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Pentapeptide

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https://www.readbyqxmd.com/read/29678128/spirpep-an-in-silico-digestion-based-platform-to-assist-bioactive-peptides-discovery-from-a-genome-wide-database
#1
Krittima Anekthanakul, Apiradee Hongsthong, Jittisak Senachak, Marasri Ruengjitchatchawalya
BACKGROUND: Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and animals. Conventional methods of identifying bioactive peptides are time-consuming and costly. To quicken the processes, several bioinformatics tools are recently used to facilitate screening of the potential peptides prior their activity assessment in vitro and/or in vivo...
April 20, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29660806/from-a-helix-to-a-small-cycle-metadynamics-inspired-%C3%AE-v%C3%AE-6-integrin-selective-ligands
#2
Francesco Saverio Di Leva, Stefano Tomassi, Salvatore Di Maro, Florian Reichart, Johannes Notni, Abha Dangi, Udaya Kiran Marelli, Diego Brancaccio, Francesco Merlino, Hans-Jürgen Wester, Ettore Novellino, Horst Kessler, Luciana Marinelli
The RGD-recognizing αvβ6 integrin has only recently emerged as a major target for cancer diagnosis and therapy. Thus, the development of selective, low molecular weight ligands of this receptor is still of great demand. Here, a metadynamics-driven design strategy allowed us to successfully convert a helical nonapeptide into a cyclic pentapeptide (6) showing remarkable potency and αvβ6 specificity. NMR and docking studies elucidated the reasons for the high affinity and selectivity of this compound, setting the ground for the rational design of new αvβ6-specific small sized peptides or even peptidomimetics...
April 16, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29651453/bacterial-cell-wall-precursor-phosphatase-assays-using-thin-layer-chromatography-tlc-and-high-pressure-liquid-chromatography-hplc
#3
Manuel Pazos, Christian Otten, Waldemar Vollmer
Peptidoglycan encases the bacterial cytoplasmic membrane to protect the cell from lysis due to the turgor. The final steps of peptidoglycan synthesis require a membrane-anchored substrate called lipid II, in which the peptidoglycan subunit is linked to the carrier lipid undecaprenol via a pyrophosphate moiety. Lipid II is the target of glycopeptide antibiotics and several antimicrobial peptides, and is degraded by 'attacking' enzymes involved in bacterial competition to induce lysis. Here we describe two protocols using thin-layer chromatography (TLC) and high pressure liquid chromatography (HPLC), respectively, to assay the digestion of lipid II by phosphatases such as Colicin M or the LXG toxin protein TelC from Streptococcus intermedius ...
March 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/29649141/anticancer-activity-of-anthopleura-anjunae-oligopeptides-in-prostate-cancer-du-145-cells
#4
Zong-Ze Wu, Guo-Fang Ding, Fang-Fang Huang, Zui-Su Yang, Fang-Miao Yu, Yu-Ping Tang, Ying-Lu Jia, Yuan-Yuan Zheng, Rui Chen
Anthopleura anjunae anti-tumor peptide (AAP-H) is a pentapeptide from the sea anemone Anthopleura anjunae with an amino acid sequence of Tyr-Val-Pro-Gly-Pro that is obtained by alkaline protease enzymatic hydrolysis extraction. In this study, we investigated the inhibitory effects of AAP-H on prostate cancer DU-145 cell proliferation using a methylthiazolyldiphenyl-tetrazolium bromide assay. Cell morphology was analyzed by hematoxylin-eosin staining, acridine orange/ethidium bromide fluorescence staining, Hoechst 33258 fluorescence staining, and scanning electron microscopy...
April 12, 2018: Marine Drugs
https://www.readbyqxmd.com/read/29644215/theoretical-and-nmr-conformational-studies-of-%C3%AE-proline-oligopeptides-with-alternating-chirality-of-pyrrolidine-units
#5
Alexey B Mantsyzov, Oleg Y Savelyev, Polina M Ivantcova, Stefan Bräse, Konstantin V Kudryavtsev, Vladimir I Polshakov
Synthetic β-peptides are potential functional mimetics of native α-proteins. A recently developed, novel, synthetic approach provides an effective route to the broad group of β-proline oligomers with alternating patterns of stereogenic centers. Conformation of the pyrrolidine ring, Z / E isomerism of β-peptide bonds, and hindered rotation of the neighboring monomers determine the spatial structure of this group of β-proline oligopeptides. Preferences in their structural organization and corresponding thermodynamic properties are determined by NMR spectroscopy, restrained molecular dynamics and quantum mechanics...
