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peptide array

Deborah A Barkley, Yekaterina Rokhlenko, Jeannette E Marine, Rachelle David, Dipankar Sahoo, Matthew D Watson, Tadanori Koga, Chinedum O Osuji, Jonathan G Rudick
Combining monodisperse building blocks that have distinct folding properties serves as a modular strategy for controlling structural complexity in hierarchically organized materials. We combine an α-helical bundle-forming peptide with selfassembling dendrons to better control the arrangement of functional groups within cylindrical nanostructures. Site-specific grafting of dendrons to amino acid residues on the exterior of the α-helical bundle yields monodisperse macromolecules with programmable folding and self-assembly properties...
October 18, 2017: Journal of the American Chemical Society
Mukesh Bhatt, Jajati K Mohapatra, Laxmi K Pandey, Nihar N Mohanty, Biswajit Das, Bikash R Prusty, Bramhadev Pattnaik
Inactivated purified whole virus vaccines are used for control of foot and mouth disease (FMD). ELISAs detecting antibodies to the nonstructural proteins (NSP), a marker of infection, are primarily used to differentiate FMD virus (FMDV) infected from vaccinated animals (DIVA). However, such DIVA assays have a limitation to their specificity since residual NSPs present in the relatively impure vaccines are suspected to induce an NSP-antibody response in the repeatedly vaccinated animals. Epitope-deleted negative marker vaccine strategy seems to have an advantage over the conventional vaccines in identifying the infected animals with accuracy...
October 14, 2017: Virus Research
Margaret R Byers, Leanne M Cornel
OBJECTIVE: Intradental sensory receptors trigger painful sensations and unperceived mechanosensitivity, but the receptor bases for those functions are only partly defined. We present new evidence here concerning complex endings of myelinated axons in rat molars. DESIGN: We sectioned mature rat jaws in sagittal and transverse planes to analyze neural immunoreactivity (IR) for parvalbumin, peripherin, neurofilament protein, neurotrophin receptors, synaptophysin, calcitonin gene-related peptide (CGRP), or mas-related g-protein-receptor-d (Mrgprd)...
September 29, 2017: Archives of Oral Biology
Márcia I Souza, Tatiana Prieto, Tiago Rodrigues, Fabio F Ferreira, Francisco B Nascimento, Anderson O Ribeiro, Emerson R Silva, Francesca Giuntini, Wendel A Alves
We present the synthesis and characterization of new peptide conjugates obtained by hierarchical co-assembly of L,L-diphenylalanine (FF) and zinc phthalocyanine complexes (ZnPc) in water. Self-assembly capabilities under defined conditions were investigated by scanning electron microscopy, and photophysical properties were evaluated using UV-Vis and fluorescence spectroscopy. AFM observations demonstrated that these ZnPcs form different highly ordered arrays on the crystalline faces of the FF microplates and that surface roughness significantly changes with the presence of differently substituted phthalocyanine units...
October 13, 2017: Scientific Reports
Palaniraja Thandapani, Anthony M Couturier, Zhenbao Yu, Xing Li, Jean-François Couture, Shawn Li, Jean-Yves Masson, Stéphane Richard
The DNA damage response (DDR) is central to the cell survival and it requires post-translational modifications, in part, to sense the damage, amplify the signaling response and recruit and regulate DNA repair enzymes. Lysine methylation of histones such as H4K20 and non-histone proteins including p53 has been shown to be essential for the mounting of the DDR. It is well-known that the lysine methyltransferase SET7 regulates the DDR, as cells lacking this enzyme are hypersensitive to chemotherapeutic drugs. To define addition substrates of SET7 involved in the DDR, we screened a peptide array encompassing potential lysine methylation sites from >100 key DDR proteins and identified peptides from 58 proteins to be lysine methylated defining a methylation consensus sequence of [S>K(-2); S>R(-1); K(0)] consistent with previous findings...
