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Jun Qu
Jun Qu speaks to Sankeetha Nadarajah, Editor of Bioanalysis: Jun Qu is the group leader of the proteomics and pharmaceutical analysis lab of SUNY-Buffalo (NY, USA) and a Professor in the Department of Pharmaceutical Sciences. His research is focused on the study of Clinical and Pharmaceutical Proteomics and Pharmaceutical Analysis using LC-MS-based strategies. His research programs include high-resolution and large-scale expression profiling of pathological proteomes, for the discovery of novel disease/therapeutics biomarkers using gel-free proteomic methods; sensitive identification, localization and quantification of post-translational modifications in tissue proteomes such as these in myocardium, using novel anti-PTM affinity capture and alternating Collision-induced dissociation/Electron transfer dissociation to obtain abundant PTM information; targeted investigation of marker proteins that are of high interests for clinical and pharmaceutical study, using highly sensitive nano-LC/SRM-based methods; and highly sensitive and accurate investigation of the PK of biotherapeutics using LC-MS...
February 16, 2018: Bioanalysis
Ruedi Aebersold, Jeffrey N Agar, I Jonathan Amster, Mark S Baker, Carolyn R Bertozzi, Emily S Boja, Catherine E Costello, Benjamin F Cravatt, Catherine Fenselau, Benjamin A Garcia, Ying Ge, Jeremy Gunawardena, Ronald C Hendrickson, Paul J Hergenrother, Christian G Huber, Alexander R Ivanov, Ole N Jensen, Michael C Jewett, Neil L Kelleher, Laura L Kiessling, Nevan J Krogan, Martin R Larsen, Joseph A Loo, Rachel R Ogorzalek Loo, Emma Lundberg, Michael J MacCoss, Parag Mallick, Vamsi K Mootha, Milan Mrksich, Tom W Muir, Steven M Patrie, James J Pesavento, Sharon J Pitteri, Henry Rodriguez, Alan Saghatelian, Wendy Sandoval, Hartmut Schlüter, Salvatore Sechi, Sarah A Slavoff, Lloyd M Smith, Michael P Snyder, Paul M Thomas, Mathias Uhlén, Jennifer E Van Eyk, Marc Vidal, David R Walt, Forest M White, Evan R Williams, Therese Wohlschlager, Vicki H Wysocki, Nathan A Yates, Nicolas L Young, Bing Zhang
Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA- and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease...
February 14, 2018: Nature Chemical Biology
Wan-Shan Yang, Mel Campbell, Hsing-Jien Kung, Pei-Ching Chang
Small ubiquitin-like modifier (SUMO) modification is an important post-translational modification (PTM) that mediates signal transduction primarily through modulating protein-protein interactions. Similar to ubiquitin modification, SUMOylation is directed by a sequential enzyme cascade including E1-activating enzyme (SAE1/SAE2), E2-conjugation enzyme (Ubc9), and E3-ligase (i.e., PIAS family, RanBP2, and Pc2). However, different from ubiquitination, an E3 ligase is non-essential for the reaction but does provide precision and efficacy for SUMO conjugation...
January 29, 2018: Journal of Visualized Experiments: JoVE
John A Carver, Heath Ecroyd, Roger J W Truscott, David C Thorn, Carl Holt
Molecular chaperone proteins perform a diversity of roles inside and outside the cell. One of the most important is the stabilization of misfolding proteins to prevent their aggregation, a process that is potentially detrimental to cell viability. Diseases such as Alzheimer's, Parkinson's, and cataract are characterized by the accumulation of protein aggregates. In vivo, many proteins are metastable and therefore under mild destabilizing conditions have an inherent tendency to misfold, aggregate, and hence lose functionality...