2018: Frontiers in Chemistry
https://www.readbyqxmd.com/read/29621526/comparative-studies-on-the-cytotoxic-effects-induced-by-nodularin-in-primary-carp-leukocytes-and-the-cells-of-the-fish-clc-line
#6
Anna Rymuszka, Anna Sieroslawska
Nodularin, one of the toxins produced by cyanobacteria commonly occurring in brackish waters, is a cyclic pentapeptide, that may exert adverse effects on animal and human health. The aim of the present study was to evaluate the cytotoxicity of nodularin on different fish cellular models. The leukocytes isolated from carp head kidney and common carp (Cyprinus carpio L.) leukocyte cell line (CLC) were incubated with the cyanotoxin at the concentrations of 0.001, 0.01, 0.05 or 0.1 μg/mL. Treatment of cells with the higher concentrations of the toxin resulted in a dramatic decrease in cell viability...
April 2, 2018: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/29618965/peptide-sharing-between-viruses-and-dlx-proteins-a-potential-cross-reactivity-pathway-to-neuropsychiatric-disorders
#7
Guglielmo Lucchese, Benjamin Stahl
The present study seeks to determine potential associations between viral infections and neuropsychiatric diseases. To address this issue, we investigated the peptide commonalities between viruses that have been related to psychiatric and neurological disorders-such as rubella, human immunodeficiency virus, and herpesviruses-and human distal-less homeobox (DLX) proteins expressed in developing brain-namely, DLX1, DLX2, DLX5, and DLX6. Peptide matching analyses revealed a high degree of pentapeptide sharing...
2018: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29615689/involvement-of-rsk1-activation-in-malformin-enhanced-cellular-fibrinolytic-activity
#8
Yukio Koizumi, Kenichiro Nagai, Lina Gao, Souichi Koyota, Tomokazu Yamaguchi, Miyuki Natsui, Yumiko Imai, Keiji Hasumi, Toshihiro Sugiyama, Keiji Kuba
Pharmacological interventions to enhance fibrinolysis are effective for treating thrombotic disorders. Utilizing the in vitro U937 cell line-based fibrin degradation assay, we had previously found a cyclic pentapeptide malformin A1 (MA1 ) as a novel activating compound for cellular fibrinolytic activity. The mechanism by which MA1 enhances cellular fibrinolytic activity remains unknown. In the present study, we show that RSK1 is a crucial mediator of MA1 -induced cellular fibrinolysis. Treatment with rhodamine-conjugated MA1 showed that MA1 localizes mainly in the cytoplasm of U937 cells...
April 3, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29615498/-chlamydia-trachomatis-dapf-encodes-a-bifunctional-enzyme-capable-of-both-d-glutamate-racemase-and-diaminopimelate-epimerase-activities
#9
George Liechti, Raghuveer Singh, Patricia L Rossi, Miranda D Gray, Nancy E Adams, Anthony T Maurelli
Peptidoglycan is a sugar/amino acid polymer unique to bacteria and essential for division and cell shape maintenance. The d-amino acids that make up its cross-linked stem peptides are not abundant in nature and must be synthesized by bacteria de novo d-Glutamate is present at the second position of the pentapeptide stem and is strictly conserved in all bacterial species. In Gram-negative bacteria, d-glutamate is generated via the racemization of l-glutamate by glutamate racemase (MurI). Chlamydia trachomatis is the leading cause of infectious blindness and sexually transmitted bacterial infections worldwide...
April 3, 2018: MBio
https://www.readbyqxmd.com/read/29613770/nanoenzyme-augmented-cancer-sonodynamic-therapy-by-catalytic-tumor-oxygenation
#10
Piao Zhu, Yu Chen, Jianlin Shi
Ultrasound (US)-triggered sonodynamic therapy (SDT) can solve the critical issue of low tissue-penetrating depth of traditional phototriggered therapies, but the SDT efficacy is still not satisfactorily high in combating cancer at the current stage. Here we report on augmenting the SDT efficacy based on catalytic nanomedicine, which takes the efficient catalytic features of nanoenzymes to modulate the tumor microenvironment (TME). The multifunctional nanosonosensitizers have been successfully constructed by the integration of a MnOx component with biocompatible/biodegradable hollow mesoporous organosilica nanoparticles, followed by conjugation with protoporphyrin (as the sonosensitizer) and cyclic arginine-glycine-aspartic pentapeptide (as the targeting peptide)...
