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Isabel Hottmann, Valentina M T Mayer, Markus B Tomek, Valentin Friedrich, Matthew B Calvert, Alexander Titz, Christina Schäffer, Christoph Mayer
Tannerella forsythia is an anaerobic, Gram-negative oral pathogen that thrives in multispecies gingival biofilms associated with periodontitis. The bacterium is auxotrophic for the commonly essential bacterial cell wall sugar N-acetylmuramic acid (MurNAc) and, thus, strictly depends on an exogenous supply of MurNAc for growth and maintenance of cell morphology. A MurNAc transporter (Tf_MurT; Tanf_08375) and an ortholog of the Escherichia coli etherase MurQ (Tf_MurQ; Tanf_08385) converting MurNAc-6-phosphate to GlcNAc-6-phosphate were recently described for T...
2018: Frontiers in Microbiology
Chongyang Wu, Huy N Hoang, Ligong Liu, David P Fairlie
A new strategy is demonstrated for making peptides helical, using a carbohydrate to bridge between sidechains at each end of a pentapeptide. CD and NMR spectra establish that both an α-helix and a 310-helix structure can form depending upon the bridge.
February 12, 2018: Chemical Communications: Chem Comm
Young-Yoon Kim, Hailan Li, Yu Seok Song, Hyo-Soon Jeong, Hye-Young Yun, Kwang Jin Baek, Nyoun Soo Kwon, Yong Kyoo Shin, Kyoung-Chan Park, Dong-Seok Kim
Since the use of animal experimentation is restricted with regard to cosmetic materials, alternative in vitro models such as skin equivalents (SEs) are needed. Laminin is one of the major non-collagenous glycoproteins. The pentapeptide YIGSR (Tyr-Ile-Gly-Ser-Arg) is a functional motif of laminin that binds to the laminin receptor. In the present study, we examined whether YIGSR could improve the reconstruction of SEs. YIGSR has no effects on monolayer cell proliferation of CCD25-Sk fibroblasts or HaCaT keratinocytes...
February 7, 2018: Journal of Tissue Viability
Baiping Mao, Caixia Liu, Wenwen Zheng, Xiaoheng Li, Renshan Ge, Haifa Shen, Xiaoling Guo, Qingquan Lian, Xian Shen, Chao Li
Regenerated silk fibroin (SF) is a natural biomacromolecule with excellent biocompatible and biodegradable properties. In this study, cyclic pentapeptide cRGDfk and Chlorin e6 (Ce6) were conjugated to SF polypeptides, and genipin was used to prepare 5-fluorouracil (5-FU) doped SF-based nanoparticles (NPs). The photodynamic therapy (PDT) potential and active targeting properties were systematically investigated in αvβ3 integrin receptor over-expressed MGC-803 cells in vitro. The results revealed that treatment with the multifunctional SF-based NPs and PDT, high level of reactive oxygen species (ROS) and cell death can be induced in MGC-803 cells...
February 3, 2018: Biomaterials
Igor Sabljić, Marko Tomin, Mihaela Matovina, Iva Sučec, Ana Tomašić Paić, Antonija Tomić, Marija Abramić, Sanja Tomić
Dipeptidyl peptidase III (DPP III) isolated from the thermophilic bacteria Caldithrix abyssi (Ca) is a two-domain zinc exopeptidase, a member of the M49 family. Like other DPPs III, it cleaves dipeptides from the N-terminus of its substrates but differently from human, yeast and Bacteroides thetaiotaomicron (mesophile) orthologs, it has the pentapeptide zinc binding motif (HEISH) in the active site instead of the hexapeptide (HEXXGH). The aim of our study was to investigate structure, dynamics and activity of CaDPP III, as well as to find possible differences with already characterized DPPs III from mesophiles, especially B...
2018: PloS One
Ali Moayedi, Leticia Mora, Maria Concepción Aristoy, Mohammad Safari, Maryam Hashemi, Fidel Toldrá
In this study, tomato seeds were obtained as by-products and submitted to fermentation with the proteolytic strain Bacillus subtilis A14h. The resulting peptide mixture was fractionated and purified through different chromatographic steps. Fractions were assayed for antioxidant and angiotensin converting enzyme (ACE)-inhibitory activities and peptides were identified by using nano-liquid chromatography coupled to mass spectrometry in tandem (nLC-MS/MS). Most of the identified peptides were smaller than 1000 Da and had different aromatic and hydrophobic amino acid residues...
