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Alireza Khataee, Saeed Sajjadi, Aliyeh Hasanzadeh, Behrouz Vahid, Sang Woo Joo
Natural Martite ore particles and graphite were modified by alternating current (AC) glow discharge plasma to form nanostructured catalyst and cathode electrode for using in the heterogeneous-electro Fenton-like (Het-EF-like) process. The performance of the plasma-treated martite (PTM) and graphite electrode (PTGE) was studied for the treatment of paraquat herbicide in a batch system. 85.78% degradation efficiency for 20 mg L(-1) paraquat was achieved in the modified process under desired operational conditions (i...
May 16, 2017: Journal of Environmental Management
Li-Ming Liu, Yan Xu, Kuo-Chen Chou
BACKGROUND: Occurring at Lys residues, the PGK (lysine phosphoglycerylation) is a special kind of post-translational modification (PTM). It may invert the charge potential of the modified residue and change the protein structures and functions, causing various diseases in liver, brain, and kidney. OBJECTIVE: From the angles of both basic research and drug development, we are facing a critical challenging problem: for an uncharacterized protein sequence containing many Lys residues, which ones can be of phosphoglycerylation, and which ones cannot? METHOD: To address this problem, we have developed a predictor called iPGK-PseAAC by incorporating into the general PseAAC (pseudo amino acid composition) with four different tiers of amino acid pairwise coupling information, where tiers 1, 2, 3, and 4 refer to the amino acid pairwise couplings between all the 1st, 2nd, 3rd, and 4th most contiguous residues along a protein segment, respectively...
May 15, 2017: Medicinal Chemistry
Alicia Sufrinko, Jamie McAllister-Deitrick, R J Elbin, Michael W Collins, Anthony P Kontos
OBJECTIVE: To determine whether family history of migraine increased the likelihood of posttraumatic migraine (PTM) symptom presentation in adolescents following concussion, and examine the influence of family history of migraine and PTM on postinjury outcomes. SETTING: Outpatient concussion clinic. PARTICIPANTS: A total of 153 patients with concussion (103 males and 50 females) aged 15.72 ± 1.48 years (range 12-18 years). DESIGN: Cross-sectional, observational study of patients presenting for initial evaluation 4...
May 17, 2017: Journal of Head Trauma Rehabilitation
Firas H Kobeissy, Joy Guingab-Cagmat, Adriaan W Bruijnzeel, Mark S Gold, Kevin Wang
Second-hand smoke (SHS) exposure leads to the death of approximately 48,000 nonsmokers per year in the United States alone. SHS exposure has been associated with cardiovascular, respiratory, and neurodegenerative diseases. While cardiac function abnormalities and lung cancer due to SHS have been well characterized, brain injury due to SHS has not undergone a full systematic evaluation. Oxidative stress and nitration have been associated with smoking and SHS exposure. Animal studies suggest that exposure to tobacco smoke increases oxidative stress...
2017: Methods in Molecular Biology
Zakey Yusuf Buuh, Zhigang Lyu, Rongsheng E Wang
Post-translational modifications (PTMs) allot versatility to the biological functions of highly conserved proteins. Recently, modifications to non-histone proteins such as methylation, acetylation, phosphorylation, glycosylation, ubiquitination, and many more have been linked to the regulation of pivotal pathways related to cellular response and stability. Due to the roles these dynamic modifications assume, their dysregulation has been associated with cancer and many other important diseases such as inflammatory disorders and neurodegenerative diseases...
May 15, 2017: Journal of Medicinal Chemistry
Yan-Xia Xu, Chen-Jia Shen, Jian-Qiang Ma, Wei Chen, Juan Mao, Yan-Yan Zhou, Liang Chen
Lysine succinylation is a novel dynamic and evolutionarily conserved post-translational modification (PTM) that regulates various biological processes. 'Anji Baicha' is an albino tea variety that exhibits temperature-based variability of leaf colour and amino acid concentrations. However, the mechanism underlying albinism in 'Anji Baicha' has not been investigated at the level of succinylation. Here, we identify 3530 lysine succinylation sites mapped to 2132 proteins in 'Anji Baicha', representing the first extensive data on the lysine succinylome in the tea plant...
May 12, 2017: Scientific Reports
Natalia A Petushkova, Victor G Zgoda, Mikhail A Pyatnitskiy, Olesya V Larina, Nadezhda B Teryaeva, Alexander A Potapov, Andrey V Lisitsa
Liquid chromatography-tandem mass spectrometry was used to analyze plasma proteins of volunteers (control) and patients with glioblastoma multiform (GBM). A database search was pre-set with a variable post-translational modification (PTM): phosphorylation, acetylation or ubiquitination. There were no significant differences between the control and the GBM groups regarding the number of protein identifications, sequence coverage or number of PTMs. However, in GBM plasma, we unambiguously observed a decreased fraction in post-translationally modified peptides identified with high quality...