September 12, 2017: Oncotarget
Prashant Kumar, Allen Takayesu, Usama Abbasi, Manu Thomas Kalathottukaren, Srinivas Abbina, Jayachandran N Kizhakkedathu, Suzana K Straus
We report the synthesis, characterization, activity and biocompatibility of a novel series of antimicrobial peptide-polymer conjugates. Using the parent peptide aurein 2.2, we designed a peptide array (~100 peptides) with single and multiple W and R mutations and identified antimicrobial peptides (AMPs) with potent activity against S. aureus. These novel AMPs were conjugated to hyperbranched polyglycerol (HPG) of different molecular weights and number of peptides to improve their antimicrobial activity and toxicity...
October 11, 2017: ACS Applied Materials & Interfaces
Leticia Mora, Tomás Bolumar, Alejandro Heres, Fidel Toldrá
Ageing is widely used in the meat industry to improve tenderness mainly as a result of the breakdown of muscular proteins through the action of endopeptidases during storage time. In addition, meat contains a large pool of other proteolytic enzymes, mainly exopeptidases, which cut from the outer edges of proteins and polypeptides generating a vast array of peptides and free amino acids. Some of these peptides could potentially exert bioactivities of interest for human health. In this study, ACE-inhibitory and antioxidant activities during meat ageing in chilled-storage at 4 °C for a period of time of 0, 1, 2, 3 and 4 weeks have been determined...
October 9, 2017: Food & Function
Yulin Yuan, Hongting Wang, Zuan-Tao Lin, Xia Hong, Mikala Heon, Tianfu Wu
Antigen arrays are fabricated using various antigens such as DNA, histones, synthetic peptides, recombinant proteins, or cell extracts to detect autoantibodies in autoimmune diseases, alloantibodies in transplantation, drug-induced antibodies or cancer-induced antibodies in blood or cell culture supernatant. In this protocol, we will provide a step-by-step executable procedure to perform antigen arrays, including antigen preparation and printing, blocking, sample loading, array detection, imaging, and data analysis...
2017: Methods in Molecular Biology
Hasan Mahmud, Frank J G Scherpen, Tiny Meeuwsen de Boer, Harm-Jan Lourens, Caroline Schoenherr, Matthias Eder, Michaela Scherr, Victor Guryev, Eveline S De Bont
The t(8;21) (q22;q22) chromosomal translocation is one of the most frequent genetic alterations in acute myeloid leukemia (AML) which has a need for improved therapeutic strategies. We found PLC-γ1 as one of the highest phosphorylated peptides in t(8;21) AML samples compared to NBM or CN-AML in our previous peptide microarray. PLC-γ1 is known to play a role in cancer progression, however, the impact of PLC-γ1 in AML is currently unknown. Therefore, we aimed to study the functional role of PLC-γ1 by investigating the cellular growth, survival and its underlying mechanism in t(8;21) AML...
September 15, 2017: Oncotarget
Prashant Sharma, Hyun Ah Cho, Jae-Won Lee, Woo Seung Ham, Bum Chul Park, Nam-Hyuk Cho, Young Keun Kim
Zinc oxide (ZnO) nanocomposites have been widely applied in biomedical fields due to their multifunctionality and biocompatibility. However, the physicochemical properties of ZnO nanocomposite involved in nano-bio interactions are poorly defined. To assess the potential applicability of ZnO nanowires for intracellular delivery of biomolecules, we examined the dynamics of cellular activity of cells growing on densely packed ZnO nanowire arrays with two different physical conformations, vertical (VNW) or fan-shaped (FNW) nanowires...
