilizing critical micelle concentration (CMC). CMC was used to differentiate performance of libraries of chemical blends. Combinatorial synthesis (or blends) and combinatorial screening were performed by utilizing robotics methodologies. The corrosion inhibitor formulations predicted by DoE were built out by using combinatorial chemical methods and the arrays of chemical formulations were screened by utilizing high throughput robotics, using CMC as the selection guide. To validate the concept, several known corrosion inhibitor formulas were selected to optimize their efficacy. Each formula contained several active ingredients and a solvent package. These raw materials were blended in random but in a control, manner using combinatorial methodologies. After formulation of a vast array of formulation by using Design Expert solvent package. These raw materials were blended in random but in a control, manner using combinatorial methodologies. After formulation of a vast array of formulation by using Design Expert (DE) software, the products were screened for by CMC using automated surface tension workstation. Several formulations with lower CMC than the reference products were selected. The selected corrosion inhibitor formulations were identified and blended in larger scales. The efficacy of these products was tested by classical laboratory testing methods such as rotating cylinder electrode (RCE) and rotating cage autoclave (RCA) to determine their performance as anti-corrosion agents. These tests were performed against the original reference corrosion inhibitor. The testing indicated that several corrosion inhibitor formulations outperform the original blend thus validating the proof of concept.
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Sarigiannis, Yiannis, Constantinos Avraamides, Spiridoula Diavoli, Ariana Robertson, Manos Vlasiou, Elena Mourelatou, and Christos Petrou. "Linear Scorpion Peptides: An unexplored pool for peptide hydrogels." In 1st International Electronic Conference on Toxins. Basel, Switzerland: MDPI, 2021. http://dx.doi.org/10.3390/iect2021-09124.
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Reissmann, Siegmund, Sebastian Kuenzel, Georg Greiner, Inge Agricola, David Pretzel, and Matthias Schmidt. "Transition metal complexes of linear and cyclic peptides and pseudopeptides." In IXth Conference Biologically Active Peptides. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2005. http://dx.doi.org/10.1135/css200508068.
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Silva, Adriana F., Marcelo D. T. Torres, Leandro S. Silva, Flávio L. Alves, Ana A. S. Pinheiro, Antonio Miranda, Margareth L. Capurro, and Vani X. Oliveira Jr. "Linear Peptides Related to Angiotensin II with Antiplasmodial Activity." In The 24th American Peptide Symposium. Prompt Scientific Publishing, 2015. http://dx.doi.org/10.17952/24aps.2015.064.
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Streuli, Alessandro, Lara Šošić, Marta Paolucci, Agathe Duda, Klaus Eyer, Pål Johansen, and Christian Steuer. "Linear peptides as IgG-epitope mimetic for allergic immunotherapy against birch pollen." In 37th European Peptide Symposium, 1155. The European Peptide Society, 2024. http://dx.doi.org/10.17952/37eps.2024.p1155.
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Kunčarová, Pavla, Elšan Nazarov, John Howl, and Jiřina Slaninová. "Full biological characterization of two linear vasopressin analogues – [Phaa,D-Tyr(Et)2,Aib4,Arg6,Tyr(NH2)9]AVP and [Phaa,D-Tyr(Et)2,Arg6,Aib7,Tyr(NH2)9]AVP." In VIth Conference Biologically Active Peptides. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 1999. http://dx.doi.org/10.1135/css199903041.
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Du, Zhenjiao, Donghai Wang, and Yonghui Li. "Comprehensive Evaluation and Comparison of Machine Learning Methods in QSAR Modeling of Antioxidant Tripeptides." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/oppq6042.
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Due to their multiple beneficial effects, antioxidant peptides have attracted increasing interest. Currently, the identification of antioxidative peptides and screening bioactive peptides are based on wet-chemistry methods which are time-consuming and highly rely on many advanced instruments and trained personnel. Compared to wet chemistry methods for preparation and screening bioactive peptides, quantitative structure-activity relationship (QSAR) analysis as an in silicon method can be more efficient and cost-effective. However, model performance of QSAR studies on antioxidant peptides was still poor due to the difficulties from data set division to regression methods. The objective of this study was to compare most popular and promising machine learning methods for antioxidant activity modeling and screening of tripeptides and identify the critical amino acid features that determine the antioxidant activity. We adopted 553 numerical indices of amino acids to characterize 130 tripeptides with known antioxidant activity from published literatures, and then six advanced feature selection methods plus pairwise correlation were used to screen the most important indices for antioxidant activity and model building. Fourteen machine learning methods were used to build models based on the six feature selection methods, respectively. Among the 84 models, the best model with R2Test of 0.847 and MSETest of 0.393 for tripeptide antioxidants was obtained based on FI-RFR plus XGB. Based on the predicted antioxidant values of 7870 unknown tripeptides, the potential high antioxidant activity tripeptides all have a tyrosine, tryptophan, or cysteine at the C-terminal position. In addition, results also showed that C-terminal amino acids contributed the most to antioxidant activity, while the central amino acid contributed the least. Non-linear regression methods were more suitable for QSAR study on antioxidant activity.
