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Pentapeptide

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https://www.readbyqxmd.com/read/28078743/bivalent-14-mer-peptide-ligands-of-cxcr4-with-polyproline-linkers-with-anti-chemotactic-activity-against-jurkat-cells
#1
Tomohiro Tanaka, Toru Aoki, Wataru Nomura, Hirokazu Tamamura
Interaction of CXCR4 with its endogenous ligand, stromal-cell derived factor-1 (SDF-1)/CXCL12, induces various physiological functions involving chemotaxis. Bivalent ligands with a polyproline helix bearing a cyclic pentapeptide, FC131, were previously shown to have higher binding affinities for CXCR4 than the corresponding monovalent ligands. Bivalent ligands based on a 14-mer peptide T140 derivative with polyproline linkers have been designed and synthesized. The activity of these peptides as well as the effect of bivalency of the ligand on CXCR4 binding has been assessed...
January 12, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28068312/mray-antibiotic-complex-reveals-details-of-tunicamycin-mode-of-action
#2
Jonna K Hakulinen, Jenny Hering, Gisela Brändén, Hongming Chen, Arjan Snijder, Margareta Ek, Patrik Johansson
The rapid increase of antibiotic resistance has created an urgent need to develop novel antimicrobial agents. Here we describe the crystal structure of the promising bacterial target phospho-N-acetylmuramoyl-pentapeptide translocase (MraY) in complex with the nucleoside antibiotic tunicamycin. The structure not only reveals the mode of action of several related natural-product antibiotics but also gives an indication on the binding mode of the MraY UDP-MurNAc-pentapeptide and undecaprenyl-phosphate substrates...
January 9, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28056488/molecular-dynamics-simulations-reveal-structural-insights-into-inhibitor-binding-modes-and-functionality-in-human-group-iia-phospholipase-a2
#3
Ryung Rae Kim, Alpeshkumar K Malde, Alireza Nematollahi, Kieran F Scott, W Bret Church
Human group IIA phospholipase A2 (hGIIA) promotes inflammation in immune-mediated pathologies by regulating the arachidonic acid pathway through both catalysis-dependent and -independent mechanisms. The hGIIA crystal structure, both alone and inhibitor-bound, together with structures of closely related snake-venom-derived secreted phospholipase enzymes has been well described. However, differentiation of biological and non-biological contacts and the relevance of structures determined from snake venom enzymes to human enzymes are not clear...
January 5, 2017: Proteins
https://www.readbyqxmd.com/read/28054413/the-importance-of-being-aib-aggregation-and-self-assembly-studies-on-conformationally-constrained-oligopeptides
#4
Mariano Venanzi, Emanuela Gatto, Fernando Formaggio, Claudio Toniolo
The role of the conformationally constrained α-aminoisobutyric acid (Aib) residue in the aggregation and self-assembly properties of oligopeptides is discussed, critically reviewing our recent work in the field. In this connection, three significant case studies are presented: (i) aggregation propensity of Aib homo-oligopeptides of different length; (ii) perturbation of the conformational and aggregation properties of Ala-based pentapeptides by a single Aib versus Ala substitution; and (iii) build up of self-assembled monolayers formed by Aib homo-hexapeptide building blocks...
January 5, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28053324/erratum-neuroprotective-pentapeptide-cn-105-improves-functional-and-histological-outcomes-in-a-murine-model-of-intracerebral-hemorrhage
#5
Beilei Lei, Michael L James, Ji Liu, Guanen Zhou, Talaignair N Venkatraman, Christopher D Lascola, Shawn K Acheson, Laura G Dubois, Daniel T Laskowitz, Haichen Wang
No abstract text is available yet for this article.
