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Relevant bibliographies by topics / Peptide substrates

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Academic literature on the topic 'Peptide substrates'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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Journal articles on the topic "Peptide substrates"

1

Hao, Yue, Elizabeth Pierce, Daniel Roe, Maho Morita, John A. McIntosh, Vinayak Agarwal, Thomas E. Cheatham, Eric W. Schmidt, and Satish K. Nair. "Molecular basis for the broad substrate selectivity of a peptide prenyltransferase." Proceedings of the National Academy of Sciences 113, no. 49 (November 21, 2016): 14037–42. http://dx.doi.org/10.1073/pnas.1609869113.

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The cyanobactin prenyltransferases catalyze a series of known or unprecedented reactions on millions of different substrates, with no easily observable recognition motif and exquisite regioselectivity. Here we define the basis of broad substrate tolerance for the otherwise uncharacterized TruF family. We determined the structures of the Tyr-prenylating enzyme PagF, in complex with an isoprenoid donor analog and a panel of linear and macrocyclic peptide substrates. Unexpectedly, the structures reveal a truncated barrel fold, wherein binding of large peptide substrates is necessary to complete a solvent-exposed hydrophobic pocket to form the catalytically competent active site. Kinetic, mutational, chemical, and computational analyses revealed the structural basis of selectivity, showing a small motif within peptide substrates that is sufficient for recognition by the enzyme. Attaching this 2-residue motif to two random peptides results in their isoprenylation by PagF, demonstrating utility as a general biocatalytic platform for modifications on any peptide substrate.

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Jabaiah, Abeer M., Jennifer A. Getz, Witold A. Witkowski, Jeanne A. Hardy, and Patrick S. Daugherty. "Identifi cation of protease exosite-interacting peptides that enhance substrate cleavage kinetics." Biological Chemistry 393, no. 9 (September 1, 2012): 933–41. http://dx.doi.org/10.1515/hsz-2012-0162.

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Abstract Many peptidases are thought to require non-active site interaction surfaces, or exosites, to recognize and cleave physiological substrates with high specifi city and catalytic effi ciency. However, the existence and function of protease exosites remain obscure owing to a lack of effective methods to identify and characterize exosite-interacting substrates. To address this need, we modifi ed the cellular libraries of peptide substrates (CLiPS) methodology to enable the discovery of exosite-interacting peptide ligands. Invariant cleavage motifs recognized by the active sites of thrombin and caspase-7 were displayed on the outer surface of bacteria adjacent to a candidate exosite-interacting peptide. Exosite peptide libraries were then screened for ligands that accelerate cleavage of the active site recognition motif using two-color fl ow cytometry. Exosite CLiPS (eCLiPS) identifi ed exosite-binding peptides for thrombin that were highly similar to a critical exosite interaction motif in the thrombin substrate, proteaseactivated receptor 1. Protease activity probes incorporating exosite-binding peptides were cleaved ten-fold faster than substrates without exosite ligands, increasing their sensitivity to thrombin activity in vitro. For comparison, screening with caspase-7 yielded peptides that modestly enhanced (two-fold) substrate cleavage rates. The eCLiPS method provides a new tool to profi le the ligand specifi city of protease exosites and to develop improved substrates.

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Masler, E. P. "Aminopeptidases inCaenorhabditis elegansandPanagrellus redivivus: detection using peptide and non-peptide substrates." Journal of Helminthology 76, no. 1 (March 2002): 45–52. http://dx.doi.org/10.1079/joh200193.

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AbstractAminopeptidase activities were detected in extracts of the free-living nematodesCaenorhabditis elegansandPanagrellus redivivususing the aminoacyl substrate L-alanine-4-nitroanilide. The activities exhibited similarities in Km (C.elegans= 2.22 mM;P.REDIVIVUS= 2.09 Mm) and specific activity (C.elegans=1.38±0.43 mAU min-1 μg-1;P. redivivus, 1.23±0.18 mAU min-1 μg-1). Each is inhibited competitively by amastatin (C. elegansIC50=0.46 μm;P. redivivusIC50=15.90 μm) and non-competitively by leuhistin (C. elegansIC50=3.00 μm;P. redivivusIC50=37.35 μm). The bioactive peptides adipokinetic hormone and substance P decrease the apparent aminopeptidase activities of each extract suggesting that the peptides compete with the Ala-pNA as substrates. With each extract, adipokinetic hormone appeared to be the more effective substrate. Digestion of adipokinetic hormone byC. elegansandP. redivivusextracts in the presence and absence of 1 mm amastatin produced distinct chromatographic profiles that suggest different digestion patterns for the two species. However, amastatin had clear effects on chromatographic profiles from each species indicating that an aminopeptidase is involved in the digestion of the peptide substrates. The data presented indicate that extracts of free-living nematodes are capable of metabolizing peptide hormones, and that this metabolism involves substrate-selective aminopeptidases.

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Rut, Wioletta, and Marcin Drag. "Human 20S proteasome activity towards fluorogenic peptides of various chain lengths." Biological Chemistry 397, no. 9 (September 1, 2016): 921–26. http://dx.doi.org/10.1515/hsz-2016-0176.

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Abstract The proteasome is a multicatalytic protease responsible for the degradation of misfolded proteins. We have synthesized fluorogenic substrates in which the peptide chain was systematically elongated from two to six amino acids and evaluated the effect of peptide length on all three catalytic activities of human 20S proteasome. In the cases of five- and six-membered peptides, we have also synthesized libraries of fluorogenic substrates. Kinetic analysis revealed that six-amino-acid substrates are significantly better for chymotrypsin-like and caspase-like activity than shorter peptidic substrates. In the case of trypsin-like activity, a five-amino-acid substrate was optimal.