October 19, 2017: Nanoscale
Kyeonga Noh, Misun Kim, Youngmi Kim, Hanearl Kim, Hyuna Kim, Jaehwan Byun, Yeongseo Park, Hansoo Lee, Yun Sil Lee, Jongseon Choe, Young Myeong Kim, Dooil Jeoung
The regulatory role of suppressor of cytokine signaling 1 (SOCS1) in inflammation has been reported. However, its role in allergic inflammation has not been previously reported. SOCS1 mediated in vitro and in vivo allergic inflammation. Histone deacetylase-3 (HDAC3), a mediator of allergic inflammation, interacted with SOCS1, and miR-384 inhibitor, a positive regulator of HDAC3, induced features of allergic inflammation in an SOCS1-dependent manner. miRNA array analysis showed that the expression of miR-122 was decreased by antigen-stimulation...
September 8, 2017: Oncotarget
Xiong Wang, Dan Liu, He-Zhou Huang, Zhi-Hao Wang, Tong-Yao Hou, Xin Yang, Pei Pang, Na Wei, Ya-Fan Zhou, Marie-Josée Dupras, Frédéric Calon, Yu-Tian Wang, Heng-Ye Man, Jian-Guo Chen, Jian-Zhi Wang, Sébastien S Hébert, Youming Lu, Ling-Qiang Zhu
BACKGROUND: Synaptic loss is an early pathological event in Alzheimer's disease (AD), but its underlying molecular mechanisms remain largely unknown. Recently, microRNAs (miRNAs) have emerged as important modulators of synaptic function and memory. METHODS: We used miRNA array and quantitative polymerase chain reaction to examine the alteration of miRNAs in AD mice and patients as well as the Morris water maze to evaluate learning and memory in the mice. We also used adeno-associated virus or lentivirus to introduce tyrosine-protein phosphatase non-receptor type 1 (PTPN1) expression of silencing RNAs...
August 10, 2017: Biological Psychiatry
Uwe Heiko Bunz, Jinsong Han, Haoran Cheng, Benhua Wang, Markus Braun, Xiaobo Fan, Markus Bender, Wei Huang, Cornelius Domhan, Walter Mier, Thomas Lindner, Kai Seehafer, Michael Wink
A negatively charged poly(para-phenyleneethynylene) (PPE) forms electrostatic complexes with four positively charged antimicrobial peptides (AMP). The AMPs quench the fluorescence of the PPE. The four partially quenched complexes discriminate fourteen different bacteria in water and in human urine by pattern based fluorescence recognition (i.e. fluorescence is turned on or off), owing to the differential binding of the AMP-PPE complexes to the components of bacterial surfaces. The different bacterial species and strains form clusters according to staining properties (Gram-positive and Gram-negative) or genetic similarity (genus, species and strain)...
September 28, 2017: Angewandte Chemie
Eike Müller, Tilo Pompe, Uwe Freudenberg, Carsten Werner
Array-format cell-culture carriers providing tunable matrix cues are instrumental in current cell biology and bioengineering. A new solvent-assisted demolding approach for the fabrication of microcavity arrays with very small feature sizes down to single-cell level (3 µm) of very soft biohybrid glycosaminoglycan-poly(ethylene glycol) hydrogels (down to a shear modulus of 1 kPa) is reported. It is further shown that independent additional options of localized conjugation of adhesion ligand peptides, presentation of growth factors through complexation to gel-based glycosaminoglycans, and secondary gel deposition for 3D cell embedding enable a versatile customization of the hydrogel microcavity arrays for cell culture studies...
September 28, 2017: Advanced Materials
Wei-Wei Li, Ming-Sheng Xia, Wen-Bin Li, Li-Wen Liu, Ying Yang, Jian-Hong Li
Cell surface structure plays a key role in Microcystis colony formation. The S-layer is a crystalline array of monomolecular proteins that constitute the outermost component of the cyanobacterial cell envelope. To date, no biochemical characterization of the S-layer protein in Microcystis has been reported. Here, we compared S-layer on the cell wall of the unicellular strain Microcystis aeruginosa PCC7806 with the colonial strain M. aeruginosa XW01. We observed crystalline S-layers in XW01 cell walls; however, similar structures were not observed in PCC7806...