January 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28043337/identification-and-expression-profiling-of-pheromone-biosynthesis-activating-neuropeptide-in-chlumetia-transversa-walker
#6
Hui Wei, Hong Chang, Lizhen Zheng, Shuo Lin, Yixin Chen, Houjun Tian, Jianwei Zhao, Yong Chen, Hongjiao Cai, Xiaojun Gu, Kadarkarai Murugan
Insect neuropeptides (NPs) in the pyrokinin/pheromone biosynthesis-activating neuropeptide (PBAN) family are actively involved in many essential endocrine functions. These peptides are potential targets in the search for novel insect control agents. This is the first report on the cloning and sequence determination of Chlumetia transversa (Walker) PBAN (Ct-PBAN) using rapid amplification of cDNA ends. The open reading frame of Ct-PBAN was 588bp in length and encoded 195 amino acids, which were assembled into five putative neuropeptides (diapause hormone homolog, α-neuropeptide, β-neuropeptide, PBAN, and γ-neuropeptide)...
January 2017: Pesticide Biochemistry and Physiology
https://www.readbyqxmd.com/read/28042435/proteomic-peptide-scan-of-porphyromonas-gingivalis-fima-type-ii-for-searching-potential-b-cell-epitopes
#7
A Lucchese, A Guida, G Capone, G Donnarumma, L Laino, M Petruzzi, R Serpico, F Silvestre, M Gargari
PURPOSE: To identify potential antigenic targets for Porphyromonas gingivalis vaccine development. MATERIALS AND METHODS: In the present study, we analyzed the Porphyromonas gingivalis, fimA type II primary amino acid sequence and characterized the similarity to the human proteome at the pentapeptide level. RESULTS: We found that exact peptide-peptide profiling of the fimbrial antigen versus the human proteome shows that only 19 out of 344 fimA type II pentapeptides are uniquely owned by the bacterial protein...
April 2016: Oral & Implantology
https://www.readbyqxmd.com/read/28040891/quantification-of-d-ala-d-lac-terminated-peptidoglycan-structure-in-vancomycin-resistant-enterococcus-faecalis-using-a-combined-solid-state-nmr-and-mass-spectrometry-analysis
#8
James D Chang, Erin C Foster, Hao Yang, Sung Joon Kim
Induction of vancomycin resistance in vancomycin-resistant enterococci (VRE) involves replacement of the D-Ala-D-Ala terminus of peptidoglycan (PG) stems with D-Ala-D-Lac, dramatically reducing the binding affinity of vancomycin to lipid II. Effects from vancomycin resistance induction on Enterococcus faecalis (ATCC 51299) were characterized using a combined solid-state NMR and LC-MS analysis. Solid-state NMR directly measured the total amounts of D-Lac and L,D-Ala metabolized from [2-13C]pyruvate, accumulated Park's nucleotide, and changes to the PG bridge-linking density during early exponential growth phase (OD660nm 0...
December 31, 2016: Biochemistry
https://www.readbyqxmd.com/read/28013436/opiorphin-in-burning-mouth-syndrome-patients-a-case-control-study
#9
Ivan Salarić, Maja Sabalić, Ivan Alajbeg
OBJECTIVES: Opiorphin is a pentapeptide isolated from human saliva that suppresses pain from chemically induced inflammation and acute physical pain. Burning mouth syndrome (BMS) is a chronic condition of a burning sensation in the mouth, where no underlying dental or medical cause can be identified. We aimed to measure the level of opiorphin in whole unstimulated (UWS) and stimulated (SWS) saliva of patients with BMS. MATERIALS AND METHODS: Originally developed and validated LC-MS/MS method was used for opiorphin quantification...
December 24, 2016: Clinical Oral Investigations
https://www.readbyqxmd.com/read/27998077/investigation-of-cellular-uptakes-of-the-in-tether-chiral-center-induced-helical-pentapeptides
#10
Kuan Hu, Wenjun Li, Mengying Yu, Chengjie Sun, Zigang Li
We recently reported that a precisely positioned in-tether chiral center can modulate backbone peptides' secondary structures, which provides an unbiased platform to evaluate peptides' biophysical properties solely imposed by secondary structure differences. In this work, we studied the cellular uptake efficiency and mechanism of epimer pairs of a panel of chirality-induced helical peptides (CIH peptides). Although the peptides' cellular uptake is a synergetic result of various factors, our results unambiguously indicate that helical content is an important factor for the cellular uptake of CIH peptides...