February 14, 2018: Accounts of Chemical Research
Ijeoma Uzoma, Jianfei Hu, Eric Cox, Shuli Xia, Jianying Zhou, Hee-Sool Rho, Catherine Guzzo, Corry Paul, Olutobi Ajala, C Rory Goodwin, Junseop Jeong, Cedric Moore, Hui Zhang, Pamela Meluh, Seth Blackshaw, Michael Matunis, Jiang Qian, Heng Zhu
Proteomics studies have revealed that SUMOylation is widely used posttranslational modification (PTM) in eukaryotes. However, how SUMO E1/2/3 complexes use different SUMO isoforms and recognize substrates remains largely unknown.  Using a human proteome microarray-based activity screen, we identified over 2,500 proteins that undergo SUMO E3-dependent SUMOylation.  We next constructed a SUMO isoform- and E3 ligase-dependent enzyme-substrate relationship network. Protein kinases were significantly enriched among SUMOylation substrates, suggesting crosstalk between tyrosine phosphorylation and SUMOylation...
February 8, 2018: Molecular & Cellular Proteomics: MCP
Zhan-Ling Liang, Dan-Dan Wu, Yue Yao, Fei-Yuan Yu, Lei Yang, Heng Wee Tan, Machteld N Hylkema, Marianne G Rots, Yan-Ming Xu, Andy T Y Lau
Cadmium (Cd), a carcinogenic toxic metal, is pervasively distributed in the soil, water and air. Chronic exposure to Cd has been correlated to lung disease development including cancers. Although many studies have been conducted to investigate the proteome response of cells challenged with Cd, the epiproteomic responses (i.e., global histone post-translational modifications [PTMs]), particularly in human lung cells, are largely unexplored. Here, we provide an epiproteome profiling of human bronchial epithelial cells (BEAS-2B) chronically treated with cadmium chloride (CdCl2 ), with the aim of identifying global epiproteomic signatures in response to Cd epigenotoxicity...
February 9, 2018: Journal of Applied Toxicology: JAT
Nima Rajabi, Iacopo Galleano, Andreas S Madsen, Christian A Olsen
Lysine residues across the proteome are modified by posttranslational modifications (PTMs) that significantly enhance the structural and functional diversity of proteins. For lysine, the most abundant PTM is ɛ-N-acetyllysine (Kac), which plays numerous roles in regulation of important cellular functions, such as gene expression (epigenetic effects) and metabolism. A family of enzymes, namely histone deacetylases (HDACs), removes these PTMs. A subset of these enzymes, the sirtuins (SIRTs), represent class III HDAC and, unlike the rest of the family, these hydrolases are NAD+-dependent...
2018: Progress in Molecular Biology and Translational Science
Ying-Wu Lin
Heme proteins are crucial for biological systems by performing diverse functions. Nature has evolved diverse approaches to fine-tune the structure and function of heme proteins, of which post-translational modification (PTM) is a primary method. As reviewed herein, a multitude of PTMs have been discovered for heme proteins in the last several decades, including heme-protein cross-links with heme side chains (Cys-heme, Tyr-heme and Asp/Glu-heme, etc) or porphyrin ring (Lys-heme and Tyr-heme, etc), heme modifications (sulfheme and nitriheme, etc), amino acids cross-links between two or among multiple residues (Cys-Cys, Tyr-His, Tyr-Cys, Met-Tyr-Trp, etc), and amino acids modifications by oxidation, nitration, phosphorylation and glycation, etc...
February 1, 2018: Archives of Biochemistry and Biophysics
Karl J Niklas, A Keith Dunker, Inmaculada Yruela
The evolution of complex multicellular life forms occurred multiple times and was attended by cell type specialization. We review seven lines of evidence indicating that intrinsically disordered/ductile proteins (IDPs) played a significant role in the evolution of multicellularity and cell type specification: (i) most eukaryotic transcription factors (TFs) and multifunctional enzymes contain disproportionately long IDP sequences (≥30 residues in length), whereas highly conserved enzymes are normally IDP region poor; (ii) ~80% of the proteome involved in development are IDPs; (iii) the majority of proteins undergoing alternative splicing (AS) of pre-mRNA contain significant IDP regions; (iv) proteins encoded by DNA regions flanking crossing-over 'hot spots' are significantly enriched in IDP regions; (v) IDP regions are disproportionately subject to combinatorial post-translational modifications (PTMs) as well as AS; (vi) proteins involved in transcription and RNA processing are enriched in IDP regions; and (vii) a strong positive correlation exists between the number of different cell types and the IDP proteome fraction across a broad spectrum of uni- and multicellular algae, plants, and animals...
