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Prakash Kulkarni, Vladimir N Uversky
A good portion of the 'protein universe' embodies the 'dark proteome'. The latter comprises proteins not amenable to experimental structure determination by existing means and inaccessible to homology modeling. Hence, the dark proteome has remained largely unappreciated. Intrinsically disordered proteins (IDPs) that lack rigid 3D structure are a major component of this dark proteome across all three kingdoms of life. Despite lack of structure, IDPs play critical roles in numerous important biological processes...
September 14, 2018: Proteomics
Karishma Bhasne, Samrat Mukhopadhyay
Protein misfolding resulting in the formation of ordered amyloid aggregates is associated with a number of devastating human diseases. Intrinsically disordered proteins (IDPs) do not autonomously fold up into a unique stable conformation and remain as an ensemble of rapidly fluctuating conformers. Many IDPs are prone to convert into the β-rich amyloid-state. One such amyloidogenic IDP is α-synuclein that is involved in Parkinson's disease. Recent studies have indicated that other neuronal proteins, especially IDPs, can co-aggregate with α-synuclein in many pathological ailments...
September 14, 2018: Proteomics
Congyan Zhang, Pingsheng Liu
The lipid droplet (LD) is an organelle with vital functions found in nearly all organisms. LD proteomic research has provided fundamentally important insights into this organelle's functions. The review provides a summary of LD proteomic studies conducted across diverse organisms and cell and tissue types. The accumulated proteomic data are reviewed for evidence of a protein targeting mechanism for the organelle. We provide hypotheses for several specific localization mechanisms based on what is known about targeting mechanisms for other organelles and vesicles...
September 14, 2018: Proteomics
Muaaz Gul Awan, Fahad Saeed
Mass Spectrometry (MS) based proteomics has become an essential tool in the study of proteins. With the advent of modern MS machines huge amounts of data is being generated which can only be processed by novel algorithmic tools. However, in the absence of data benchmarks and ground truth datasets algorithmic integrity testing and reproducibility is a challenging problem. To this end, we present MaSS-Simulator, which is an easy to use simulator and can be configured to simulate MS/MS datasets for a wide variety of conditions with known ground truths...
September 14, 2018: Proteomics
Laura Carcangiu, Salvatore Pisanu, Silvia Tore, Maria Filippa Addis, Eric Zini, Sergio Uzzau, Daniela Pagnozzi
In veterinary medicine, assay performance is often affected by the lack of species-specific diagnostic tools. Reliable biomarkers might be identified by investigating biological fluids of the species of interest, but protein sequence databases are often incomplete and human-specific devices for reducing sample complexity might fail when applied to animal plasma. Here, seven commercial methods based on different capturing agents (anti-human antibodies, affinity ligands, mixture of antibodies and ligands, and combinatorial peptide ligand libraries) were applied to cat plasma and evaluated in terms of yield, identified proteins/ peptides, and relative abundance by high resolution shotgun proteomics and label-free quantitation...
September 14, 2018: Proteomics
Parimal Samir, Christopher M Brown, Rahul Rahul, Ming Sun, Bingxin Shen, Wen Li, Joachim Frank, Andrew J Link
The regulatory role of the ribosome in gene expression has come into sharper focus. It has been proposed that ribosomes are dynamic complexes capable of changing their protein composition in response to enviromental stimuli. We applied mass spectrometry to identify quantitative changes in the protein composition of S. cerevisiae 80S ribosomes in response to different environmental stimuli. Using quantitative mass spectrometry, we found that the paralog yeast ribosomal proteins RPL8A (eL8A) and RPL8B (eL8B) change their relative proportions in the 80S ribosome when yeast is switched from growth in glucose to glycerol...
September 13, 2018: Proteomics
Gang Hu, Kui Wang, Jiangning Song, Vladimir N Uversky, Lukasz Kurgan
Growth rate of the protein sequence universe dramatically exceeds the speed of expansion for the protein structure universe, generating an immense dark proteome that includes proteins with unknown structure. We perform a whole-proteome scale analysis of 5.4 million proteins from 987 proteomes in the three domains of life and viruses to systematically dissect an interplay between structural coverage, degree of putative intrinsic disorder, and predicted propensity for structure determination. We found that Archaean and Bacterial proteomes have relatively high structural coverage and low amounts of disorder, whereas Eukaryotic and Viral proteomes are characterized by a broad spread of structural coverage and higher disorder levels...