2017: PloS One
Bing-Jie Chen, Thomas Chuen Lam, Long-Qian Liu, Chi-Ho To
Gene expression is the process by which genetic information is used for the synthesis of a functional gene product, and ultimately regulates cell function. The increase of biological complexity from genome to proteome is vast, and the post-translational modification (PTM) of proteins contribute to this complexity. The study of protein expression and PTMs has attracted attention in the post‑genomic era. Due to the limited capability of conventional biochemical techniques in the past, large‑scale PTM studies were technically challenging...
June 2017: Molecular Medicine Reports
Abdollah Dehzangi, Yosvany López, Sunil Pranit Lal, Ghazaleh Taherzadeh, Jacob Michaelson, Abdul Sattar, Tatsuhiko Tsunoda, Alok Sharma
Post-translational modification (PTM) is a covalent and enzymatic modification of proteins, which contributes to diversify the proteome. Despite many reported PTMs with essential roles in cellular functioning, lysine succinylation has emerged as a subject of particular interest. Because its experimental identification remains a costly and time-consuming process, computational predictors have been recently proposed for tackling this important issue. However, the performance of current predictors is still very limited...
May 5, 2017: Journal of Theoretical Biology
Eun Ju Kim
O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) are the only enzymes that regulate the dynamics of protein O-GlcNAcylation. Protein O-GlcNAcylation is an important post-translational modification (PTM) of nuclear and cytoplasmic proteins with O-linked ß-N-acetyl-glucosamine (O-GlcNAc). O-GlcNAc and its enzymes are involved in a wide variety of cellular processes and are linked to the pathological progression of chronic diseases. Considering their emerging biological significance, systematic and rapid methods to determine the activities of OGT and OGA have become essential and several chemical/biochemical methods for measuring these enzymes' activities have been developed...
May 5, 2017: Chembiochem: a European Journal of Chemical Biology
Rod Chalk
Mass spectrometry is a generic technique for the structural and functional analysis of purified proteins. Instrument capabilities and the possibilities of intact protein, peptide fragmentation and native analyses are discussed. Detailed experimental protocols are described for the most commonly applied techniques of protein identification, posttranslational modification (PTM) characterization, PTM mapping, native mass spectrometry, and analysis of membrane proteins using electrospray mass spectrometry.
2017: Methods in Molecular Biology
Shorouk Fahmy-Garcia, Marjolein van Driel, Janneke Witte-Buoma, Heike Walles, Johannes Ptm van Leeuwen, Gerjo van Osch, Eric Farrell
Currently, autografts still represent the gold standard treatment for the repair of large bone defects. However, these are associated with donor site morbidity, increased pain, cost and recovery time. The ideal therapy would use biomaterials combined with bone growth factors to induce and instruct bone defect repair without the need to harvest patient tissue. In this line, BMPs have been the most extensively used agents for clinical bone repair, but at supraphysiological doses that are not without risk. Because of the need to eliminate the risks of BMP2 use in vivo, we assessed the ability of three putative osteogenic factors, Nell-1, HMGB1 and CCN2, to enhance the essential processes for bone defect repair in vitro and compared them to BMP2...
May 2, 2017: Tissue Engineering. Part A
BingHua Wang, Minghui Wang, Ao Li
Protein post-translational modification (PTM) is an important mechanism that is involved in the regulation of protein function. Considering the high-cost and labor-intensive of experimental identification, many computational prediction methods are currently available for the prediction of PTM sites by using protein local sequence information in the context of conserved motif. Here we proposed a novel computational method by using the combination of multiple kernel support vector machines (SVM) for predicting PTM sites including phosphorylation, O-linked glycosylation, acetylation, sulfation and nitration...
2017: PeerJ
Ying Li, Xueya Zhou, Zichao Zhai, Tingting Li
Post-translational modifications (PTMs) add a further layer of complexity to the proteome and regulate a wide range of cellular protein functions. With the increasing number of known PTM sites, it becomes imperative to understand their functional interplays. In this study, we proposed a novel analytical strategy to explore functional relationships between PTM sites by testing their tendency to be modified together (co-occurrence) under the same condition, and applied it to proteome-wide human phosphorylation data collected under 88 different laboratory or physiological conditions...