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TOOMIK, Reet, and Pia EK. "A potent and highly selective peptide substrate for protein kinase C assay." Biochemical Journal 322, no. 2 (March 1, 1997): 455–60. http://dx.doi.org/10.1042/bj3220455.

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Protein kinases exhibit substrate specificities that are often primarily determined by the amino acids around the phosphorylation sites. Peptides corresponding to protein kinase C phosphorylation sites in several different proteins were synthesized on SPOTs membrane which has recently been found to be applicable for studies of protein kinase specificity. After phosphorylation with protein kinase C, we chose the best phosphorylated peptides for the investigation of the importance of amino acids immediately adjacent to the phosphorylation site. The selectivity of the best protein kinase C substrates from this study was analysed with protein kinases A, CK1 and CK2. According to these tests, the most favourable characteristics of SPOTs-membrane-associated peptides were demonstrated by peptide KRAKRKTAKKR. Kinetic analysis of peptide phosphorylation with protein kinase C revealed an apparent Km of 0.49±0.13 μM and Vmax of 10.0±0.5 nmol/min per mg with soluble peptide KRAKRKTAKKR. In addition, we assayed several other soluble peptides commonly used as protein kinase C substrates. Peptide KRAKRKTAKKR showed the lowest Km and the highest Vmax/Km value in comparison with peptides FKKSFKL, pEKRPSQRSKYL and KRAKRKTTKKR. Furthermore, of the peptides tested, KRAKRKTAKKR was the most selective substrate for protein kinase C. The favourable kinetic parameters combined with the selectivity should make the KRAKRKTAKKR peptide useful as a substrate for protein kinase C in the assays of both purified enzyme and in crude cell extracts.

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Ng, Sandy Y. M., David J. VanDyke, Bonnie Chaban, John Wu, Yoshika Nosaka, Shin-Ichi Aizawa, and Ken F. Jarrell. "Different Minimal Signal Peptide Lengths Recognized by the Archaeal Prepilin-Like Peptidases FlaK and PibD." Journal of Bacteriology 191, no. 21 (August 28, 2008): 6732–40. http://dx.doi.org/10.1128/jb.00673-09.

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ABSTRACT In Archaea, the preflagellin peptidase (a type IV prepilin-like peptidase designated FlaK in Methanococcus voltae and Methanococcus maripaludis) is the enzyme that cleaves the N-terminal signal peptide from preflagellins. In methanogens and several other archaeal species, the typical flagellin signal peptide length is 11 to 12 amino acids, while in other archaea preflagellins possess extremely short signal peptides. A systematic approach to address the signal peptide length requirement for preflagellin processing is presented in this study. M. voltae preflagellin FlaB2 proteins with signal peptides 3 to 12 amino acids in length were generated and used as a substrate in an in vitro assay utilizing M. voltae membranes as an enzyme source. Processing by FlaK was observed in FlaB2 proteins containing signal peptides shortened to 5 amino acids; signal peptides 4 or 3 amino acids in length were unprocessed. In the case of Sulfolobus solfataricus, where the preflagellin peptidase PibD has broader substrate specificity, some predicted substrates have predicted signal peptides as short as 3 amino acids. Interestingly, the shorter signal peptides of the various mutant FlaB2 proteins not processed by FlaK were processed by PibD, suggesting that some archaeal preflagellin peptidases are likely adapted toward cleaving shorter signal peptides. The functional complementation of signal peptidase activity by FlaK and PibD in an M. maripaludis ΔflaK mutant indicated that processing of preflagellins was detected by complementation with either FlaK or PibD, yet only FlaK-complemented cells were flagellated. This suggested that a block in an assembly step subsequent to signal peptide removal occurred in the PibD complementation.

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Balasuriya, Nileeka, Norman E. Davey, Jared L. Johnson, Huadong Liu, Kyle K. Biggar, Lewis C. Cantley, Shawn Shun-Cheng Li, and Patrick O'Donoghue. "Phosphorylation-dependent substrate selectivity of protein kinase B (AKT1)." Journal of Biological Chemistry 295, no. 24 (April 29, 2020): 8120–34. http://dx.doi.org/10.1074/jbc.ra119.012425.

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Protein kinase B (AKT1) is a central node in a signaling pathway that regulates cell survival. The diverse pathways regulated by AKT1 are communicated in the cell via the phosphorylation of perhaps more than 100 cellular substrates. AKT1 is itself activated by phosphorylation at Thr-308 and Ser-473. Despite the fact that these phosphorylation sites are biomarkers for cancers and tumor biology, their individual roles in shaping AKT1 substrate selectivity are unknown. We recently developed a method to produce AKT1 with programmed phosphorylation at either or both of its key regulatory sites. Here, we used both defined and randomized peptide libraries to map the substrate selectivity of site-specific, singly and doubly phosphorylated AKT1 variants. To globally quantitate AKT1 substrate preferences, we synthesized three AKT1 substrate peptide libraries: one based on 84 “known” substrates and two independent and larger oriented peptide array libraries (OPALs) of ∼1011 peptides each. We found that each phospho-form of AKT1 has common and distinct substrate requirements. Compared with pAKT1T308, the addition of Ser-473 phosphorylation increased AKT1 activities on some, but not all of its substrates. This is the first report that Ser-473 phosphorylation can positively or negatively regulate kinase activity in a substrate-dependent fashion. Bioinformatics analysis indicated that the OPAL-activity data effectively discriminate known AKT1 substrates from closely related kinase substrates. Our results also enabled predictions of novel AKT1 substrates that suggest new and expanded roles for AKT1 signaling in regulating cellular processes.

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Srinivasan, J., M. Koszelak, M. Mendelow, Y. G. Kwon, and D. S. Lawrence. "The design of peptide-based substrates for the cdc2 protein kinase." Biochemical Journal 309, no. 3 (August 1, 1995): 927–31. http://dx.doi.org/10.1042/bj3090927.