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Emerine, R., J. Jacob, O. Akiode, S. Idell, G. Florova, and A. A. Komissarov. "Short Linear Peptides Protect Fibrinolysis From Inactivation With Up To 8-fold PAI-1 In Vitro." In American Thoracic Society 2024 International Conference, May 17-22, 2024 - San Diego, CA. American Thoracic Society, 2024. http://dx.doi.org/10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a2504.
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Whiting, Amanda L., Francisco Aguilar-Alonso, Joseph J. Mitala, and Federico Bernal. "Abstract 5235: Affecting activity of the linear ubiquitin chain assembly complex (LUBAC) with stapled alpha-helical peptides." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-5235.
Full textReports on the topic "Linear peptides"
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Altstein, Miriam, and Ronald Nachman. Rationally designed insect neuropeptide agonists and antagonists: application for the characterization of the pyrokinin/Pban mechanisms of action in insects. United States Department of Agriculture, October 2006. http://dx.doi.org/10.32747/2006.7587235.bard.
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The general objective of this BARD project focused on rationally designed insect neuropeptide (NP) agonists and antagonists, their application for the characterization of the mechanisms of action of the pyrokinin/PBAN (PK-PBAN) family and the development of biostable, bioavailable versions that can provide the basis for development of novel, environmentally-friendly pest insect control agents. The specific objectives of the study, as originally proposed, were to: (i) Test stimulatory potencies of rationally designed backbone cyclic (BBC) peptides on pheromonotropic, melanotropic, myotropic and pupariation activities; (ii) Test the inhibitory potencies of the BBC compounds on the above activities evoked either by synthetic peptides (PBAN, LPK, myotropin and pheromonotropin) or by the natural endogenous mechanism; (iii) Determine the bioavailability of the most potent BBC compounds that will be found in (ii); (iv) Design, synthesize and examine novel PK/PBAN analogs with enhanced bioavailability and receptor binding; (v) Design and synthesize ‘magic bullet’ analogs and examine their ability to selectively kill cells expressing the PK/PBAN receptor. To achieve these goals the agonistic and antagonistic activities/properties of rationally designed linear and BBC neuropeptide (NP) were thoroughly studied and the information obtained was further used for the design and synthesis of improved compounds toward the design of an insecticide prototype. The study revealed important information on the structure activity relationship (SAR) of agonistic/antagonistic peptides, including definitive identification of the orientation of the Pro residue as trans for agonist activity in 4 PK/PBANbioassays (pheromonotropic, pupariation, melanotropic, & hindgut contractile) and a PK-related CAP₂b bioassay (diuretic); indications that led to the identification of a novel scaffold to develop biostbiostable, bioavailable peptidomimetic PK/PBANagonists/antagonists. The work led to the development of an arsenal of PK/PBAN antagonists with a variety of selectivity profiles; whether between different PKbioassays, or within the same bioassay between different natural elicitors. Examples include selective and non-selective BBC and novel amphiphilic PK pheromonotropic and melanotropic antagonists some of which are capable of penetrating the moth cuticle in efficacious quantities. One of the latter analog group demonstrated unprecedented versatility in its ability to antagonize a broad spectrum of pheromonotropic elicitors. A novel, transPro mimetic motif was proposed & used to develop a strong, selective PK agonist of the melanotropic bioassay in moths. The first antagonist (pure) of PK-related CAP₂b diuresis in flies was developed using a cisPro mimetic motif; an indication that while a transPro orientation is associated with receptor agonism, a cisPro orientation is linked with an antagonist interaction. A novel, biostablePK analog, incorporating β-amino acids at key peptidase-susceptible sites, exhibited in vivo pheromonotropic activity that by far exceeded that of PBAN when applied topically. Direct analysis of neural tissue by state-of-the-art MALDI-TOF/TOF mass spectrometry was used to identify specific PK/PK-related peptides native to eight arthropod pest species [house (M. domestica), stable (S. calcitrans), horn (H. irritans) & flesh (N. bullata) flies; Southern cattle fever tick (B. microplus), European tick (I. ricinus), yellow fever mosquito (A. aegypti), & Southern Green Stink Bug (N. viridula)]; including the unprecedented identification of mass-identical Leu/Ile residues and the first identification of NPs from a tick or the CNS of Hemiptera. Evidence was obtained for the selection of Neb-PK-2 as the primary pupariation factor of the flesh fly (N. bullata) among native PK/PK-related candidates. The peptidomic techniques were also used to map the location of PK/PK-related NP in the nervous system of the model fly D. melanogaster. Knowledge of specific PK sequences can aid in the future design of species specific (or non-specific) NP agonists/antagonists. In addition, the study led to the first cloning of a PK/PBAN receptor from insect larvae (S. littoralis), providing the basis for SAR analysis for the future design of 2ⁿᵈgeneration selective and/or nonselective agonists/antagonists. Development of a microplate ligand binding assay using the PK/PBAN pheromone gland receptor was also carried out. The assay will enable screening, including high throughput, of various libraries (chemical, molecular & natural product) for the discovery of receptor specific agonists/antagonists. In summary, the body of work achieves several key milestones and brings us significantly closer to the development of novel, environmentally friendly pest insect management agents based on insect PK/PBANNPs capable of disrupting critical NP-regulated functions.