May 2017: PLoS Computational Biology
Jesse J McClure, Elizabeth S Inks, Cheng Zhang, Yuri K Peterson, Jiaying Li, Kalyan Chundru, Bradley Lee, Ashley Buchanan, Shiqin Miao, C James Chou
The acetylation status of lysine residues on histone proteins has long been attributed to a balance struck between the catalytic activity of histone acetyl transferases and histone deacetylases (HDAC). HDACs were identified as the sole removers of acetyl post-translational modifications (PTM) of histone lysine residues. Studies into the biological role of HDACs have also elucidated their role as removers of acetyl PTMs from lysine residues of nonhistone proteins. These findings, coupled with high-resolution mass spectrometry studies that revealed the presence of acyl-group PTMs on lysine residues of nonhistone proteins, brought forth the possibility of HDACs acting as removers of both acyl- and acetyl-based PTMs...
May 4, 2017: ACS Chemical Biology
Juliette J Commodore, Xinyao Jing, Carolyn J Cassady
RATIONALE: Production of multiply protonated ions by electrospray ionization (ESI) is important to the analysis of peptides by mass spectrometry. For small neutral and acidic peptides, addition of chromium(III) greatly increases the intensity of doubly protonated ions. The current study examines instrumental and solution parameters that maximize peptide ion charge by ESI. METHODS: The neutral and basic heptapeptides AAAAAAA (A7) and AAAKAAA (A3KA3) were used as test compounds and electrosprayed from a solution containing chromium(III) nitrate at a peptide to metal molar ratio of 1:10...
April 29, 2017: Rapid Communications in Mass Spectrometry: RCM
Jishan Wu, Xiaojin Wu, Jun Oh Kim, Samara Medina, Francisco J Ramírez, Paula Mayorga Burrezo, Shaofei Wu, Zheng Long Lim, Christoph Lambert, Juan Casado, Dongho Kim
We report a general building block 2, tri(4-iodo-2,3,5,6-tetrachlorophenyl)methane, for the synthesis of various π-conjugated polychlorotriphenylmethyl (PTM) radicals. Three push-pull type triphenylamine-substituted PTM radicals with different substitution pattern were prepared, and they all exhibited intense inter-valence charge-transfer bands and large two-photon absorption (TPA) cross sections. Moreover, increase of solvent polarity also resulted in improved TPA response. The charge transfer character of the relevant excited states provokes the efficient photo-generation of charges, anions in the PTM and cations in the amine arms, driven by the amphoteric redox character and the small coupling between donor and acceptor...
April 28, 2017: Chemistry: a European Journal
Subhasish Saha, Wenjun Zhang, Guangtao Zhang, Yiguang Zhu, Yuchan Chen, Wei Liu, Chengshan Yuan, Qingbo Zhang, Haibo Zhang, Liping Zhang, Weimin Zhang, Changsheng Zhang
Polycyclic tetramate macrolactams (PTMs) are a growing class of natural products and are derived from a hybrid polyketide synthase (PKS)/non-ribosomal peptide synthetase (NRPS) pathway. PTM biosynthetic gene clusters are conserved and widely distributed in bacteria, however, most of them remain silent. Herein we report the activation of a PTM gene cluster in marine-derived Streptomyces pactum SCSIO 02999 by promoter engineering and heterologous expression, leading to the discovery of six new PTMs, pactamides A-F (11-16), with potent cytotoxic activity upon several human cancer cell lines...
February 1, 2017: Chemical Science
Xavier Gallart-Palau, Aida Serra, Siu Kwan Sze
Characterization of protein deamidation is imperative to decipher the role(s) and potentialities of this protein posttranslational modification (PTM) in human pathology and other biochemical contexts. In order to perform characterization of protein deamidation, we have recently developed a novel long-length electrostatic repulsion-hydrophilic interaction chromatography-tandem mass spectrometry (LERLIC-MS/MS) method which can separate the glutamine (Gln) and asparagine (Asn) isoform products of deamidation from model compounds to highly complex biological samples...
April 9, 2017: Journal of Visualized Experiments: JoVE
Stamatios Liokatis
Asymmetrically modified nucleosomes contain the two copies of a histone (sister histones) decorated with distinct sets of Post-translational Modifications (PTMs). They are newly identified species with unknown means of establishment and functional implications. Current analytical methods are inadequate to detect the copy-specific occurrence of PTMs on the nucleosomal sister histones. This protocol presents a biochemical method for the in vitro reconstitution of nucleosomes containing differentially isotope-labeled sister histones...
March 26, 2017: Journal of Visualized Experiments: JoVE
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