June 1, 2018: Food Chemistry
Akira Katsuyama, Satoshi Ichikawa
Muraymycins, isolated from a culture broth of Streptomyces sp., are members of a class of naturally occurring nucleoside antibiotics. They are strong inhibitors of the phospho-MurNAc-pentapeptide translocase (MraY), which is responsible for the peptidoglycan biosynthesis. Since MraY is an essential enzyme among bacteria, muraymycins are expected to be a novel antibacterial agent. In this review, our efforts to synthesize muraymycin D2, simplify the chemical structure, improve antibacterial spectrum, and solve the X-ray crystal structure of the muraymycin D2/MraY complex are described...
2018: Chemical & Pharmaceutical Bulletin
Jia-Jung Ho, Ayanjeet Ghosh, Tianqi O Zhang, Martin T Zanni
Two-dimensional sum-frequency generation spectroscopy (2D SFG) is used to study the structures of the pentapeptide FGAIL on hydrogen bond promoting surfaces. FGAIL is the most amyloidogenic portion of the human islet amyloid polypeptide (hIAPP or amylin). In the presence of a pure gold surface, FGAIL does not form ordered structures. When the gold is coated with a self-assembled monolayer of mercaptobenzoic acid (MBA), 2D SFG spectra reveal features associated with β-sheets. Also observed are cross peaks between the FGAIL peptides and the carboxylic acid groups of the MBA monolayer, indicating that the peptides are in close contact with the surface headgroups...
January 25, 2018: Journal of Physical Chemistry. A
Noelia Bernardo-Garcia, Kiran V Mahasenan, Maria T Batuecas, Mijoon Lee, Dusan Hesek, Denisa Petráčková, Linda Doubravová, Pavel Branny, Shahriar Mobashery, Juan A Hermoso
Transpeptidases, members of the penicillin-binding protein (PBP) families, catalyze crosslinking of the bacterial cell wall. This transformation is critical for the survival of bacteria and it is the target of inhibition by -lactam antibiotics. We report herein our structural insights into catalysis by the essential PBP2x of Streptococcus pneumoniae by disclosing a total of four X-ray structures, two computational models based on the crystal structures and molecular-dynamics simulations. The X-ray structures are for the apo PBP2x, the enzyme modified covalently in the active site by oxacillin (a penicillin antibiotic), the enzyme modified by oxacillin in the presence of a synthetic tetrasaccharide surrogate for the cell-wall peptidoglycan and a non-covalent complex of cefepime (a cephalosporin antibiotic) bound to the active site...
January 22, 2018: ACS Chemical Biology
Rahul Goel, Charu Garg, Hemant Kumar Gautam, Ashwani Kumar Sharma, Pradeep Kumar, Alka Gupta
The present article describes designing and fabrication of nanostructures from a mixed α/β-pentapeptide, Lys-βAla-βAla-Lys-βAla, which majorly contains non-natural β-alanine residues in the backbone with two α-lysine residues at 1- and 4-positions. The amphiphilic pentapeptide showed the ability to self-assemble into cationic nanovesicles in an aqueous solution. The average size of peptide nanostructures was found to be ~270 nm with a very high cationic charge of ~+40 mV. TEM micrographs revealed the average size of the same nanostructures ~80 nm bearing vesicular morphology...
January 17, 2018: International Journal of Biological Macromolecules
Zijian Liu, Hidetoshi Noda, Masakatsu Shibasaki, Naoya Kumagai
Waste-free catalytic assembly of α-amino acids is fueled by a multiboron catalyst that features a characteristic B3NO2 heterocycle, providing a versatile catalytic protocol wherein functionalized natural α-amino acid units are accommodated and commonly used protecting groups are tolerated. The facile dehydrative conditions eliminate the use of engineered peptide coupling reagents, exemplifying a greener catalytic alternative for peptide coupling. The catalysis is sufficiently robust to enable pentapeptide synthesis, constructing all four amide bond linkages in a catalytic fashion...
January 17, 2018: Organic Letters
Yuliya V Samoylova, Ksenia N Sorokina, Margarita V Romanenko, Valentin N Parmon
A new esterase gene from thermophilic bacteria Ureibacillus thermosphaericus was cloned into the pET32b vector and expressed in Escherichia coli BL21(DE3). Alignment of the estUT1 amino acid sequence revealed the presence of a novel canonical pentapeptide (GVSLG) and 41-47% identity to the closest family of the bacterial lipases XIII. Thus the esterase estUT1 from U. thermosphaericus was assigned as a member of the novel family XVIII. It also showed a strong activity toward short-chain esters (C2-C8), with the highest activity for C2...