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The substrate sequence specificity of the cdc2 protein kinase from Pisaster ochraceus has been evaluated. The peptide, Ac-Ser-Pro-Gly-Arg-Arg-Arg-Arg-Lys-amide, serves as an efficient cdc2 kinase substrate with a Km of 1.50 +/- 0.04 microM and a Vmax. of 12.00 +/- 0.18 mumol/min per mg. The amino acid sequence of this peptide is not based on any sequence in a known protein substrate of the cyclin-dependent kinase, but rather was designed from structural attributes that appear to be important in the majority of cdc2 substrates. The cyclin-dependent enzyme is remarkably indiscriminate in its ability to recognize and phosphorylate peptides that contain an assortment of structurally diverse residues at the P-2, P-1 and P+2 positions. However, peptides that contain a free N-terminal serine or lack an arginine at the P+4 position are relatively poor substrates. These aspects of the substrate specificity of the cdc2 protein kinase are compared and contrasted with the previously reported substrate specificity of a cdc2-like protein kinase from bovine brain [Beaudette, Lew and Wang (1993) J. Biol. Chem. 268, 20825-20830].

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Ting, Yi Tian, Paul W. R. Harris, Gaelle Batot, Margaret A. Brimble, Edward N. Baker, and Paul G. Young. "Peptide binding to a bacterial signal peptidase visualized by peptide tethering and carrier-driven crystallization." IUCrJ 3, no. 1 (January 1, 2016): 10–19. http://dx.doi.org/10.1107/s2052252515019971.

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Bacterial type I signal peptidases (SPases) are membrane-anchored serine proteases that process the signal peptides of proteins exported via the Sec and Tat secretion systems. Despite their crucial importance for bacterial virulence and their attractiveness as drug targets, only one such enzyme, LepB from Escherichia coli, has been structurally characterized, and the transient nature of peptide binding has stymied attempts to directly visualize SPase–substrate complexes. Here, the crystal structure of SpsB, the type I signal peptidase from the Gram-positive pathogen Staphylococcus aureus, is reported, and a peptide-tethering strategy that exploits the use of carrier-driven crystallization is described. This enabled the determination of the crystal structures of three SpsB–peptide complexes, both with cleavable substrates and with an inhibitory peptide. SpsB–peptide interactions in these complexes are almost exclusively limited to the canonical signal-peptide motif Ala-X-Ala, for which clear specificity pockets are found. Minimal contacts are made outside this core, with the variable side chains of the peptides accommodated in shallow grooves or exposed faces. These results illustrate how high fidelity is retained despite broad sequence diversity, in a process that is vital for cell survival.

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Stensland, Maria E., Sylvie Pollmann, Øyvind Molberg, Ludvig M. Sollid, and Burkhard Fleckenstein. "Primary sequence, together with other factors, influence peptide deimination by peptidylarginine deiminase-4." Biological Chemistry 390, no. 2 (February 1, 2009): 99–107. http://dx.doi.org/10.1515/bc.2009.019.

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Abstract Enzymes of the peptidylarginine deiminase (PAD) family catalyze the posttranslational deimination of polypeptide-bound arginine residues. Here, we report the selection of peptide substrates by PAD-4, an isoform thought to be involved in the pathogenesis of rheumatoid arthritis. First, we investigated whether PAD-4-mediated deimination is influenced by the nature of amino acid residues flanking the targeted arginine. Using two peptide substrates, residues in positions -2, -1, +1, and +2 relative to the central arginine targeted by PAD-4 were systematically replaced by all natural l-amino acids except cysteine. Each peptide was treated with recombinant human PAD-4 and deimination was analyzed by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. In all four flanking positions, amino acids which positively or negatively influenced deimination were identified. We next designed peptides with expected high or low deimination rates and determined their Km and kcat values. These peptides showed PAD-4 substrate behavior as predicted, demonstrating that residues flanking the targeted arginine are important for deimination. Further truncation of peptide substrates suggested additional effects on deimination by residues outside the -2 to +2 region. Finally, we observed that a methylated lysine residue flanking the targeted arginine influences PAD-4-mediated deimination, also suggesting that posttranslational modifications can affect substrate efficiency.

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Dissertations / Theses on the topic "Peptide substrates"

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Murphy, Diarmaid Joseph. "Intracellular delivery of peptide carriers, substrates and inhibitors." Thesis, Queen's University Belfast, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.479407.

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Noble, J. E. "Fluorescent peptide substrates for protein phosphates and protein kinases." Thesis, Imperial College London, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.406155.

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Loney, Charles Nicholas. "Characterization of Polyproline Peptide Monolayers on Metal / Metal Oxide Substrates." Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case159163938348028.

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4

Lou, Qiang 1962. "Identification of peptide substrates and development of pseudosubstrate-based peptide inhibitors for p60(C-SRC) protein tyrosine kinase." Diss., The University of Arizona, 1996. http://hdl.handle.net/10150/282230.