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Altstein, Miriam, and Ronald J. Nachman. Rational Design of Insect Control Agent Prototypes Based on Pyrokinin/PBAN Neuropeptide Antagonists. United States Department of Agriculture, August 2013. http://dx.doi.org/10.32747/2013.7593398.bard.
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The general objective of this study was to develop rationally designed mimetic antagonists (and agonists) of the PK/PBAN Np class with enhanced bio-stability and bioavailability as prototypes for effective and environmentally friendly pest insect management agents. The PK/PBAN family is a multifunctional group of Nps that mediates key functions in insects (sex pheromone biosynthesis, cuticular melanization, myotropic activity, diapause and pupal development) and is, therefore, of high scientific and applied interest. The objectives of the current study were: (i) to identify an antagonist biophores (ii) to develop an arsenal of amphiphilic topically active PK/PBAN antagonists with an array of different time-release profiles based on the previously developed prototype analog; (iii) to develop rationally designed non-peptide SMLs based on the antagonist biophore determined in (i) and evaluate them in cloned receptor microplate binding assays and by pheromonotropic, melanotropic and pupariation in vivo assays. (iv) to clone PK/PBAN receptors (PK/PBAN-Rs) for further understanding of receptor-ligand interactions; (v) to develop microplate binding assays for screening the above SMLs. In the course of the granting period A series of amphiphilic PK/PBAN analogs based on a linear lead antagonist from the previous BARD grant was synthesized that incorporated a diverse array of hydrophobic groups (HR-Suc-A[dF]PRLa). Others were synthesized via the attachment of polyethylene glycol (PEG) polymers. A hydrophobic, biostablePK/PBAN/DH analog DH-2Abf-K prevented the onset of the protective state of diapause in H. zea pupae [EC50=7 pmol/larva] following injection into the preceding larval stage. It effectively induces the crop pest to commit a form of ‘ecological suicide’. Evaluation of a set of amphiphilic PK analogs with a diverse array of hydrophobic groups of the formula HR-Suc-FTPRLa led to the identification of analog T-63 (HR=Decyl) that increased the extent of diapause termination by a factor of 70% when applied topically to newly emerged pupae. Another biostablePK analog PK-Oic-1 featured anti-feedant and aphicidal properties that matched the potency of some commercial aphicides. Native PK showed no significant activity. The aphicidal effects were blocked by a new PEGylated PK antagonist analog PK-dF-PEG4, suggesting that the activity is mediated by a PK/PBAN receptor and therefore indicative of a novel and selective mode-of-action. Using a novel transPro mimetic motif (dihydroimidazole; ‘Jones’) developed in previous BARD-sponsored work, the first antagonist for the diapause hormone (DH), DH-Jo, was developed and shown to block over 50% of H. zea pupal diapause termination activity of native DH. This novel antagonist development strategy may be applicable to other invertebrate and vertebrate hormones that feature a transPro in the active core. The research identifies a critical component of the antagonist biophore for this PK/PBAN receptor subtype, i.e. a trans-oriented Pro. Additional work led to the molecular cloning and functional characterization of the DH receptor from H. zea, allowing for the discovery of three other DH antagonist analogs: Drosophila ETH, a β-AA analog, and a dF analog. The receptor experiments identified an agonist (DH-2Abf-dA) with a maximal response greater than native DH. ‘Deconvolution’ of a rationally-designed nonpeptide heterocyclic combinatorial library with a cyclic bis-guanidino (BG) scaffold led to discovery of several members that elicited activity in a pupariation acceleration assay, and one that also showed activity in an H. zea diapause termination assay, eliciting a maximal response of 90%. Molecular cloning and functional characterization of a CAP2b antidiuretic receptor from the kissing bug (R. prolixus) as well as the first CAP2b and PK receptors from a tick was also achieved. Notably, the PK/PBAN-like receptor from the cattle fever tick is unique among known PK/PBAN and CAP2b receptors in that it can interact with both ligand types, providing further evidence for an evolutionary relationship between these two NP families. In the course of the granting period we also managed to clone the PK/PBAN-R of H. peltigera, to express it and the S. littoralis-R Sf-9 cells and to evaluate their interaction with a variety of PK/PBAN ligands. In addition, three functional microplate assays in a HTS format have been developed: a cell-membrane competitive ligand binding assay; a Ca flux assay and a whole cell cAMP ELISA. The Ca flux assay has been used for receptor characterization due to its extremely