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https://www.readbyqxmd.com/read/28734205/identification-of-mycobacterium-tuberculosis-enoyl-acyl-carrier-protein-reductase-inhibitors-a-combined-in-silico-and-in-vitro-analysis
#1
Mohsin Y Lone, Mohd Athar, Vivek K Gupta, Prakash C Jha
Mycobacterium tuberculosis (Mtb), had developed evolutionary changes in its genome to adapt for survival and thereby generated multi-drug resistant strains. However, novel drug targets that remained unchanged for their biochemical role has impressed the research community to target such proteins. The comprehensive analysis of multiple protein targets has influenced us to make a consensus structural rule exploited by pharmacophore and other allied techniques from a large repository of protein structures. In this pursuit, we made a retrospective analysis of pharmacophores mapped from the tuberculosis structural proteome and identified unique patterns that can be employed for the novel molecules design...
July 14, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28732263/proteomic-analysis-of-naturally-occurring-boron-tolerant-plant-gypsophila-sphaerocephala-l-in-response-to-high-boron-concentration
#2
Huseyin Tombuloglu, Guzin Tombuloglu, Mehmet Serdal Sakcali, Ali Turkan, Khalid Rehman Hakeem, Hesham F Alharby, Shah Fahd, Waseem Mohammed Abdul
Gypsophila sphaerocephala is a naturally Boron (B) tolerant species that can grow around the B mining areas in Turkey, where the B concentration in soil reaches a lethal dose for plants (up to ∼8900mgkg(-1) (∼140mM). While its interesting survival capacity in extremely B containing soils, any molecular research has been conducted to understand its high tolerance mechanism yet. In the present study, we have performed a proteomic analysis of this plant to understand its high tolerance towards B-stress. Seedlings of G...
July 4, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28732011/proteomics-analysis-reveals-a-dynamic-diurnal-pattern-of-photosynthesis-related-pathways-in-maize-leaves
#3
Dan Feng, Yanwei Wang, Tiegang Lu, Zhiguo Zhang, Xiao Han
Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions...
2017: PloS One
https://www.readbyqxmd.com/read/28731711/identification-of-proteomic-features-to-distinguish-benign-pulmonary-nodules-from-lung-adenocarcinoma
#4
Simona G Codreanu, Megan D Hoeksema, Robbert J C Slebos, Lisa J Zimmerman, S M Jamshedur Rahman, Ming Li, Sheau-Chiann Chen, Heidi Chen, Rosana Eisenberg, Daniel C Liebler, Pierre P Massion
We hypothesized that distinct protein expression features of benign and malignant pulmonary nodules may reveal novel candidate biomarkers for the early detection of lung cancer. We performed proteome profiling by liquid chromatography-tandem mass spectrometry to characterize 34 resected benign lung nodules, 24 early stage untreated lung adenocarcinomas (ADCs) and biopsies of bronchial epithelium. Group comparisons identified 65 proteins that differentiate nodules from ADCs and normal bronchial epithelium, and 66 proteins that differentiate ADCs from nodules and normal bronchial epithelium...
July 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28730955/itraq-based-proteomic-analysis-of-appsw-ind-mice-provides-insights-into-the-early-changes-in-alzheimer-s-disease
#5
Nan Li, Pinghong Hu, Tiantian Xu, Huan Chen, Xiaoying Chen, Jianwen Hu, Xifei Yang, Lei Shi, Jian-Hong Luo, Junyu Xu
BACKGROUND: Several proteins have been identified as potential diagnostic biomarkers in imaging, genetic, or proteomic studies in Alzheimer disease (AD) patients and mouse models. However, biomarkers for presymptom diagnosis of AD are still under investigation, as are the presymptom molecular changes in AD pathogenesis. OBJECTIVE: In this study, we aim to analyzed the early proteomic changes in APPSw,Ind mice and to conduct further functional studies on interesting proteins...
July 19, 2017: Current Alzheimer Research
https://www.readbyqxmd.com/read/28730820/tryptic-peptides-bearing-c-terminal-dimethyllysine-need-be-considered-during-the-analysis-of-lysine-dimethylation-in-proteomic-study
#6
Ming Chen, Min Zhang, Linhui Zhai, Hao Hu, Ping Liu, Minjia Tan
Lysine methylation plays important roles in structural and functional regulation of chromatin. Although trypsin is the most widely used protease in mass spectrometry-based proteomic analysis for lysine methylation substrates, the proteolytic activity of trypsin on dimethylated lysine residues remains an arguable issue. In this study, we tested the ability of trypsin to cleave dimethylated lysine residues in synthetic peptides, purified albumin and whole cell lysate, and found that the C-terminal of dimethylated lysine residue could be cleaved in a protein sequence-dependent manner...