April 5, 2018: ACS Nano
https://www.readbyqxmd.com/read/29608300/structure-activity-relationship-study-of-cyclic-pentapeptide-ligands-for-atypical-chemokine-receptor-3-ackr3
#11
Haruka Sekiguchi, Tomoko Kuroyanagi, David Rhainds, Kazuya Kobayashi, Yuka Kobayashi, Hiroaki Ohno, Nikolaus Heveker, Kenichi Akaji, Nobutaka Fujii, Shinya Oishi
The atypical chemokine receptor 3 (ACKR3)/CXC chemokine receptor 7 (CXCR7) recognizes stromal cell-derived factor 1 (SDF-1)/CXCL12 and is involved in a number of physiological and pathological processes. Here, we investigated the SAR of the component amino acids in a ACKR3-selective ligand, FC313 [cyclo(-D-Tyr-L-Arg-L-MeArg-L-Nal(2)-L-Pro-)], for the devel-opment of highly active ACKR3 ligands. Notably, modification at the L-Pro position with a bulky hydrophobic side chain led to improved bioactivity toward ACKR3...
April 2, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29603545/tunable-pentapeptide-self-assembled-%C3%AE-sheet-hydrogels
#12
David E Clarke, Christopher D J Parmenter, Oren A Scherman
Oligopeptide-based supramolecular hydrogels hold promise in a range of applications. The gelation of these systems is hard to control with minor alterations in the peptide sequence significantly influencing the self-assembly process. This makes sequence design difficult whereby typical self-assembly rules cannot be applied. We explored the design of pentapeptide sequences with different charge distributions and discovered that they formed robust, pH-responsive hydrogels. Through altering the concentration and charge distribution of the peptide sequence, we demonstrated that the stiffness of the hydrogels can be tuned across two orders of magnitude (2-200 kPa)...
March 30, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29601819/the-crystal-structure-and-oligomeric-form-of-escherichia-colil-d-carboxypeptidase-a
#13
Karen Meyer, Christine Addy, Satoko Akashi, David I Roper, Jeremy R H Tame
Bacterial peptidoglycan is constructed by cross-linking sugar chains carrying pentapeptide building blocks with two d-alanine residues at the C-terminus. Incorporation into the polymer and subsequent breakdown of peptidoglycan releases a tetrapeptide with a single d-alanine residue. Removal of this residue is necessary for the tripeptide to receive a new D-Ala-D-Ala dipeptide in the synthetic pathway, but proteases are generally unable to work with substrates having residues of unusual chirality close to the scissile bond...
March 27, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29589926/designing-well-structured-cyclic-pentapeptides-based-on-sequence-structure-relationships
#14
Diana P Slough, Sean M McHugh, Ashleigh E Cummings, Peng Dai, Bradley L Pentelute, Joshua A Kritzer, Yu-Shan Lin
Cyclic peptides are a promising class of molecules for unique applications. Unfortunately, cyclic peptide design is severely limited by the difficulty in predicting the conformations they will adopt in solution. In this work, we use explicit-solvent molecular dynamics simulations to design well-structured cyclic peptides by studying their sequence-structure relationships. Critical to our approach is an enhanced sampling method that exploits the essential transitional motions of cyclic peptides to efficiently sample their conformational space...
March 28, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29582500/the-stereodynamics-of-macrocyclic-succinimide-thioethers
#15
Stefan Lenz, Philip Horx, Armin Geyer
Maleimide-thiol coupling is a popular bioconjugation strategy, but little is known about the stereoselectivity and the stereodynamics of the succinimide thioether formed in a biopolymer environment. We used thiol 1,4-addition for the macrocyclisation of 5 designed pentapeptides with the ringsize of hexapeptides because they incorporate the succinimide thioether (4-8). Both succinimide diastereomers are observed in the constrained macrocyclic rings in each case. In spite of the low diastereoselectivity of the macrocyclisation reaction, there is a significant influence of the amino acid environment on the epimerization rate of the succinimide...