high sensitivity. Computer homology studies were carried out to predict both receptor’s SAR and based on this analysis 8 mutants have been generated. The bioavailability of small linear antagonistic peptides has been evaluated and was found to be highly effective as sex pheromone biosynthesis inhibitors. The activity of 11 new amphiphilic analogs has also been evaluated. Unfortunately, due to a problem with the Heliothis moth colony we were unable to select those with pheromonotropic antagonistic activity and further check their bioavailability. Six peptides exhibited some melanotropic antagonistic activity but due to the low inhibitory effect the peptides were not further tested for bioavailability in S. littoralis larvae. Despite the fact that no new antagonistic peptides were discovered in the course of this granting period the results contribute to a better understanding of the interaction of the PK/PBAN family of Nps with their receptors, provided several HT assays for screening of libraries of various origin for presence of PK/PBAN-Ragonists and antagonists and provided important practical information for the further design of new, peptide-based insecticide prototypes aimed at the disruption of key neuroendocrine physiological functions in pest insects.
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Pizarro, Shelly Ann. Spectroscopic study of the light-harvesting protein C-phycocyanin associated with colorless linker peptides. Office of Scientific and Technical Information (OSTI), May 2000. http://dx.doi.org/10.2172/764396.
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Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593390.bard.
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The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mutant receptors, cell lines and pheromone glands (at tissue and organism levels) against selected, designed compounds to confirm if compounds are agonists or antagonists. (2) The elucidation ofthemolecular regulationmechanisms of PBAN-R by:(a) age-dependence of gene expression; (b) the effect of hormones and; (c) PBAN-R characterization in male hair-pencil complexes. Background to the topic Insects have several closely related G protein-coupled receptors (GPCRs) belonging to the pyrokinin/PBAN family, one with the ligand pheromone biosynthesis activating neuropeptide or pyrokinin-2 and another with diapause hormone or pyrokinin-1 as a ligand. We were unable to identify the diapause hormone receptor from Helicoverpa zea despite considerable effort. A third, related receptor is activated by a product of the capa gene, periviscerokinins. The pyrokinin/PBAN family of GPCRs and their ligands has been identified in various insects, such as Drosophila, several moth species, mosquitoes, Triboliumcastaneum, Apis mellifera, Nasoniavitripennis, and Acyrthosiphon pisum. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates pheromone production in moths plus other functions indicating the pleiotropic nature of these ligands. Based on the alignment of annotated genomic sequences, the primary and secondary structures of the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors found in vertebrates. Major conclusions, solutions, achievements Evolutionary trace analysisof receptor extracellular domains exhibited several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding. Through site-directed point mutations, the 3rd extracellular domain of PBAN-R was shown to be critical for ligand selection. We identified three receptors that belong to the PBAN family of GPCRs and a partial sequence for the periviscerokinin receptor from the European corn borer, Ostrinianubilalis. Functional expression studies confirmed that only the C-variant of the PBAN-R is active. We identified a non-peptide agonist that will activate the PBAN-receptor from H. zea. We determined that there is transcriptional control of the PBAN-R in two moth species during the development of the pupa to adult, and we demonstrated that this transcriptional regulation is independent of juvenile hormone biosynthesis. This transcriptional control also occurs in male hair-pencil gland complexes of both moth species indicating a regulatory role for PBAN in males. Ultimate confirmation for PBAN's function in the male tissue was revealed through knockdown of the PBAN-R using RNAi-mediated gene-silencing. Implications, both scientific and agricultural The identification of a non-peptide agonist can be exploited in the future for the design of additional compounds that will activate the receptor and to elucidate the binding properties of this receptor. The increase in expression levels of the PBAN-R transcript was delineated to occur at a critical period of 5 hours post-eclosion and its regulation can now be studied. The mysterious role of PBAN in the males was elucidated by using a combination of physiological, biochemical and molecular genetics techniques.