September 27, 2017: Current Microbiology
Jin-Hee Lee, Bing Yang, Anastasia J Lindahl, Nathan Damaschke, Melissa D Boersma, Wei Huang, Eva Corey, David F Jarrard, John M Denu
There is a tremendous need for novel strategies aimed at directly assessing activities of histone modifiers to probe epigenetic determinants associated with disease progression. Here, we developed a high-throughput peptide microarray assay to identify altered histone lysine (de)acetylation activity in prostate cancer (PCa). This microarray-based activity assay revealed up-regulated histone acetyltransferase (HAT) activity against specific histone H3 sites in a castrate-resistant (CR) PCa cell line compared to its hormone-sensitive (HS) isogenic counterpart...
October 11, 2017: ACS Chemical Biology
Michael D Olp, Nan Zhu, Brian C Smith
Recent proteomic studies discovered histone lysines are modified by acylations beyond acetylation. These acylations derive from acyl-CoA metabolites, potentially linking metabolism to transcription. Bromodomains bind lysine acylation on histones and other nuclear proteins to influence transcription. However, the extent bromodomains bind non-acetyl acylations is largely unknown. Also unclear are the effects of neighboring post-translational modifications, especially within heavily modified histone tails. Using peptide arrays, binding assays, sucrose gradients, and computational methods, we quantified 10 distinct acylations for binding to the bromodomain and extraterminal domain (BET) family...
October 5, 2017: Biochemistry
Kaori Fujiwara, Takuya Inoue, Yujiro Henmi, Yoshimasa Hirata, Yutaka Naka, Azusa Hara, Kazuki Kakimoto, Sadaharu Nouda, Toshihiko Okada, Ken Kawakami, Toshihisa Takeuchi, Kazuhide Higuchi
The relationship between type 2 diabetes mellitus and intestinal neoplasia has been shown epidemiologically. A high-fat diet (HFD) is also known to promote insulin resistance, which is a risk factor for intestinal neoplasia. Dipeptidyl peptidase-4 (DPP-4) inhibitors are used in the clinic for the treatment of type 2 diabetes and also to prolong the effects of glucagon-like peptide-1 (GLP-1). However, since the intestinotrophic hormone GLP-2 and chemokines, such as CXCL5 and stromal cell-derived factor-1 (SDF-1), are also substrates of DPP-4, DPP-4 inhibitors may increase the risk of intestinal carcinogenesis...
October 2017: Oncology Letters
Chunqiu Zhang, Ramim Shafi, Ayala Lampel, Douglas MacPherson, Charalampos G Pappas, Vishal Narang, Tong Wang, Charles Maldarelli, Rein V Ulijn
The reversible regulation of catalytic activity is a feature found in natural enzymes which is not commonly observed in artificial catalytic systems. Here, we fabricate an artificial hydrolase with pH-switchable activity, achieved by introducing a catalytic histidine residue at the terminus of a pH-responsive peptide. The peptide exhibits a conformational transition from random coil to β-sheet by changing the pH from acidic to alkaline. The β-sheet self-assembles to form long fibrils with the hydrophobic edge and histidine residues extending in an ordered array as the catalytic microenvironment, which shows significant esterase activity...
September 22, 2017: Angewandte Chemie
Sarah E Wood, Gaurav Sinsinbar, Sushanth Gudlur, Madhavan Nallani, Che-Fan Huang, Bo Liedberg, Milan Mrksich
Identifying peptide substrates that are efficiently cleaved by proteases gives insights into substrate recognition and specificity, guides development of inhibitors, and improves assay sensitivity. Peptide arrays and SAMDI mass spectrometry were used to identify a tetrapeptide substrate exhibiting high activity for the bacterial outer-membrane protease (OmpT). Analysis of protease activity for the preferred residues at the cleavage site (P1, P1') and nearest-neighbor positions (P2, P2') and their positional interdependence revealed FRRV as the optimal peptide with the highest OmpT activity...
September 20, 2017: Angewandte Chemie
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