December 21, 2016: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/27997165/aromatic-aromatic-interactions-enable-%C3%AE-helix-to-%C3%AE-sheet-transition-of-peptides-to-form-supramolecular-hydrogels
#11
Jie Li, Xuewen Du, Saqib Hashim, Adrianna Shy, Bing Xu
Isolated short peptides usually are unable to maintain their original secondary structures due to the lack of the restriction from proteins. Here we show that two complementary pentapeptides from a β-sheet motif of a protein, being connected to an aromatic motif (i.e., pyrene) at their C-terminal, self-assemble to form β-sheet like structures upon mixing. Besides enabling the self-assembly to result in supramolecular hydrogels upon mixing, aromatic-aromatic interactions promote the pentapeptides transform from α-helix to β-sheet conformation...
December 22, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27987382/effect-of-4-methoxy-1-methyl-2-oxopyridine-3-carbamide-on-s-aureus-by-inhibiting-udp-murnac-pentapeptide-peptidyl-deformylase-and-uridine-monophosphate-kinase
#12
Vimjam Swarupa, Abhijit Chaudhury, Potukuchi Venkata Gurunadha Krishna Sarma
AIMS: The present study is aimed to investigate the anti-S. aureus and anti-biofilm properties of 4-Methoxy-1-Methyl-2-Oxopyridine-3-Carbamide (MMOXC) on S. aureus UDP-MurNAc-Pentapeptide (MurF), Peptidyl deformylase (PDF) and Uridine monophosphate kinase (UMPK). METHODS AND RESULTS: The in vitro efficacy of MMOXC was evaluated using qPCR, in vitro assays and broth micro dilution methods. Further, minimum inhibitory concentration (MIC), IC50 and zone of inhibition (ZOI) were recorded in addition to anti-biofilm property...
December 17, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27973909/effective-riemannian-diffusion-model-for-conformational-dynamics-of-biomolecular-systems
#13
Ashkan Fakharzadeh, Mahmoud Moradi
We present a Riemannian formalism for effective diffusion of biomolecules in collective variable spaces that provides a robust framework for conformational free energy calculation methods. Unlike their Euclidean counterparts, the Riemannian potential of mean force (PMF) and minimum free energy path (MFEP) are invariant under coordinate transformations. The presented formalism can be readily employed to modify the collective variable based enhanced sampling techniques, such as umbrella sampling (US) commonly used in biomolecular simulations, to take into account the role of intrinsic geometry of collective variable space...
December 15, 2016: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/27973857/cyclizing-pentapeptides-mechanism-and-application-of-dehydrophenylalanine-as-a-traceless-turn-inducer
#14
Diane N Le, Jan Riedel, Natalia Kozlyuk, Rachel W Martin, Vy M Dong
Dehydrophenylalanine is used as a traceless turn-inducer in the total synthesis of dichotomin E. Macrocyclization of the monomer is achieved in high yields and selectivity over cyclodimerization under conditions 100 times more concentrated than previously achieved. The enamide facilitates ring closing, and Rh-catalyzed hydrogenation of the unsaturated cyclic peptide results in selective formation of the natural product or its epimer, depending on our choice of phosphine ligand. NMR analysis and molecular modeling revealed that the linear peptide adopts a left-handed α-turn that preorganizes the N- and C-termini toward macrocyclization...
December 14, 2016: Organic Letters
https://www.readbyqxmd.com/read/27926796/novel-umami-ingredients-umami-peptides-and-their-taste
#15
REVIEW
Yin Zhang, Chandrasekar Venkitasamy, Zhongli Pan, Wenlong Liu, Liming Zhao
Umami substances are very important for food seasoning and healthy eating. In addition to monosodium glutamate and some nucleotides, recent investigations have revealed that several peptides also exhibit umami taste. In recent years, 52 peptides have been reported to show umami taste, including 24 dipeptides, 16 tripeptides, 5 octapeptides, 2 pentapeptides, 2 hexapeptides, 1 tetrapeptide, 1 heptapeptide, and 1 undecapeptide. Twenty of these peptides have been examined for the present of umami taste. In this review, we have listed these umami peptides based on their category, source, taste, and threshold concentration...