February 1, 2018: Journal of Experimental Botany
Lin Qiu, Kai Tian, Zhongqing Wen, Youchao Deng, Dingding Kang, Haoyu Liang, Xiangcheng Zhu, Ben Shen, Yanwen Duan, Yong Huang
Several sulfur-containing platensimycin (PTM) and platencin (PTN) analogues, with activities comparable to the parent natural products, have recently been discovered from microorganisms, implying a biomimetic route to diversify the PTM and PTN scaffolds for structure-activity relationship study. We present here a substrate-directed and scaleable semisynthetic strategy to make PTM and PTN sulfur analogues with excellent diasteroselectivity, without using any chiral catalysts. Most of the sulfur analogues showed strong activities against clinical Staphylococcus aureus isolates, with minimum inhibitory concentrations of 0...
February 1, 2018: Journal of Natural Products
Shuai Zhao, Baichao Zhang, Mo Yang, Jinsong Zhu, Haitao Li
Histone post-translational modifications (PTMs) and their recognition by histone readers exert crucial functions in eukaryotes. Despite extensive studies, conservation and diversity of histone PTM regulation between animals and plants remain less explored because of a lack of systematic knowledge of histone readers in plants. Based on a high-throughput surface plasmon resonance imaging (SPRi) platform, we report the lab-on-chip profiling of interactions between 204 putative reader domains and 11 types of histone peptides in Arabidopsis thaliana...
January 23, 2018: Cell Reports
Angélica Torres-Arroyo, Arturo Ruiz-Lara, Adriana Castillo-Villanueva, Sara Teresa Méndez-Cruz, Sara Elvia Espinosa-Padilla, Francisco Javier Espinosa-Rosales, Flora Zarate-Mondragón, Roberto Cervantes-Bustamante, Vanessa Bosch-Canto, Iris Vizzuett-López, Juan Carlos Ordaz-Fávila, Jesús Oria-Hernández, Horacio Reyes-Vivas
Proteomics is the study of the expression of changes and post-translational modifications (PTM) of proteins along a metabolic condition either normal or pathological. In the field of health, proteomics allows obtaining valuable data for treatment, diagnosis or pathophysiological mechanisms of different illnesses. To illustrate the aforementioned, we describe two projects currently being performed at the Instituto Nacional de Pediatría: The immuno-proteomic study of cow milk allergy and the Proteomic study of childhood cataract...
May 2017: Boletín Médico del Hospital Infantil de México
Camilla Thygesen, Inga Boll, Bente Finsen, Maciej Modzel, Martin R Larsen
Exploring post-translational modifications (PTMs) with the use of mass spectrometry (PTMomics) is a rapidly developing area, with methods for discovery/quantification being developed and advanced on a regular basis. PTMs are highly important for the regulation of protein function, interaction and activity, both in physiological and disease states. Changes in PTMs can either cause, or be the result of a disease, making them central for biomarker studies and studies of disease pathogenesis. Recently, it became possible to study multiple PTMs simultaneously from low amount of sample material, thereby increasing coverage of the PTMome obtainable from a single sample...
January 27, 2018: Expert Review of Proteomics
Will McIntyre, Rachel Netzband, Gaston Bonenfant, Jason M Biegel, Clare Miller, Gabriele Fuchs, Eric Henderson, Manoj Arra, Mario Canki, Daniele Fabris, Cara T Pager
More than 140 post-transcriptional modifications (PTMs) are known to decorate cellular RNAs, but their incidence, identity and significance in viral RNA are still largely unknown. We have developed an agnostic analytical approach to comprehensively survey PTMs on viral and cellular RNAs. Specifically, we used mass spectrometry to analyze PTMs on total RNA isolated from cells infected with Zika virus, Dengue virus, hepatitis C virus (HCV), poliovirus and human immunodeficiency virus type 1. All five RNA viruses significantly altered global PTM landscapes...