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Carrigee, Lyndsay, Carina Jung, Matthew Carr, and Karl Indest. Bacterial remediation of microsystin-HAB toxins utilizing microcystinase (MlrA). Engineer Research and Development Center (U.S.), April 2025. https://doi.org/10.21079/11681/49673.
Full textAbstract:
Microcystins are a class of hepatotoxins produced by some harmful algal bloom–associated cyanobacteria and are the most reported toxins in freshwaters. Their cyclic structure makes them resistant to conventional methods used in water treatment operations (boiling, chlorination, and UV treatment). Some bacteria can naturally degrade microcystins via the mlrABCD cluster, a pathway initiated by the primary enzyme microcystinase (MlrA). MlrA linearizes the cyclic microcystin, greatly reducing its toxicity. Protein fusion was employed to produce a recombinant MlrA enzyme fused to maltose-binding protein ([MBP] MBP-MlrA) and to evaluate long-term enzymatic stabilization and reconstitution for future applications. MBP-MlrA degraded cyclic microcystin in vitro and demonstrated stability across a range of biological pHs. At a concentration of 0.61 ng/μl in buffer, MBP-MlrA achieved and maintained an average degradation rate of approximately 101.95 μM/h/ng of protein across fifteen freeze/thaw cycles. Stability assays demonstrated that enzyme activity was preserved over 5 months at −20°C. Results also demonstrated the effectiveness of MBP-MlrA to linearize microcystin upwards of 55.59 μM/h/ng of protein at the bench scale in both buffer and various freshwater matrices. The presence of the linear metabolite is of concern regarding intermediate toxicity, and future studies to incorporate the MlrB peptidase are discussed.
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Sooksai, Sarintip, Nanthika Khongchareonporn, Aphichart Karnchanatat, Shongchan Phuthong, Sajee Noitang, and Sawanan Thongyoo. Enhancement of recombinant monomeric insulin production in methylotrophic yeasts by increasing copy number of gene : Completed research report (2nd year). Chulalongkorn University, 2016. https://doi.org/10.58837/chula.res.2016.59.
Full textAbstract:
Insulin is a hormone that is produced in pancreas. It is important for regulation of blood sugar level. The active form of insulin is monomer which contains 51 amino acids in two peptide chains. Currently, improvement of insulin production was done by using recombinant DNA technology in bacteria and yeasts. The obtained recombinant insulin is easier to be purified than the pancreatic insulin. This research has been using the recombinant yeast, Pichia pastoris KM71H (TP1), which has a cassette of monomeric insulin precursor (MIP) to produce recombinant MIP. The recombinant MIP was induced to be expressed by 0.5% methanol in MMH medium. The recombinant MIP expression was detected and quantitatively determination by dot-blot analysis and indirect competitive ELISA, respectively. The expression level of recombinant MIP was 16 mg/L. The molecular weight of MIP that was determined by MALDI-TOF mass spectra technique is 5756.95 Da. The recombinant MIP was purified from culture broth by two steps, i.e. SP sepharose fast flow cation exchange chromatography and 10 kDa Amicon centrifugal molecular weight cutoff. Afterwards, it was converted to active form by TPCK tryptic hydrolysis. The tryptic digested MIP was used to test the activity through the expression of glucose transporter 4 (GLUT4) gene in H9c2 (2-1) rat myocardial cell line by real-time PCR. The results showed that the active MIP (11.20 ug/L) induced the expression of GLUT4 gene and the glucose in culture medium of H9c2 (2-1) cell line significantly reduced when the cell line was treated with the active MIP at the concentration 0.70 to 11.20 ug/L.
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Aly, Radi, James H. Westwood, and Carole L. Cramer. Novel Approach to Parasitic Weed Control Based on Inducible Expression of Cecropin in Transgenic Plants. United States Department of Agriculture, May 2003. http://dx.doi.org/10.32747/2003.7586467.bard.