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Protein tyrosine kinases (PTKs) mediate important signaling events associated with cellular growth, differentiation, and mitogenesis. The p60c-src protein is the first described cellular protein tyrosine kinase. Human p60c-src PTK has been implicated in the development of colon and breast cancer, and leukemia. However, the exact physiological role of p60c-src PTK or its physiological target proteins are not well known, and the mechanism by which the p60c-src PTK activity is regulated is not completely understood. Peptide substrates can be used to determine the substrate specificity and kinetic parameters, and therefore to provide important information for understanding of the physiological role and mechanism of action of this enzyme. Peptide substrates can also be used to develop pseudosubstrate-based peptide inhibitors for p60c-src PTK. Combinatorial peptide library methods have proven to be very powerful in identifying ligands for receptors and in discovering peptide substrates for protein kinases. In this dissertation, a "one-bead one-compound" combinatorial peptide library method was applied to identify peptide substrates for p60c-src PTK, the structure-activity relationship of the identified peptide substrates was studied, and the pseudosubstrate-based peptide inhibitors for p60c-src PTK were developed. Using the "one-bead one-compound" combinatorial peptide library method, a novel peptide, YIYGSFK, was identified as an efficient substrate for p60c-src PTK. The structure-activity relationship study was performed on over 70 analogs of YIYGSFK. It was determined that -Ile-Tyr- were the two critical residues required for activity. Based on this dipeptide motif a secondary library was synthesized (XIYXXXX, wherein X = all 19 eukaryotic amino acids except cysteine, I = isoleucine, Y = tyrosine) and screened with p60c-src PTK. One of the identified peptides, GIYWHHY, was found to be more efficient for p60c-src PTK than the parental compound, YIYGSFK. Several potent psedosubstrate based inhibitors were developed using GIYWHHY as a template. Some of the more potent inhibitors have branched structure indicating the enzyme active site can accommodate more than a linear motif. These data demonstrate that the "one-bead one-compound" combinatorial library method is a powerful tool to discover novel peptide substrates, and to develop pseudosubstrate-based peptide inhibitors for PTKs.

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Umeobika, Ugochukwu Christian. "Solid phase peptide synthesis of substrates for the chemoenzymatic generation of cyanobactins analogues." Thesis, University of Aberdeen, 2017. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=233678.

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Ribosomal synthesized and post translational modified peptide natural products have attracted a lot of interest in the past decade. Backbone cyclization of the translated linear peptides is generally catalysed by specific enzymes giving them peptidase resistance, thermodynamic stability and various other physiological activities. These features have made backbone cyclic peptide to become an attractive resource for drug discovery. Here, we described the synthesis of linear peptides containing natural and unnatural residues and its biosynthetic mechanism to generate man-made cyclic peptides. In this thesis we used SPPS to make short and medium linear peptide chains, we purified them using HPLC, and analysed them using MS. We incorporated unnatural residues such as homocysteine, homoserine, aminoalanine, propargyl glycine and the substrates were subjected to different enzymatic reaction such as prenylation, heterocyclization and macrocyclization modification reactions to generate small macrocycles (4-6 residues), prenylated linear peptides, and patellamime analogues. The final products were analysed using LC-MS. In our results, we verified that kawaguchipeptin (kgp) gene cluster is responsible for the production of kawaguchipeptins through heterologous expression of the kgp gene cluster in Escherichia coli. The KgpF prenyltransferase was overexpressed and was shown to prenylate C-3 of Trp residues in both linear and cyclic peptides in vitro. We also found out that PatGmac can macrocyclise short peptides (4-6 residues) to generate small macrocyclic peptides. We also tested the flexibility of OscGmac using unnatural amino acid residues such as pseudoprolines and pipecolic acid that can mimic the heterocyle incorporated as the final residue in the natural product. Our results show that OscGmac recognises pseudoprolines before AYD(G) to process a linear peptide.

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Balmer, J. N. "Using peptide libraries to search for the substrates of ABH1 and Ofd2." Thesis, University of Cambridge, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596327.

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ABH1 and Ofd2 are human and Schizosaccharomyces pombe members of the 2-oxyglutarate-iron(II)-dependent dioxygenase family respectively. Little is known about these proteins, and no substrates for them have been identified. Using positionally addressable synthesis of peptides on a cellulose membrane (SPOT synthesis) random peptide libraries were generated. These were screened with ABH1 and Ofd2 using a 2-oxoglutarate turnover assay, to generate preferred sequence motifs. The motifs were searched against protein databases to create a list of potential substrates. The potential substrates were tested both for binding and activity. Several highly active peptides were systematically mutated in an attempt to further define the preferred motifs. These sequence preferences were used to conduct another search of the protein databases. Ultimately none of the sequences studied could be confirmed as substrates, however, refinement of the technique used could produce a viable method of identifying unknown substrates.

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Page, Timothy C. M. "Mechanism based inhibitors of tyrosine kinases." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.260163.

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Wang, Peng. "Screening Combinatorial Peptide Library for Optimal Enzyme Substrates and High Affinity Protein Ligands." The Ohio State University, 2003. http://rave.ohiolink.edu/etdc/view?acc_num=osu1039797438.

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Mongeon, Vanessa. "Elucidating the Biochemical and Structural Features Required for SMYD5 Mediated Methylation of Histone H4 and Other Potential Substrates." Thesis, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31321.

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Lysine methylation modulates diverse biological processes and is catalyzed by SET domain methyltransferases such as the SMYDs (SMYD1-5), which possess a SET domain split by a MYND motif. Through association with NCoR, the H4 Lys20 methyltransferase activity of SMYD5 represses inflammation by restricting TLR-4 mediated expression in macrophages, yet biochemical and structural features required for SMYD5 methylation activity remain elusive. To determine how SMYD5 catalyses methylation, crystallization screens were conducted with SMYD5 in complex with the co-factor AdoMet and histone H4. Screens yielded lead conditions but no crystals. To determine the motif recognized by SMYD5 and decipher its methylome, peptide arrays were conducted to produce a methylation motif used to identify putative substrates. Surprisingly, arrays revealed that substitution of Lys16, not Lys20, is detrimental to SMYD5 activity. Further enzymatic assays are required to determine if SMYD5 methylates residues other than Lys20 on the H4 tail, or if structural determinants or interacting partners restrict methylation of target lysines.

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Canu, Nicolas. "New insights into the recognition of the substrates of cyclodipeptide synthases." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS580.