July 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28730805/integrating-discovery-driven-proteomics-and-selected-reaction-monitoring-to-develop-a-non-invasive-assay-for-geoduck-reproductive-maturation
#7
Emma B Timmins-Schiffman, Grace A Crandall, Brent Vadopalas, Michael E Riffle, Brook L Nunn, Steven Roberts
Geoduck clams (Panopea generosa) are an increasingly important fishery and aquaculture product along the eastern Pacific coast from Baja California, Mexico to Alaska. These long-lived clams are highly fecund, though sustainable hatchery production of genetically diverse larvae is hindered by the lack of sexual dimorphism, resulting in asynchronous spawning of broodstock, unequal sex ratios, and low numbers of breeders. Development of assays of gonad physiology could indicate sex and maturation stage, as well as be used to assess the status of natural populations...
July 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28730497/databases-and-computational-tools-for-evolutionary-analysis-of-protein-phosphorylation
#8
Chris Soon Heng Tan
Advancements in MS-based phospho-proteomics techniques have helped uncover hundred thousands of protein phosphorylation sites in human and various model organisms. The majority of these sites are uncharacterized. The sheer number of uncharacterized sites necessitates systematic approaches to prioritize sites for more in-depth annotation. Analyzing the phosphorylation and sequence conservation of uncharacterized sites across species can help reveal a subset of the functionally important phosphorylation events...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730491/development-of-selected-reaction-monitoring-methods-to-systematically-quantify-kinase-abundance-and-phosphorylation-stoichiometry-in-human-samples
#9
Kirsten Beck, Nathan Camp, Michael Bereman, James Bollinger, Jarrett Egertson, Michael MacCoss, Alejandro Wolf-Yadlin
Protein phosphorylation, one of the most common types of post-translational modifications, is the central regulatory mechanism of cellular signaling networks. In human cells, thousands of proteins are continuously and dynamically phosphorylated and dephosphorylated at specific sites and times in response to external and internal stimuli. Reversible phosphorylation is facilitated by the action of two protein superfamilies: kinases and phosphatases. Kinases play an essential role in almost every relevant physiological process in human cells and their deregulation is linked to pathologies ranging from cancer to autoimmune diseases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730490/mass-spectrometry-analysis-of-spatial-protein-networks-by-colocalization-analysis-cola
#10
Faraz K Mardakheh
A major challenge in systems biology is comprehensive mapping of protein interaction networks. Crucially, such interactions are often dynamic in nature, necessitating methods that can rapidly mine the interactome across varied conditions and treatments to reveal change in the interaction networks. Recently, we described a fast mass spectrometry-based method to reveal functional interactions in mammalian cells on a global scale, by revealing spatial colocalizations between proteins (COLA) (Mardakheh et al., Mol Biosyst 13:92-105, 2017)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730489/identification-of-plant-kinase-substrates-based-on-kinase-assay-linked-phosphoproteomics
#11
Chuan-Chih Hsu, Justine V Arrington, Liang Xue, W Andy Tao
Protein phosphorylation is one of the key events in the regulation of plant physiological responses to diverse environmental stimuli. As crucial regulators of phosphorylation, protein kinases have been linked to the control of seed germination, flowering, and stress responses. Identifying downstream substrates of kinases is important for dissecting kinase-substrate networks as well as delineating the underlying defense mechanisms in response to extracellular stimulation. Despite the fact that thousands of kinase-substrate networks have been identified in mammalian cells, the downstream substrates of important plant kinases are still elusive...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730488/absolute-phosphorylation-stoichiometry-analysis-by-motif-targeting-quantitative-mass-spectrometry
#12
Chia-Feng Tsai, Wei-Chi Ku, Yu-Ju Chen, Yasushi Ishihama
Direct measurement of site-specific phosphorylation stoichiometry can unambiguously distinguish whether the degree of phosphorylation is regulated by upstream kinase/phosphatase activity or by transcriptional regulation to alter protein expression level. Here, we describe a motif-targeting quantitative proteomic approach that integrates dephosphorylation, isotope tag labeling, and enzymatic kinase reaction for large-scale phosphorylation stoichiometry measurement of the human proteome.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730487/a-methodology-for-comprehensive-analysis-of-toll-like-receptor-signaling-in-macrophages
#13
Marijke Koppenol-Raab, Aleksandra Nita-Lazar
A combination of high-throughput, multiplexed, quantitative methods with computational modeling and statistical approaches is required to obtain system-level understanding of biological function. Mass spectrometry (MS)-based proteomics has emerged as a preferred tool for the analysis of changes in protein abundance and their post-translational modification (PTM) levels at a global scale, comparable with genomic experiments and generating data suitable for use in mathematical modeling of signaling pathways. Here we describe a set of parallel bottom-up proteomic approaches to detect and quantify the global protein changes in total intracellular proteins, their phosphorylation, and the proteins released by active and passive secretion or shedding mechanisms (referred to as the secretome as reviewed in Makridakis and Vlahou, J Proteome 73:2291-2305, 2010) in response to the stimulation of Toll-like receptors (TLRs) with specific ligands in cultured macrophages...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730485/targeted-analysis-of-phosphotyrosine-signaling-by-multiple-reaction-monitoring-mass-spectrometry