Full textAbstract:
Our overall goal was to engineer crop plants with enhanced resistance to Orobanche (broomrape) based on the inducible expression of sarcotoxin-like peptide (SLP). A secondary objective was to localize small proteins such as SLP in the host-parasite union in order to begin characterizing the mechanism of SLP toxicity to Orobanche. We have successfully accomplished both of these objectives and have demonstrated that transgenic tobacco plants expressing SLP under control of the HMG2 promoter show enhanced resistance to O. aegyptiaca and O. ramosa . Furthermore, we have shown that proteins much larger than the SLP move into Orobanche tubercles from the host root via either symplastic or apoplastic routes. This project was initiated with the finding that enhanced resistance to Orobanche could be conferred on tobacco, potato, and tomato by expression of SLP (Sarcotoxin IA is a 40-residue peptide produced as an antibiotic by the flesh fly, Sarcophaga peregrina ) under the control of a low-level, root-specific promoter. To improve the level of resistance, we linked the SLP gene to the promoter from HMG2, which is strongly inducible by Orobanche as it parasitizes the host. The resulting transgenic plants express SLP and show increased resistance to Orobanche. Resistance in this case is manifested by increased growth and yield of the host in the presence of the parasite as compared to non-transgenic plants, and decreased parasite growth. The mechanism of resistance appears to operate post-attachment as the parasite tubercles attached to the transgenic root plants turned necrotic and failed to develop normally. Studies examining the movement of GFP (approximately 6X the size of SLP) produced in tobacco roots showed accumulation of green fluorescence in tubercles growing on transformed plants but not in those growing on wild-type plants. This accumulation occurs regardless of whether the GFP is targeted to the cytoplasm (translocated symplastically) or the apoplastic space (translocated in xylem). Plants expressing SLP appear normal as compared to non-transgenic plants in the absence of Orobanche, so there is no obvious unintended impact on the host plant from SLP expression. This project required the creation of several gene constructs and generation of many transformed plant lines in order to address the research questions. The specific objectives of the project were to: 1. Make gene constructs fusing Orobanche-inducible promoter sequences to either the sarcotoxin-like peptide (SLP) gene or the GFP reporter gene. 2. Create transgenic plants containing gene constructs. 3. Characterize patterns of transgene expression and host-to-parasite movement of gene products in tobacco ( Nicotiana tabacum L.) and Arabidopsis thaliana (L.). 4. Characterize response of transgenic potato ( Solanum tuberosum L.) and tomato ( Lycopersicon esculentum Mill .) to Orobanche in lab, greenhouse, and field. Objectives 1 and 2 were largely accomplished during the first year during Dr. Aly's sabbatical visit to Virginia Tech. Transforming and analyzing plants with all the constructs has taken longer than expected, so efforts have concentrated on the most important constructs. Work on objective 4 has been delayed pending the final results of analysis on tobacco and Arabidopsis transgenic plants. The implications of this work are profound, because the Orobanche spp. is an extremely destructive weed that is not controlled effectively by traditional cultural or herbicidal weed control strategies. This is the first example of engineering resistance to parasitic weeds and represents a unique mode of action for selective control of these weeds. This research highlights the possibility of using this technique for resistance to other parasitic species and demonstrates the feasibility of developing other novel strategies for engineering resistance to parasitic weeds.
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Dolja, Valerian V., Amit Gal-On, and Victor Gaba. Suppression of Potyvirus Infection by a Closterovirus Protein. United States Department of Agriculture, March 2002. http://dx.doi.org/10.32747/2002.7580682.bard.
Full textAbstract:
The plant virus family Polyviridae is the largest and most destructive of all plant viruses. Despite the continuous effort to develop resistant plant varieties, there is a desperate need for novel approaches conferring wide-range potyvirus resistance. Based on experiments with the tobacco etch potyvirus (TEV)-derived gene expression vector, we suggested approach for screening of the candidate resistance genes. This approach relies on insertion of the genes into a virus vector and evaluation of the phenotypes of the resulting recombinant viruses. The genes which suppress infection by the recombinant virus are selected as candidates for engineering transgenic resistance. Our analysis of the TEV variants expressing proteins of the beet yellows closterovirus (BYV) revealed that one of those, the leader proteinase (L-Pro), strongly and specifically interfered with the hybrid TEV infection. Since closterovirus L-Pro is evolutionary related to potyviral helper component-proteinase (HC-Pro), we suggested that the L-Pro interfered with HC-Pro function via a trans-dominant inhibitory effect. Based on these findings, we proposed to test two major hypotheses. First, we suggested that L-Pro-mediated suppression of potyvirus infection is a general phenomenon effective against a range of potyviruses. The second hypothesis stated that the suppression effect can be reproduced in transgenic plants expressing L-Pro, and can be utilized for generation of resistance to potyviruses. In accord with these hypotheses, we developed two original objectives of our proposal: A) to determine the range of the closterovirus-derived suppression of potyviral infection, and B) to try and utilize the L-Pro-mediated suppression for the development of transgenic resistance to potyviruses. In the first phase of the project, we have developed all major tools and technologies required for successful completion of the proposed research. These included TEV and ZYMV vectors engineered to express several closteroviral L-Pro variants, and generation of the large collection of transgenic plants. To our satisfaction, characterization of the