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Les cyclodipeptides constituent, avec leurs dérivés plus complexes les dicétopiperazines (DKP), une importante famille de produits naturels, synthétisés essentiellement par des micro-organismes. Une approche intéressante pour synthétiser une grande diversité de DKP consiste à étudier et manipuler les voies de biosynthèse de ces molécules. Les synthases de cyclodipeptides (CDPS) constituent une famille d’enzymes dédiés à la production de cyclodipeptides, qui ont la particularité d’utiliser les ARNt aminoacylés (AA-ARNt) comme substrats. Afin d’exploiter complètement le potentiel de ces enzymes, il est nécessaire de mieux comprendre leur spécificité, notamment vis-à-vis de substrats non naturels. Dans cette thèse, nous avons tout d’abord démontré que les CDPS sont capables d’incorporer des acides aminés non naturels, en utilisant la promiscuité des aminoacyl-ARNt synthétases (AARS) d’Escherichia coli. Puis nous avons amélioré notre compréhension de la reconnaissance de la partie ARNt des susbtrats par les CDPS. En utilisant les flexizymes, des ribozymes à activité AARS, nous avons généré des analogues d’AA-ARNt avec des parties ARNt tronquées. Nous avons pu montrer que des « mini AA-ARNt » reproduisant les 7 paires de bases du bras accepteur des ARNt sont d’aussi bons substrats que les AA-ARNt complets, ce qui suggère que les CDPS interagissent principalement avec les bras accepteurs de leurs substrats ARNt
Cyclodipeptides and their complex derivatives, the diketopiperazines (DKPs), constitute a large class of natural products with diverse and noteworthy pharmacological activities observed for many naturally occurring DKPs. A promising approach to generate diverse DKPs is to study and manipulate DKP biosynthetic pathways. Cyclodipeptide synthases (CDPSs) constitute an enzyme family dedicated to the synthesis of cyclodipeptides, with the particularity to use aminoacylated-tRNAs (AA-tRNAs) as substrates. In order to unlock the biosynthetic potential of these enzymes, better understanding their specificity, in particular towards non-natural substrates, is required.In this thesis, we first significantly expanded the diversity of cyclodipeptides accessible with CDPSs by showing that CDPSs could incorporate non-canonical amino acids, through the use of the promiscuity of E. coli aminoacyl-tRNA synthetases. Then, we gave new insights into the recognition by CDPSs of the tRNA moieties of their substrates. By using an innovative RNA acylation strategy based on a class of ribozymes called flexizymes, we generated analogues of AA-tRNAs with truncated RNA moieties. Among these “AA-minitRNAs”, we showed that those mimicking the entire 7 bp stems of tRNAs are as good substrates as AA-tRNAs, which suggests that CDPSs interact mainly with the acceptor arms of tRNAs and paves the way for promising biophysical and structural studies

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Books on the topic "Peptide substrates"

1

Balanced Nutrition and Therapy (1986 Erlangen, Germany). Dipeptides as new substrates in nutrition therapy =: Peptide als neue Substrate in der Ernährungstherapie. Basel: Karger, 1987.

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2

Shao, Jiahong. Identification of peptide substrates of calcium-dependent protein kinase from random peptide phage display libraries and phosphorylation studies of the peptide substrate in transgenic tobacco cells. 1999.

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Furst, P., and W. Fekl. Dipeptides As New Substrates in Nutrition Therapy/Peptide Als Neue Substrate in Der Ernahrungstherapie: Balanced Nutrition and Therapy : Iv. International ... to Infusion Therapy and Clinica). S Karger Pub, 1987.

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A, Adibi S., ed. Dipeptides as new substrates in nutrition therapy: Balanced nutrition and therapy : IV. international symposium, Erlangen, July 10-12, 1986 = Peptide als neue Substrate in der Ernährungstherapie : bilanzierte Ernährung in der Therapie. Basel: Karger, 1987.

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Nutt, David J., and Liam J. Nestor. Appetite hormones and addiction. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198797746.003.0012.

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Many of the same behavioural and brain disturbances observed in addiction are also seen in obesity and binge-eating disorder. This suggests that there are shared neural substrates between substance addiction and compulsive food consumption. Food intake and appetite are regulated by numerous appetite hormones that exert their effects through brain systems involved in reward sensitivity, stress, impulsivity, and compulsivity. There is now emerging evidence that appetite hormones (e.g. ghrelin, glucagon-like peptide-1, orexin) can modulate addictive behaviours (e.g. craving) and the intake of alcohol and drugs. Therefore, there is an emerging shift into a new field of testing drugs that affect appetite hormones and their receptors in the brain, and their use in regulating the brain mechanisms that lead to relapse in addiction disorders.

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Koob, George F. The Neurobiology of Reward and Stress and Its Relevance for Understanding Drug-Seeking and Dependence Symptomatology. Edited by Kenneth J. Sher. Oxford University Press, 2014. http://dx.doi.org/10.1093/oxfordhb/9780199381678.013.013.

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Drug addiction can be conceptualized as a disorder that progresses from neurobiological mechanisms involved in positive reinforcement to mechanisms involved in negative reinforcement. Neurobiological substrates for the positive reinforcement of drug abuse involve activation of the brain’s incentive salience and reward systems, such as dopamine and opioid peptides, and neurobiological substrates for the negative reinforcement of drug addiction involve the brain stress systems, such as corticotropin-releasing factor (CRF), norepinephrine, and dynorphin in the ventral striatum and extended amygdala. Decreased function of brain antistress systems further contributes to motivational dysfunction. A brain stress response system is hypothesized to be dysregulated by acute excessive drug intake, sensitized during repeated withdrawal, persist into protracted abstinence, and contribute to the allostatic changes in motivation associated with addiction. From a theoretical perspective, the combination of loss of reward function and recruitment of brain stress systems drives the compulsivity of addiction and provides a rich neurobiological substrate for therapeutic interventions.