January 2017: Journal of Food Science
https://www.readbyqxmd.com/read/27909427/biocombinatorial-synthesis-of-novel-lipopeptides-by-com-domain-mediated-reprogramming-of-the-plipastatin-nrps-complex
#16
Hongxia Liu, Ling Gao, Jinzhi Han, Zhi Ma, Zhaoxin Lu, Chen Dai, Chong Zhang, Xiaomei Bie
Both donors and acceptors of communication-mediating (COM) domains are essential for coordinating intermolecular communication within nonribosomal peptides synthetases (NRPSs) complexes. Different sets of COM domains provide selectivity, allowing NRPSs to utilize different natural biosynthetic templates. In this study, novel lipopeptides were synthesized by reprogramming the plipastatin biosynthetic machinery. A Thr-to-Asp point mutation was sufficient to shift the selectivity of the donor COM domain of ppsB toward that of ppsD...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27890013/in-silico-characterization-of-a-hypothetical-protein-rv1288-of-mycobacterium-tuberculosis-containing-an-esterase-signature-and-an-uncommon-lyte-domain
#17
Arbind Kumar, Pratibha Maan, Gurpreet Singh, Jagdeep Kaur
BACKGROUND: Death toll due to tuberculosis is still rising day by day. Whole genome sequence of Mycobacterium tuberculosis has provided a platform to conduct research in order to identify the probable drug target. OBJECTIVES: Out of 4000 gene products of M. tuberculosis, approximately 40% of proteins are annotated as hypothetical. Identifying and characterizing these proteins could provide a new prescriptive for developing new TB drugs. Rv1288, a protein of M. tuberculosis H37Rv has been annotated as a hypothetical protein in database...
November 24, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27887965/muropeptide-signature-of-inhibitors-of-protein-synthesis-correlates-with-%C3%AE-lactam-synergism-against-methicillin-resistant-staphylococcus-aureus
#18
Bertrand Guignard, Paul A Majcherczyk, Cédric Monachon, Jacques Vouillamoz, Philippe Moreillon
Quinupristin/dalfopristin (Q/D) and β-lactams interact positively against methicillin-resistant Staphylococcus aureus (MRSA). The effect extends to other inhibitors of protein synthesis, but not to inhibitors of polynucleotide synthesis or assembly, or to Q/D plus non-β-lactam cell wall inhibitors. Moreover, electron microscopy studies have correlated this effect with a thickened cell wall. In this study, we sought to determine whether inhibitors of protein synthesis might produce a specific peptidoglycan muropeptide signature that would correlate with their positive β-lactam interaction...
January 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/27879684/role-of-osteogenic-growth-peptide-ogp-and-ogp-10-14-in-bone-regeneration-a-review
#19
REVIEW
Suzane C Pigossi, Marcell C Medeiros, Sybele Saska, Joni A Cirelli, Raquel M Scarel-Caminaga
Bone regeneration is a process that involves several molecular mediators, such as growth factors, which directly affect the proliferation, migration and differentiation of bone-related cells. The osteogenic growth peptide (OGP) and its C-terminal pentapeptide OGP(10-14) have been shown to stimulate the proliferation, differentiation, alkaline phosphatase activity and matrix mineralization of osteoblastic lineage cells. However, the exact molecular mechanisms that promote osteoblastic proliferation and differentiation are not completely understood...
November 22, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27878897/minimal-immune-determinants-connect-zika-virus-human-cytomegalovirus-and-toxoplasma-gondii-to-microcephaly-related-human-proteins
#20
Guglielmo Lucchese, Darja Kanduc
Aiming at the molecular definition of the relationship(s) between prenatal infections and fetal microcephaly and using pentapeptides as minimal immune determinants, we analyzed the peptide matching between proteins from infectious agents involved in microcephalic syndromes (namely Zika virus, human Cytomegalovirus, and Toxoplasma gondii) and human proteins that, when altered, have been specifically associated with microcephaly. We report that an unexpected high number of epitopic pentapeptides (ie, 34) are common to the three fetopathogenic agents and repeatedly occur throughout an important number of microcephaly-related human proteins...
November 23, 2016: American Journal of Reproductive Immunology: AJRI
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