infection phenotypes exhibited by chimeric TEV and ZYMV variants confirmed our first hypothesis. For instance, similar to TEV-L- Pro(BYV) chimera, ZYMV-L-Pro(LIYV) chimera was debilitated in its systemic spread. In contrast, ZYMV-GUS chimera (positive control) was competent in establishing vigorous systemic infection. These and other results with chimeric viruses indicated that several closteroviral proteinases inhibit long-distance movement of the potyviruses upon co-expression in infected plants. In order to complete the second objective, we have generated ~90 tobacco lines transformed with closteroviral L-Pro variants, as well as ~100 lines transformed with BYV Hsp70-homolog (Hsp70h; a negative control). The presence and expression of the trans gene in each line was initially confirmed using RT-PCR and RNA preparations isolated from plants. However, since detection of the trans gene-specific RNA can not guarantee production of the corresponding protein, we have also generated L-Pro- and Hsp70h-specific antisera using corresponding synthetic peptides. These antisera allowed us to confirm that the transgenic plant lines produced detectable, although highly variable levels of the closterovirus antigens. In a final phase of the project, we tested susceptibility of the transgenic lines to TEV infection. To this end, we determined that the minimal dilution of the TEV inoculum that is still capable of infecting 100% of nontransgenic plants was 1:20, and used 10 plants per line (in total, ~2,000 plants). Unfortunately, none of the lines exhibited statistically significant reduction in susceptibility. Although discouraging, this outcome prompted us to expand our experimental plan and conduct additional experiments. Our aim was to test if closteroviral proteinases are capable of functioning in trans. We have developed agroinfection protocol for BYV, and tested if co- expression of the L-Pro is capable of rescuing corresponding null-mutant. The clear-cut, negative results of these experiments demonstrated that L-Pro acts only in cis, thus explaining the lack of resistance in our transgenic plants. We have also characterized a collection of the L-Pro alanine- scanning mutants and found direct genetic evidence of the requirement for L-Pro in virus systemic spread. To conclude, our research supported by BARD confirmed one but not another of our original hypotheses. Moreover, it provided an important insight into functional specialization of the viral proteinases and generated set of tools and data with which we will be able to address the molecular mechanisms by which these proteins provide a variety of critical functions during virus life cycle.
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Tucker, Mark L., Shimon Meir, Amnon Lers, Sonia Philosoph-Hadas, and Cai-Zhong Jiang. Elucidation of signaling pathways that regulate ethylene-induced leaf and flower abscission of agriculturally important plants. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597929.bard.
Full textAbstract:
The Problem: Abscission is a highly regulated process, occurring as a natural terminal stage of development, in which various organs are separated from the parent plant. In most plant species, the process is initiated by a decrease in active auxin in the abscission zone (AZ) and an increase in ethylene, and may be accelerated by postharvest or environmental stresses. Another potential key regulator in abscission is IDA (Inflorescence Deficient in Abscission), which was identified as an essential peptide signal for floral organ abscission in Arabidopsis. However, information is still lacking regarding the molecular mechanisms integrating all these regulators. In our previous BARD funded research we made substantial progress towards understanding these molecular events in tomato, and the study is still in progress. We established a powerful platform for analysis of genes for regulatory proteins expressed in AZ. We identified changes in gene expression for several transcription factors (TFs) directly linked to ethylene and auxin signaling and several additional regulatory proteins not so obviously linked to these hormones. Moreover, we demonstrated using a virus-induced gene silencing (VIGS) assay that several play a functional role in the onset of abscission. Based on these results we have selected 14 genes for further analysis in stably transformed tomato plants. All 14 genes were suppressed by RNA interference (RNAi) using a constitutive promoter, and 5 of them were also suppressed using an abscission-specific promoter. Transformations are currently at different stages of progress including some lines that already display an abscission phenotype. Objectives: We propose here to (1) complete the functional analysis of the stably transformed tomato plants with T2 lines and perform transcriptome analysis using custom abscission-specific microarrays; (2) conduct an indepth analysis of the role of IDA signaling in tomato leaf and flower abscission; (3) perform transcriptome and proteome analyses to extend the earlier gene expression studies to identify transcripts and proteins that are highly specific to the separation layer (i.e., target cells for cell separation) prior to the onset of abscission; (4) extend and compliment the work in tomato using a winnowed set of genes in soybean. Methodology: Next Generation Sequencing (NGS) of mRNA will be used to further increase the list of abscission-associated genes, and for preparation of a custom tomato abscission microarray to test altered gene expression in transgenic plants. Tandem mass spectrometry (LC-MS/MS) of protein extracts from leaf petiole, flower pedicel and their AZ tissues will be used to identify the proteome of the AZ before and during abscission. AZ-specific gene promoters will be used in stably transformed tomato plants to reduce non-target phenotypes. The bean pod mottle virus (BPMV) plasmid vectors will be used for VIGS analysis in soybean. Expected Contribution: Our study will provide new insights into the regulation of ethylene-induced abscission by further revealing the role of key regulators in the process. This will permit development of novel techniques for manipulating leaf and flower abscission, thereby improving the postharvest performance of agriculturally important crops.