September 10, 2018: Proteomics
Haitao Ge, Longfa Fang, Xiahe Huang, Jinlong Wang, Weiyang Chen, Yuanya Zhang, Xiaorong Wang, Na Sui, Wu Xu, Qingfang He, Yingchun Wang
The histidine kinase Hik33 plays a central role in acclimation to changing environments in cyanobacteria. Deletion of hik33 induces strong stress-like response in Synechocystis sp. PCC 6803 (Synechocystis) as represented by repressed photoautotrophic growth and photosynthesis, and differential expression of stress responsive proteins. In contrast, the photomixotrophic growth of the hik33-deletion mutant (Δhik33) with glucose as the exogenous carbon source is only marginally repressed. To investigate how glucose rescue the growth of Δhik33, we quantitatively analyzed the proteomes of the photomixotrophically-growing wild type (WT) and the mutant strains of Synechocystis...
September 8, 2018: Proteomics
Liangjie Niu, Xiangru Xu, Hui Liu, Xiaolin Wu, Wei Wang
Comparative proteomics is widely used to detect protein changes, especially differential abundance proteins (DAPs) that are involved in plant responses to development, disease, or environment. Once DAPs are identified, it is essential to validate any change in their abundance, and their role in the biological process under study. In addition to common confirmation by qRT-PCR, immunoblot and multiple reaction monitoring analysis, here we propose that enzyme activity assay (EAA) can be complementary to the standard proteomics results, especially regarding the elucidation of protein (enzyme) function and the mechanism of enzyme-associated biochemical or metabolic pathways...
September 4, 2018: Proteomics
Wenjuan Zhang, Naizhong Song, Haijiao Zheng, Wei Feng, Qiong Jia
In this study, we prepared poly(glycidyl methacrylate-ethyleneglycol dimethacrylate) (poly(GMA-EDMA)) monolith functionalized with cobalt phthalocyanine tetracarboxylic acid (CoPcTc). The polymer monolithic material was used for glycopeptides enrichment coupled with MALDI-TOF MS. By taking advantage of cobalt phthalocyanine including hydrogen bonds between isoindole subunits of phthalocyanine and glycans, coordination interaction between cobalt and glycopeptides, the monolithic material was successfully applied to the enrichment of glycopeptides efficiently and selectively...
September 4, 2018: Proteomics
Tara Basavanhally, Renée Fonseca, Vladimir N Uversky
Recently, genome-wide association study reveals a significant association between specific single nucleotide polymorphisms (SNPs) in men and their sexual orientation. These SNPs (rs9547443 and rs1035144) reside in the intergenic region between the SLITRK5 and SLITRK6 genes and in the intronic region of the TSHR gene and might affect functionality of SLITRK5, SLITRK6, and TSHR proteins that are engaged in tight control of key developmental processes, such as neurite outgrowth and modulation, cellular differentiation, and hormonal regulation...
August 29, 2018: Proteomics
Brett Janis, Clinton Belott, Michael A Menze
This review compares the molecular strategies employed by anhydrobiotic invertebrates to survive extreme water stress. Intrinsically disordered proteins (IDPs) play a central role in desiccation tolerance in all species investigated. Various hypotheses about the functions of anhydrobiosis-related intrinsically disordered (ARID) proteins, including late embryogenesis abundant (LEA) and tardigrade-specific intrinsically disordered proteins, were evaluated by broad sequence characterization. A surprisingly wide range in sequence characteristics including hydropathy and the frequency and distribution of charges was discovered...
August 24, 2018: Proteomics
Jonathan K Williams, Xue Yang, Jean Baum
Several intrinsically disordered proteins have been implicated in the process of amyloid fibril formation in neurodegenerative disease, and developing approaches to inhibit the aggregation of these intrinsically disordered proteins is critical for establishing effective therapies against disease progression. The aggregation pathway of the intrinsically disordered protein alpha-synuclein, which is implicated in several neurodegenerative diseases known as synucleinopathies, has been extensively characterized...
August 24, 2018: Proteomics
Yadong Wang, Chuang Liu, Jinzhe Du, Jingliang Huang, Shuce Zhang, Rongqing Zhang
Limpets are marine mollusks using mineralized teeth, one of the hardest and strongest biomaterials, to feed on algae on intertidal rocks. However, most of studies only focuses on the ultrastructure and chemical composition of the teeth while the molecular information is largely unknown, limiting our understanding of this unique and fundamental biomineralization process. In this study, we investigated the microstructure, proteomics and crystallization in the teeth of limpet Cellana toreuma. It is found that the limpets formed alternatively tricuspid teeth and unicuspid teeth...