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d'Avila-Levy, Claudia M. Applications of Zymography (Substrate-SDS-PAGE) for Peptidase Screening in a Post-Genomic Era. INTECH Open Access Publisher, 2012.

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Book chapters on the topic "Peptide substrates"

1

Kirschke, H., and B. Wiederanders. "Chromogenic Peptide Substrates." In Proteolytic Enzymes, 11–29. Berlin, Heidelberg: Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/978-3-642-59816-6_2.

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Brandt, Inger, Anne-Marie Lambeir, Marie-Berthe Maes, Simon Scharpé, and Ingrid De Meester. "Peptide Substrates of Dipeptidyl Peptidases." In Advances in Experimental Medicine and Biology, 3–18. Boston, MA: Springer US, 2006. http://dx.doi.org/10.1007/0-387-32824-6_1.

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Mitin, Yu V., E. Yu Gorbunova, N. I. Evgrafova, and N. P. Zapevalova. "Enzymatic peptide synthesis with nonspecific trypsin substrates." In Peptide Chemistry 1992, 182–84. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1474-5_54.

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Mitin, Y. V., E. Y. Gorbunova, N. I. Evgrafova, and N. P. Zapevalova. "Enzymatic peptide synthesis with nonspecific trypsin substrates." In Peptides 1992, 417–18. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1470-7_183.

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Mitin, Y. V., V. Schellenberger, U. Schellenberger, H. D. Jakubke, and N. P. Zapevalova. "Protease catalyzed peptide synthesis using inverse substrates." In Peptides 1990, 287–88. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3034-9_122.

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Eubanks, Shad R., Derek S. Towery, Foe S. Tjoeng, Steven P. Adams, Dwight A. Towler, Emily Jackson-Machelski, Luis Glaser, and Jeffrey I. Gordon. "Peptide substrates and inhibitors of N-myristoyl transferase." In Peptides, 566–69. Dordrecht: Springer Netherlands, 1988. http://dx.doi.org/10.1007/978-94-010-9595-2_169.

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Juliano, M. A., M. C. F. Oliveira, F. Filira, B. Scolaro, R. Rocchi, and L. Juliano. "Glyco-peptide substrates and their hydrolysis by proteases." In Peptides 1994, 731–32. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-1468-4_336.

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Toth, Mihaly V., Francis Chiu, George Glover, Stephen B. H. Kent, Lee Ratner, Nancy Vander Heyden, Jeremy Green, Daniel H. Rich, and Garland R. Marshall. "Inhibitors of HIV protease based on modified peptide substrates." In Peptides, 835–38. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-010-9060-5_280.

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Zhang, Ruo-heng, Xue Ge, Xiao-jie Xu, and You-qi Tang. "Kinetic investigation of the chromogenic peptide substrates for chymotrypsin." In Peptides, 278–79. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-010-9066-7_81.

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Stawikowski, Maciej J., Anna M. Knapinska, and Gregg B. Fields. "Determining the Substrate Specificity of Matrix Metalloproteases using Fluorogenic Peptide Substrates." In Methods in Molecular Biology, 137–83. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6863-3_8.

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Conference papers on the topic "Peptide substrates"

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Sato, Daisuke, Wu Zhe, and Tamaki Kato. "Detection of Protease Activity by Concentration Quenching-Based Substrates." In The 24th American Peptide Symposium. Prompt Scientific Publishing, 2015. http://dx.doi.org/10.17952/24aps.2015.139.

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Stüber, W., D. Schiwek, U. Becker, and N. Heimburger. "NEW CHROMOGENIC SUBSTRATES FOR THE DETERMINATION OF COAGULATION AND FIBRINOLYSIS ENZYMES." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644323.

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A new type of chromogenic substraces based on derivatives of phenoxazine is presented. Particularly interesting is the blue dye 7-amino-3-diethylamino-8-methylphenoxazine (ADMP) with a molar extinktion coefficient of about 80,000 at 624 nm. Peptides were linked to the aminogroup of the dye and red coloured substrates were obtained with a λmax value of about 540 nm. On account of the distinct difference of the λmax values and the negligable influence of the absorption peaks of the acylated and the free dye this chromophore is suitable for the synchesis of substrates. Besides the spectral properties of chese new chromogenic peptides we determined their characce-riscics using serine proteases involved in the process of coagu-lacion and fibrinolysis. In comparison co para-nitroaniline substrates the introduction of the relatively bulky ADMP into the peptide sequence led to products with superior properties in respect of sensitivity and specificity.It was found that the ADMP substrates are particularly favourable for the determination of thrombin, urokinase and activated protein C in the presence of other proteases.

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Gunawan, Steven, Yunting Luo, Yuan Ren, Harshani R. Lawrence, Jerry Wu, and Nicholas J. Lawrence. "Abstract 4547: Preparation of peptide-based Shp2 substrates with phosphatase activity-dependent fluorescence." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-4547.

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Boriack-Sjodin, Ann, Lei Jin, Suzanne L. Jacques, Allison Drew, Margaret Porter Scott, Scott Ribich, and Oscar Moradei. "Abstract 2437: Crystal structures of CARM1 bound to sinefungin and diverse peptide substrates." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-2437.

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Suttie, W. J., A. Cheung, and M. G. Wood. "ENZYMOLOGY OF THE VITAMIN K-DEPENDENT CARBOXYLASE: CURRENT STATUS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643991.