#14
Leo S Payne, Paul H Huang
Phosphoproteomics is an important tool for the unbiased investigation of signaling network activation and has particular application to unraveling aberrant signaling driving cancer progression. However, validating the behavior of specific phosphosites across multiple experimental conditions remains challenging, due to limitations inherent in discovery-based proteomic workflows and the limited availability of high-quality antibodies required for alternative, immunoaffinity-based methods. Targeted phosphoproteomics enables specific phosphosites to be quantified reproducibly across multiple experimental conditions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730483/characterization-of-the-phospho-adhesome-by-mass-spectrometry-based-proteomics
#15
Joseph Robertson, Jonathan D Humphries, Nikki R Paul, Stacey Warwood, David Knight, Adam Byron, Martin J Humphries
Integrin adhesion receptors engage with their extracellular matrix (ECM) ligands, initiating intracellular signaling pathways that regulate a range of fundamental cell functions. Protein kinases and phosphatases play an integral role in integrin adhesion-mediated signaling. However, until recently, knowledge of the phosphorylation sites regulated downstream of integrin ligation was limited to candidate-based approaches and did not support a system-level understanding of the molecular mechanisms through which ECM engagement influences cell behavior...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730482/cell-specific-labeling-for-analyzing-bidirectional-signaling-by-mass-spectrometry
#16
Christopher J Tape, Claus Jørgensen
Cell-specific proteome labeling enables global proteome-wide analysis of cell signaling in heterotypic co-cultures. Such approaches have provided unique insight in contact-initiated receptor tyrosine kinase signaling, transfer of proteomic material between heterotypic cells, and interactions between normal and oncogenic cells. Here we describe current methods for cell-specific labeling of heterotypic cells with isotopic labeled amino acids (e.g., SILAC and CTAP). We outline the advantages and disadvantages of individual approaches, describe typical experimental scenarios, and discuss where each experimental approach is optimally applied...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730476/proteomic-profiling-of-protein-kinase-inhibitor-targets-by-mass-spectrometry
#17
Martin Golkowski, Dustin J Maly, Shao-En Ong
Identifying cellular targets of bioactive small molecules from large-scale screening campaigns can be a significant bottleneck in developing novel therapeutics. Our rapid small-molecule target profiling protocol combines affinity enrichment and SILAC for proteomic identification of small molecule-protein interactions. Selective interactions are easily discernable from nonspecific protein binding by quantitative ratios. Using kinase inhibitors as an example, we provide an optimized protocol featuring on-bead protein digestion and single nano-flow liquid chromatographic-mass spectrometric (LC-MS) analyses, consequently increasing analytical throughput and sensitivity over gel-based sample preparation methods for rapid profiling of kinase inhibitor targets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730336/serologic-markers-of-autism-spectrum-disorder
#18
REVIEW
T V Khramova, Anna L Kaysheva, Y D Ivanov, T O Pleshakova, I Y Iourov, S G Vorsanova, Y B Yurov, A A Schetkin, A I Archakov
According to WHO data, about 67 million people worldwide are affected by autism, and this number grows by 14% annually. Among the possible causes of autism are genetic modifications, organic lesions of the central nervous system, metabolic disorders, influence of viral and bacterial infections, chemical influence to the mother's body during pregnancy, etc. The conducted research shows that research papers published until today do not name any potential protein markers that meet the requirements of the basic parameters for evaluating the efficiency of disease diagnostics, in particular high sensitivity, specificity, and accuracy...
July 20, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/28730086/peptidome-profiling-of-human-serum-of-uveal-melanoma-patients-based-on-magnetic-bead-fractionation-and-mass-spectrometry
#19
Xiang-Yu Shi, Qing Li, Wen-Bin Wei, Li-Ming Tao
AIM: To find new biomarkers for uveal melanoma (UM) by analyzing the serum peptidome profile. METHODS: Proteomic spectra in patients with UM before and after operation were analyzed and compared with those of healthy controls. Magnetic affinity beads were used to capture serum peptides and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometer were used to compile serum peptide profiles. RESULTS: A panel of 49 peptides were differentially expressed between UM patients and controls, of which 33 peptides were of higher intensities in patient group and 16 peptides were of higher intensities in control group...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28730077/proteomic-profiling-of-early-degenerative-retina-of-rcs-rats
#20
Zhi-Hong Zhu, Yan Fu, Chuan-Huang Weng, Cong-Jian Zhao, Zheng-Qin Yin
AIM: To identify the underlying cellular and molecular changes in retinitis pigmentosa (RP). METHODS: Label-free quantification-based proteomics analysis, with its advantages of being more economic and consisting of simpler procedures, has been used with increasing frequency in modern biological research. Dystrophic RCS rats, the first laboratory animal model for the study of RP, possess a similar pathological course as human beings with the diseases. Thus, we employed a comparative proteomics analysis approach for in-depth proteome profiling of retinas from dystrophic RCS rats and non-dystrophic congenic controls through Linear Trap Quadrupole - orbitrap MS/MS, to identify the significant differentially expressed proteins (DEPs)...
2017: International Journal of Ophthalmology
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