August 24, 2018: Proteomics
Marisa J Stachowski, Ronald J Holewinski, Eric Grote, Vidya Venkatraman, Jennifer E Van Eyk, Jonathan A Kirk
Cardiac dyssynchrony arises from conduction abnormalities during heart failure and worsens morbidity and mortality. Cardiac resynchronization therapy (CRT) re-coordinates contraction using bi-ventricular pacing, but the cellular and molecular mechanisms involved remain largely unknown. The aim is to determine how dyssynchronous heart failure (HFdys ) alters the phospho-proteome and how CRT interacts with this unique phospho-proteome by analyzing Ser/Thr and Tyr phosphorylation. Phospho-enriched myocardium from dog models of Control, HFdys , and CRT is analyzed via MS...
August 20, 2018: Proteomics
Ranran Sun, Gaofeng Cui, Yaoyao Chen, Benshui Shu, Guohua Zhong, Xin Yi
Biopesticides are considered as an alternative to synthetic pesticide with a focus on increasing agricultural productivity as well as maintaining the ecosystem. Prior to application, its potential mechanism should be clearly addressed. Here, the effects of azadirachtin on the reproductive behavior in male Spodoptera litura (Fabricius) are determined. To further explore its molecular mechanism, an iTRAQ (isobaric tags for relative and absolute quantitation) based approach is applied to identify the differentially expressed proteins regulated by azadirachtin at two developmental stages...
August 10, 2018: Proteomics
Vera L Maria, David Licha, Janeck J Scott-Fordsmand, Christian G Huber, Mónica J B Amorim
The transcriptome of the ecotoxicological model Enchytraeus crypticus (known as potworm) is well studied, but the downstream changes at the protein level remained a gap. Changes in the protein regulation following exposure to CuO nanomaterial (NM) and Cu salt (CuCl2 ) are investigated. HPLC-MS/MS using tandem mass tags is used. CuO NM elicits higher number of differentially expressed proteins (DEPs) compared to CuCl2 with little to no overlap of proteins. CuO NM causes more stress response mechanisms, with good agreement between DEPs, genes, and metabolites...
August 10, 2018: Proteomics
Fengdi Li, Yacui Wang, Yu Li, Hongpu Yang, Hongmei Wang
Psoriasis is a common chronic autoimmune skin disease involving the activation of T cells. To explore the proteomic signature of peripheral blood mononuclear cells, a quantitative analysis of their global proteome was conducted in samples from Chinese patients with new-onset psoriasis (n = 31) and healthy controls (n = 32) using an integrated quantitative approach with tandem mass tag labeling and LC-MS/MS. Protein annotation, unsupervised hierarchical clustering, functional classification, functional enrichment and cluster, and protein-protein interaction analyses were performed...
August 9, 2018: Proteomics
Mainak Guharoy, Tamas Lazar, Peter Tompa
The 20S proteasome is known to degrade intrinsically disordered proteins (IDPs) via an ubiquitin-independent, disorder-driven mechanism. Unless protected within protein complexes or macromolecular assemblies, certain IDPs can undergo degradation mediated directly by the 20S core particle. In this issue of Proteomics, Myers et al. utilize a proteomics approach to identify ∼500 IDP substrates of the 20S proteasome. Bioinformatics analyses of these substrates demonstrate a large fraction of highly disordered RNA-binding proteins, enriched in low-complexity, prion-like domains...
August 2, 2018: Proteomics
Gabriela Seabra, Ana Caroline B Falvella, Paul C Guest, Daniel Martins-de-Souza, Valéria de Almeida
Interest in the modulation of endocannabinoid signaling has increased since the discovery of receptors for compounds of Cannabis sativa. Endocannabinoids are crucial neuromodulators of many brain functions and changes in the ligands and their receptors have been associated with psychiatric disorders, such as schizophrenia. Genetic, neuroimaging, and behavioral studies have reinforced the role of endocannabinoids in the pathobiology of schizophrenia. However, molecular pathways and biological processes involved in cannabinoid effects are not totally understood...
August 2, 2018: Proteomics
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