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The vitamin K-dependent microsomal carboxylase converts glutamyl residues in precursor proteins to γ-carboxyglutamyl (Gla) residues in completed proteins. The enzyme activity is present in significant activities in most non-skeletal tissues but has been studied most extensively in rat and bovine liver. Early studies of the enzyme utilized bound precursors of vitamin K-dependent clotting factors as substrates for the enzyme and demonstrated that the enzyme requires the reduced form of vitamin K (vitamin KH2), O2, and CO2. Subsequent investigations have taken advantage of the observation that the enzyme will carboxylate low-molecular-weight peptide substrates with Glu-Glu sequences. Utilizing a substrate such as Phe-Leu-Glu-Glu-Leu, it has been possible to demonstrate that γ-C-H release from the Glu residue of a substrate is independent of CO2 concentration. The formation of vitamin K 2,3-epoxide can also be demonstrated in a crude microsomal system, and it can be shown that the formation of this metabolite can be stimulated by the presence of a peptide substrate of the carboxylase. These observations have led to the general hypothesis that the mechanism of action of the enzyme involves interaction of vitamin KH2 with O2 to form an oxygenated intermediate that can interact with a substrate Glu residue to abstract a γ-hydrogen and in the process he converted to vitamin K epoxide (KO). The current evidence suggests that, either directly or indirectly, removal of the γ-C-H results in the formation of a carbanion at the γ-position of the Glu residue which can interact with CO2 to form Gla. The Glu residue intermediate which is formed can be demonstrated to partition between accepting a proton in the media to reform Glu, or interacting with CO2 to form Gla. Current data do not distinguish between the direct formation of a carbanion coupled to proton removal, or the participation of a reduced intermediate. Recent studies have demonstrated that the enzyme will carry out a partial reaction, the formation of vitamin K epoxide, at a decreased rate in the absence of a Glu site substrate. Epoxide formation under these conditions has the same for O2 as the carboxylation reaction and is inhibited in the same manner as the carboxylation reaction. In the presence of saturating concentrations of a Glu site substrate and C02, the ratio of KO formed, γ-C-H released, and C02 formed is 1:1:1. However, KO formation can be uncoupled from and proceeds at a higher rate than γ-C-H bond cleavage and Gla formation at low Glu site substrate concentrations. At saturating concentrations of CO2, Gla formation is equivalent to γ-C-H bond cleavage, and this unity is not altered by variations in vitamin KH2 or peptide substrate concentrations. Natural compounds with vitamin K activity are 2-Me-l,4-naphthoquinones with a polyprenyl side chain at the 3-position. Studies of vitamin K analogs have demonstrated that a 2-Me group is essential for activity but that the group at the 3-position can vary significantly. Modification of the aromatic ring of the naphthoquinone nucleus by methyl group substitution can result in alterations of either the rate of the carboxylation reaction or the apparent affinity of the enzyme for the vitamin. Studies of a large number of peptide substrates have failed to reveal any unique primary amino acid sequence which is a signal for carboxylation. However, current evidence from a number of sources suggests that a basic amino acid rich "propeptide" region of the intracellular form of the vitamin K-dependent proteins is an essential recognition site for the enzyme. This region of the precursor is lost in subsequent processing, and the manner in which it directs this posttranslational event is not yet clarified. Supported by NIH grant AM-14881.

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Hurley, Margaret M., and Michael S. Sellers. "Prediction of protein-peptide interactions: application of the XPairIt API to anthrax lethal factor and substrates." In SPIE Defense, Security, and Sensing, edited by Brian M. Cullum and Eric S. McLamore. SPIE, 2013. http://dx.doi.org/10.1117/12.2014767.

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Liu, Hua-zhen, Wei Chen, Qi-ying Liu, Xia Zhang, Li-xiu Wang, and Cheng-wu Chi. "A NEW PEPTIDE THROMBIN INHIBITOR FROM STREPTOMYCES GRISEUS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644330.

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A new peptide thrombin inhibitor was found in the Streptomyces griseus strain 254 isolated from a soil sample from Tongan, Fujian province, China, the inhibitor being a secondary metabolic product. The production of the inhibitor reached a maximum after 3 days culture of bacteria at 28°C in a rotary shaker. The inhibitor excreted in the culture filtrate was purified by absorption on macroporous resin, followed by ion exchange chromatography on DEAE-52, CM-32 cellulose, affinity chromatography on the immobilized thrombin and high performance liquid chromatography. The amino acid composition of the inhibitor was determined to be Val(2), Met(l), Ile(l), Leu(2) and Arg (1), similar to that of the amino acid residues around the reactive site of human antithrombin III, the critical plasma inhibitor of thrombin. The NH2-terminal residue of the inhibitor seems to be blocked by the alkyl group due to the negative reaction to ninhydrin, whereas the COO-terminal residue is most likely to be arginal because of that Arg was not found in the amino acid analysis, unless the peptide was oxidized by performic acid before acid hydrolysis. The chromogen substrates Bz-Phe-Val-Arg-PNA and Bz-Gly-Pro-Lys-PNA were used to determine the thrombin and plasmin activities, respectively. Besides thrombin, the purified inhibitor also exhibits a weak inhibitory activities on trypsin and much weak on plasmin, but not on chymotrypsin and other protein-ases.

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Vojtěchová, Martina, Zdena Tuháčková, Jan Hlaváček, Jiří Velek, and Vlasta Sovová. "The v-Src and c-Src tyrosine kinases immunoprecipitated from Rous sarcoma virus-transformed cells display different specificities to three commonly used peptide substrates." In VIIIth Conference Biologically Active Peptides. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2003. http://dx.doi.org/10.1135/css200306119.

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Vermeer, C., BA M. Soute, and MM W. Ulrich. "IN VITRO CARBOXYLATION OF EXOGENOUS PROTEIN SUBSTRATES BY VITAMIN K-DEPENDENT CARBOXYLASE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643994.