March 27, 2018: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/29580681/head-to-tail-macrocyclization-of-cysteine-free-peptides-using-an-o-aminoanilide-linker
#16
Takumi Ohara, Masato Kaneda, Tomo Saito, Nobutaka Fujii, Hiroaki Ohno, Shinya Oishi
A head-to-tail macrocyclization protocol for the preparation of cysteine-free cyclic peptides was investigated. The o-aminoanilide linker constructed in the peptide sequence by a standard Fmoc-based peptide synthesis procedure was subjected to nitrite-mediated activation under acidic conditions toward N-acyl benzotriazole as the active ester species. The subsequent cyclization smoothly proceeded by neutralization in the presence of additives such as 1-hydroxybenzotriazole (HOBt) and 1-hydroxy-7-azabenzotriazole (HOAt) to afford the expected cyclic pentapeptide, a CXCR4 antagonist...
March 14, 2018: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29559839/synthesis-and-in-vitro-experiments-of-carcinoma-vascular-endothelial-targeting-polymeric-nano-micelles-combining-small-particle-size-and-supermagnetic-sensitivity
#17
Yi Zhang, Jielin Pan, Qilan Xu, Hao Li, Jianhao Wang, Chao Zhang, Guobin Hong
Objective: To construct carcinoma vascular endothelial-targeted polymeric nanomicelles with high magnetic resonance imaging (MRI) sensitivity and to evaluate their biological safety and in vitro tumor-targeting effect, and to monitor their feasibility using clinical MRI scanner. Method: Amphiphilic block copolymer, poly(ethylene glycol)- b -poly(ε-caprolactone) (PEG-PCL) was synthesized via the ring-opening polymerization of ε-caprolactone (CL) initiated by poly(ethylene glycol) (PEG), in which cyclic pentapeptide Arg-Gly-Asp (cRGD) was conjugated with the terminal of hydrophilic PEG block...
2018: International Journal of Medical Sciences
https://www.readbyqxmd.com/read/29552219/a-ly-15-a-novel-cyclic-pentapeptide-that-inhibits-b16-cell-proliferation-and-migration-and-induces-cell-apoptosis
#18
Xuan Wang, Xiangli Yao, Shiming Fan, Chenshuang Xiang, Runjiao Liu, Juan Feng, Jing Huang, Shouxin Liu
Melanoma is highly resistant to most traditional treatments; therefore, its incidence and mortality rates are rapidly increasing. The effect of a novel sansalvamide A analogue named LY-15 on the growth and induction of apoptosis in B16 cancer cells was investigated in vitro . The inhibitory effects of LY-15 on B16 cells occurred in a concentration- and time-dependent manner. The B16 cells were cultured in various concentrations of LY-15 (5, 15 and 25 µM), and the ameliorating effect of LY-15 was evaluated using apoptotic protein markers B-cell lymphoma 2 (Bcl-2), Bcl-2-associated X protein (Bax), caspase-3 and caspase-9...
April 2018: Oncology Letters
https://www.readbyqxmd.com/read/29548784/high-expression-of-integrin-%C3%AE-v%C3%AE-3-enables-uptake-of-targeted-fluorescent-probes-into-ovarian-cancer-cells-and-tumors
#19
Scott K Shaw, Cynthia L Schreiber, Felicia M Roland, Paul M Battles, Seamus P Brennan, Simon J Padanilam, Bradley D Smith
The cell line OVCAR-4 was recently ranked as one of the most representative cell lines for high grade serous ovarian cancer (HGSOC). However, little work has been done to assess the susceptibility of OVCAR-4 cells and tumors to the more common types of molecular targeting. Proteome profiles suggest OVCAR-4 express high levels of integrin αvβ3 receptors. Using flow cytometry with fluorescent antibodies we determined that OVCAR-4 cells have high number of integrin αvβ3 receptors ([9.8 ± 2.5] × 104 /cell) compared to the well-characterized cell line U87-MG ([5...
March 6, 2018: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29548439/secondary-structure-changes-induced-by-pulsed-electric-field-affect-antioxidant-activity-of-pentapeptides-from-pine-nut-pinus-koraiensis-protein
#20
Rong Liang, Sheng Cheng, Xiuying Wang
We used a pulsed electric field (PEF) to treat four pentapeptides with similar amino acid sequences (KCHKP, KCHQP, QCHKP, and QCHQP). We then evaluated antioxidant activity of the pentapeptides according to ferric reducing antioxidant power (FRAP) and hydroxyl radical scavenging capacity. Structures of the peptides were determined by high performance liquid chromatography (HPLC), mid-infrared (MIR), circular dichroism (CD) spectroscopy, and nuclear magnetic resonance (NMR). The results indicated that antioxidant activities of KCHQP and QCHKP were increased by PEF, whereas those of KCHKP and QCHQP were reduced...
July 15, 2018: Food Chemistry
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