January 24, 2018: Nucleic Acids Research
Agnieszka Anna Rawłuszko-Wieczorek, Franziska Knodel, Raluca Tamas, Arunkumar Dhayalan, Albert Jeltsch
BACKGROUND: Protein posttranslational modifications (PTMs) occur broadly in the human proteome, and their biological outcome is often mediated indirectly by reader proteins that specifically bind to modified proteins and trigger downstream effects. Particularly, many lysine methylation sites among histone and nonhistone proteins have been characterized; however, the list of readers associated with them is incomplete. RESULTS: This study introduces a modified yeast three-hybrid system (Y3H) to screen for methyllysine readers...
January 25, 2018: Epigenetics & Chromatin
Bruno Raposo, Patrick Merky, Christina Lundqvist, Hisakata Yamada, Vilma Urbonaviciute, Colin Niaudet, Johan Viljanen, Jan Kihlberg, Bruno Kyewski, Olov Ekwall, Rikard Holmdahl, Johan Bäcklund
Establishing effective central tolerance requires the promiscuous expression of tissue-restricted antigens by medullary thymic epithelial cells. However, whether central tolerance also extends to post-translationally modified proteins is not clear. Here we show a mouse model of autoimmunity in which disease development is dependent on post-translational modification (PTM) of the tissue-restricted self-antigen collagen type II. T cells specific for the non-modified antigen undergo efficient central tolerance...
January 24, 2018: Nature Communications
Megan Garland, Christopher J Schulze, Ian T Foe, Wouter A van der Linden, Matthew A Child, Matthew Bogyo
Protein palmitoylation is a dynamic post-translational modification (PTM) important for cellular functions such as protein stability, trafficking, localization, and protein-protein interactions. S-palmitoylation occurs via the addition of palmitate to cysteine residues via a thioester linkage, catalyzed by palmitoyl acyl transferases (PATs), with removal of the palmitate catalyzed by acyl protein thioesterases (APTs) and palmitoyl-protein thioesterases (PPTs). Tools that target the regulators of palmitoylation-PATs, APTs and PPTs-will improve understanding of this essential PTM...
2018: PloS One
Henrick Horita, Andy Law, Kim Middleton
It is now well-appreciated that post-translational modifications (PTMs) play an integral role in regulating a protein's structure and function, which may be essential for a given protein's role both physiologically and pathologically. Enrichment of PTMs is often necessary when investigating the PTM status of a target protein, because PTMs are often transient and relatively low in abundance. Many pitfalls are encountered when enriching for a PTM of a target protein, such as buffer incompatibility, the target protein antibody is not IP-compatible, loss of PTM signal, and others...
January 8, 2018: Journal of Visualized Experiments: JoVE
Rahul S Kathayat, Yang Cao, Pablo D Elvira, Patrick A Sandoz, María-Eugenia Zaballa, Maya Z Springer, Lauren E Drake, Kay F Macleod, F Gisou van der Goot, Bryan C Dickinson
The reversible modification of cysteine residues by thioester formation with palmitate (S-palmitoylation) is an abundant lipid post-translational modification (PTM) in mammalian systems. S-palmitoylation has been observed on mitochondrial proteins, providing an intriguing potential connection between metabolic lipids and mitochondrial regulation. However, it is unknown whether and/or how mitochondrial S-palmitoylation is regulated. Here we report the development of mitoDPPs, targeted fluorescent probes that measure the activity levels of "erasers" of S-palmitoylation, acyl-protein thioesterases (APTs), within mitochondria of live cells...
January 23, 2018: Nature Communications
Danielle Moncrieffe, Mark C Parkin, David Cowan
RATIONALE: Procollagen III amino-terminal propeptide (P-III-NP) is currently monitored in human doping control as a biomarker for growth hormone administration and also in clinical diagnostics using immunoassays. Drawbacks to this approach have been highlighted, and research is ongoing to develop a mass spectrometric method to complement these methods. However, a lack of traceable reference material, the presence of post translational modifications (PTMs), and small blood concentration implicate the development of targeted analytical methods for P-III-NP quantification...
January 23, 2018: Rapid Communications in Mass Spectrometry: RCM
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