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In vivo treatment of experimental animals with vitamin K-antagonists induces the accumulation of non-carboxylated coagulation factor precursors in the liver, where they are tightly bound to vitamin K-dependent carboxylase. If hepatic carboxylase is isolated from warfarin-treated animals, it is obtained therefore almost exclusively in the form of an enzyme/substrate complex. If carboxylase is prepared from non-treated animals, on the other hand, the resulting enzyme is predominantly substrate-free. Small substrates like F L E E L or decarboxylated osteocalcinare carboxylated equally well by both types of carboxylase, but protein substrates(Mr > 30 000) are recognized exclusively by substrate-free carboxylase.Initial attempts to purify carboxylasewere performed with livers from warfarin-treated cows as a starting material. Antibodies against the normal blood coagulation factors crossreact with the hepatic precursor proteins so that the enzyme/substrate complexes could be specifically extracted from detergent-solubilized microsomes by the substrate/antibody interaction. This procedure resulted ina substantial purification of carboxylase, but because its endogenous substrate remained firmly bound, even after it had been carboxylated in vitro, the enzyme system was not suitable for the carboxylation of protein substrates.Therefore a second strategy was developed by which substrate-free carboxylase (from normal livers) was partly purified by sequential extraction of the microsomal membranes with detergents, followed by ammonium sulfate precipitation and size exclusion chromatography.This procedure resulted in a soluble carboxylase complex, still consisting of 7 proteins and phosphatidylcholine. Although further dissociation of the complex resulted in a complete loss of activity, it is not sure if all components play a role in the carboxylation reaction. Exogenous substrates which could be carboxylated by substrate-free carboxylase were: the penta-peptide F L E E L, descarboxyprothrombin from bovine plasma, thermally decarboxylated osteocalcin from bovine bone and non-car-boxy lated coagulaton factor precursors which had been produced by recombinant-DNA techniques in various laboratories. The . efficiency of CO^ incorporation was: 1 mole per 100 moles of F L E E L, 1 mole per 240 moles of descarboxy-prothrombin, 1 mole per mole of decarboxylated osteocalcin and 8 moles per mole of a recombinant factor IX precursor. We assume that the high efficiency with which the recombinant coagulation factor precursors were carboxylated is due to the presence of at least part of their leader sequence. The importance of the aminoacid chain preceding the first carboxylatable Glu residue is demonstrated by the fact that descarboxylated osteocalcin of bovine origin is carboxylated with a relatively high efficiency, whereas descarboxylated osteocalcin from monkey bone is not recognized atal.. Yet the only difference between the two substrates is found in their aminoacids 3 and 4, whereas the first carboxylatable Glu occurs at position 17. It seems, therefore, that the aminoacids 1-16 in bovine osteocalcin mimic to some extent part of the leader sequence in the coagulation factor precursors. Chemical or biochemical modification of decarboxylated osteocalcin might reveal which structural features contribute to its recognition by hepatic carboxylase.The optimal conditions for carboxylation include a high concentration of dithiols (e.g. DTT) and under these conditions disulfide bridges are reduced. Obviously this will lead to a complete destruction of the biological activity of various carboxylated products. Therefore we have searched for a more natural reducing system and it was found that the bacterial thioredoxin/thiore-doxin-reductase system in the presence of 40 uM NADFH was able to replace DTT in the reaction mixtures. Since a comparable system also occurs in calf liver it seems not unlikely that this is the physiological counterpart of the dithiols used in vitro.

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Fay, P. J., S. I. Chavin, and F. J. Walker. "INACTIVATION OF FACTOR VIII BY ACTIVATED PROTEIN C AND PROTEIN S." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644770.

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Human factor VIII has been isolated from factor VIII concentrates. The isolated protein is composed of a heavy chain and light chain. The heavy chain was heterogenous with respect to molecular weight ranging from 110-170 kDa. The light chain appeared as a 81/84 kDa dimer, 'when factor VIII was treated with activated protein C in the presence of calcium and phospholipids factor VIII procoagulant activity was rapidly lost. Analysis of the activated protein C catalyzed cleavage products of factor VIII indicated that loss of activity was correlated with cleavage of the heavy chains. The heavy chains appeared to be converted into 93 kDa and 53 kDa peptides. A separate factor VIII preparation has been prepared that contained only a 93 kDa heavy chain as well as the 81/83 kDa light chain. When this preparation was inactivated with activated protein C, a pathway in which the 93 kDa peptide was degraded into a 68 kDa peptide which was subsequently degraded into 48 and 23 kDa polypeptides. This result suggested that the 53 kDa polypeptide was not derived from the 93 kDa domain of the heavy chain, but must have been derived from the variable molecular weight portion of the heavy chain. These results suggest that activated protein C catalyzed a minimum of four cleavages in the heavy chain. Activated protein C did not appear to alter the factor VIII light chain. Protein S has been observed to be a protein cofactor both the anticoagulant and proteolytic action of activated protein C with factor Va. It is thought that protein S forms a lipid bound complex with activated protein C which then can rapidly inactivate factor Va. When factor VIII was inactivated in the presence of both activated protein C and protein S the rate of activity loss was enhanced. The effect of protein S could be observed on the cleavage of the heavy chains and on secondary cleavages of the smaller products including the 93, 68, and 53 kDa polypeptides. In an analogous reaction, the addition of factor Xa has been observed to inhibit the inactivation of factor Va by activated protein C. The addition of factor IX to the factor Vlll-activated protein C reaction mixture resulted in the inhibition of factor VIII inactivation. The effect of factor IX was dose dependent. Finally, as both factor Va and factor VIII have structural similarities and are substrates for activated protein C the possibility that they might compete as substrates was tested. Factor VIII was observed to compete with factor Va for activated protein C. The concentration dependence of factor VIII inhibition of factor Va inactivation suggested that factor VIII and factor Va were equivalent substrates for activated protein C.

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