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Funkenstein, Bruria, and Shaojun (Jim) Du. Interactions Between the GH-IGF axis and Myostatin in Regulating Muscle Growth in Sparus aurata. United States Department of Agriculture, March 2009. http://dx.doi.org/10.32747/2009.7696530.bard.
Full textAbstract:
Growth rate of cultured fish from hatching to commercial size is a major factor in the success of aquaculture. The normal stimulus for muscle growth in growing fish is not well understood and understanding the regulation of muscle growth in fish is of particular importance for aquaculture. Fish meat constitutes mostly of skeletal muscles and provides high value proteins in most people's diet. Unlike mammals, fish continue to grow throughout their lives, although the size fish attain, as adults, is species specific. Evidence indicates that muscle growth is regulated positively and negatively by a variety of growth and transcription factors that control both muscle cell proliferation and differentiation. In particular, growth hormone (GH), fibroblast growth factors (FGFs), insulin-like growth factors (IGFs) and transforming growth factor-13 (TGF-13) play critical roles in myogenesis during animal growth. An important advance in our understanding of muscle growth was provided by the recent discovery of the crucial functions of myostatin (MSTN) in controlling muscle growth. MSTN is a member of the TGF-13 superfamily and functions as a negative regulator of skeletal muscle growth in mammals. Studies in mammals also provided evidence for possible interactions between GH, IGFs, MSTN and the musclespecific transcription factor My oD with regards to muscle development and growth. The goal of our project was to try to clarify the role of MSTNs in Sparus aurata muscle growth and in particular determine the possible interaction between the GH-IGFaxis and MSTN in regulating muscle growth in fish. The steps to achieve this goal included: i) Determining possible relationship between changes in the expression of growth-related genes, MSTN and MyoD in muscle from slow and fast growing sea bream progeny of full-sib families and that of growth rate; ii) Testing the possible effect of over-expressing GH, IGF-I and IGF-Il on the expression of MSTN and MyoD in skeletal muscle both in vivo and in vitro; iii) Studying the regulation of the two S. aurata MSTN promoters and investigating the possible role of MyoD in this regulation. The major findings of our research can be summarized as follows: 1) Two MSTN promoters (saMSTN-1 and saMSTN-2) were isolated and characterized from S. aurata and were found to direct reporter gene activity in A204 cells. Studies were initiated to decipher the regulation of fish MSTN expression in vitro using the cloned promoters; 2) The gene coding for saMSTN-2 was cloned. Both the promoter and the first intron were found to be polymorphic. The first intron zygosity appears to be associated with growth rate; 3) Full length cDNA coding for S. aurata growth differentiation factor-l I (GDF-II), a closely related growth factor to MSTN, was cloned from S. aurata brain, and the mature peptide (C-terminal) was found to be highly conserved throughout evolution. GDF-II transcript was detected by RT -PCR analysis throughout development in S. aurata embryos and larvae, suggesting that this mRNA is the product of the embryonic genome. Transcripts for GDF-Il were detected by RT-PCR in brain, eye and spleen with highest level found in brain; 4) A novel member of the TGF-Bsuperfamily was partially cloned from S. aurata. It is highly homologous to an unidentified protein (TGF-B-like) from Tetraodon nigroviridisand is expressed in various tissues, including muscle; 5) Recombinant S. aurata GH was produced in bacteria, refolded and purified and was used in in vitro and in vivo experiments. Generally, the results of gene expression in response to GH administration in vivo depended on the nutritional state (starvation or feeding) and the time at which the fish were sacrificed after GH administration. In vitro, recombinantsaGH activated signal transduction in two fish cell lines: RTHI49 and SAFI; 6) A fibroblastic-like cell line from S. aurata (SAF-I) was characterized for its gene expression and was found to be a suitable experimental system for studies on GH-IGF and MSTN interactions; 7) The gene of the muscle-specific transcription factor Myogenin was cloned from S. aurata, its expression and promoter activity were characterized; 8) Three genes important to myofibrillogenesis were cloned from zebrafish: SmyDl, Hsp90al and skNAC. Our data suggests the existence of an interaction between the GH-IGFaxis and MSTN. This project yielded a great number of experimental tools, both DNA constructs and in vitro systems that will enable further studies on the regulation of MSTN expression and on the interactions between members of the GHIGFaxis and MSTN in regulating muscle growth in S. aurata.