January 12, 2018: Extremophiles: Life Under Extreme Conditions
Siamak Semsary, Ivana Crnovčić, Ronja Driller, Joachim Vater, Bernhard Loll, Ullrich Keller
X-type actinomycins (Acms) contain 4-hydroxyproline (Acm X0) or 4-oxoproline (Acm X2) in their ß-pentapeptide lactone rings whereas their α-ring contains proline. We demonstrate that these Acms are formed through asymmetric condensation of Acm half molecules (Acm halves) containing proline with 4-hydroxyproline- or 4-oxo-proline-containing Acm halves. In turn we show - using an artificial Acm half analogue (PPL 1) with proline in its peptide chain - its conversion into the 4-hydroxyproline and 4-oxoproline-containing Acm halves, PPL 0 and PPL 2, in mycelial suspensions of Streptomyces antibioticus...
January 12, 2018: Chembiochem: a European Journal of Chemical Biology
R Otter, K Klinker, D Spitzer, M Schinnerer, M Barz, P Besenius
We report the synthesis of ABA' triblock peptide-polysarcosine-peptide conjugates featuring two complementary phenylalanine-histidine pentapeptide strands A/A'. These sequences encode for antiparallel β-sheet formation into folded conjugates, which promote the self-assembly into polysarcosine-shielded core-shell nanorods. These do not cause aggregation of serum proteins in human blood plasma underlining an enhanced stability.
December 18, 2017: Chemical Communications: Chem Comm
Alejandra P Frasch, León A Bouvier, Florencia M Oppenheimer, Maria Aparecida Juliano, Luiz Juliano, Adriana K Carmona, Juan José Cazzulo, Gabriela T Niemirowicz
Metallocarboxypeptidases (MCPs) of the M32 family, while broadly distributed among prokaryotic organisms, have so far been only found in a few eukaryotes including trypanosomatids. Among these organisms are human and animal pathogens of medical relevance such as Trypanosoma brucei and Trypanosoma cruzi, the respective causative agents of sleeping sickness and Chagas disease. The M32 MCP orthologues found in these parasites share 72% protein sequence identity. They also present a cytosolic localization, a similar pattern of expression and a marked preference for Arg/Lys residues at P1'...
December 12, 2017: Molecular and Biochemical Parasitology
Steve Catarino, Paulo Pereira, Henrique Girão
Chaperone-mediated autophagy (CMA) is a selective form of autophagy in which cytosolic proteins bearing a pentapeptide motif biochemically related to the KFERQ sequence, are recognized by the heat shock protein family A member 8 (HSPA8) chaperone, delivered to the lysomal membrane, and directly translocated across the lysosomal membrane by a protein complex containing lysosomal associated membrane protein 2a (Lamp2a). Since its discovery over two decades ago, the importance of this pathway in cell proteostasis has been made increasingly apparent...
December 12, 2017: Essays in Biochemistry
Konda Mani Saravanan, A Keith Dunker, Sankaran Krishnaswamy
More than sixty prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the world-wide web. Nearly, all of these predictors give balanced accuracies in the ~65% to ~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions...
December 11, 2017: Journal of Biomolecular Structure & Dynamics
T Rytömaa, K Grip-Rytömaa
OBJECTIVES: When rat chloroleukaemia (CHL) cells are grown undisturbed in a confined space, a genomic long interspersed nuclear element (LINE) is transcriptionally activated at a relatively low population density, followed by the retrotransposition of LINE and population death. This death programme is fundamentally different from conventional cell death pathways. MATERIALS AND METHODS: This work is essentially based on the re-analysis of relevant, old experimental data...
December 10, 2017: Cell Proliferation
Andrea Pizzi, Valentina Dichiarante, Giancarlo Terraneo, Pierangelo Metrangolo
Amyloidogenic peptide fragment KLVFF (H2 N-Lys-Leu-Val-Phe-Phe-COOH, Aβ16-20 ), the core-sequence of the polypeptide Aβ40, is a well-studied model for amyloid formation. However, due to its low crystallinity, detailed atomic information of KLVFF structure is lacking. Here we report the high-resolution single-crystal X-ray structure of two monohalogenated KLVFF derivatives, KLVFF(I) and KLVFF(Br). The obtained results highlight how halogenation is a good strategy to promote crystallization and facilitate the phase determination of KLVFF(I) and KLVFF(Br) fragments...
November 27, 2017: Biopolymers
Aleksandra Kotynia, Edward Krzyżak, Elżbieta Kamysz, Małgorzata Sobocińska, Justyna Brasuń
Three novel analogues of salivary peptides as sialorphin (QHNPR) and opiorphin (QRFSR) were synthesized by the solid-phase method. The sequences of these ligands were following: AHNPR, QANPR and QRFPR. The aim of our work was investigation in what way some structural modifications may impact on coordination abilities of studied peptides. In this work we presented the interaction of pentapeptides with copper(II) ions in wide range of pH. To determine the coordination model of ligands there were carried out several studies by spectroscopy (UV-Vis, CD) methods and potentiometric measurements...
2017: International Journal of Peptide Research and Therapeutics
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