Post-translational attachment of lipids to proteins is found in all organisms, and is important for many biological processes. Acylation with myristic and palmitic acids are among the most common ...lipid modifications, and understanding reversible protein palmitoylation dynamics has become a particularly important goal. Linking acyltransferase enzymes to disease states can be challenging due to a paucity of robust models, compounded by functional redundancy between many palmitoyl transferases; however, in cases such as Wnt or Hedgehog signalling, small molecule inhibitors have been identified, with some progressing to clinical trials. In this review, we present recent developments in our understanding of protein acylation in human health and disease through use of chemical tools, global profiling of acylated proteomes, and functional studies of specific protein targets.
Studies have recently identified new enzymes responsible for adding or removing fatty acyl post-translational modifications, along with small-molecule ‘chemical tools’ to modulate the activity of several of these enzymes.
The advent of chemical tagging methodologies, in combination with proteomic analysis, has enhanced our understanding of the scope and importance of long-chain acylation across the cellular proteome, including in the dynamic nature of modifications.
Investigations of fatty-acylated substrate proteins have shown a wide range of outcomes from modifications, including effects in protein secretion, signalling, folding, and stability.
Fatty acyl transferases have been implicated in a growing number of disease states, where chemical tools and proteomic profiling technologies provide insight into the mechanism and potential therapeutic benefit of targeting such enzymes.
Protein N-myristoylation is a ubiquitous co- and post-translational modification that has been implicated in the development and progression of a range of human diseases. Here, we report the global ...N-myristoylated proteome in human cells determined using quantitative chemical proteomics combined with potent and specific human N-myristoyltransferase (NMT) inhibition. Global quantification of N-myristoylation during normal growth or apoptosis allowed the identification of >100 N-myristoylated proteins, >95% of which are identified for the first time at endogenous levels. Furthermore, quantitative dose response for inhibition of N-myristoylation is determined for >70 substrates simultaneously across the proteome. Small-molecule inhibition through a conserved substrate-binding pocket is also demonstrated by solving the crystal structures of inhibitor-bound NMT1 and NMT2. The presented data substantially expand the known repertoire of co- and post-translational N-myristoylation in addition to validating tools for the pharmacological inhibition of NMT in living cells.
Sized satellite images (pyramids) are not widely used in classification due to their dissimilarity with respect to the original image. But varied size images can reduce the cost, the time and mass ...storage of the classification system and can give us an initial impression of the result. This research work is an investigation to study the dependency upon varied size images in classification instead of using the original satellite image. The reference map is prepared to study the performance of the proposed system. Then, the varied size image is constructed for each band of the satellite image. Then, the classification is carried out using competitive learning neural networks (CLNN) method for all digital image pyramids, either the original satellite image or its sized images. The last step is the evaluation of the studied elements such as accuracy, classification time and storage volume. Some resized images are useful in such application, so the study suggests which size suits such applications.
Perturbed cellular protein homeostasis (proteostasis) and mitochondrial dysfunction play an important role in neurodegenerative diseases, however, the interplay between these two phenomena remains ...unclear. Mitochondrial dysfunction leads to a delay in mitochondrial protein import, causing accumulation of non-imported mitochondrial proteins in the cytosol and challenging proteostasis. Cells respond by increasing proteasome activity and molecular chaperones in yeast and C. elegans. Here, we demonstrate that in human cells mitochondrial dysfunction leads to the upregulation of a chaperone HSPB1 and, interestingly, an immunoproteasome-specific subunit PSMB9. Moreover, PSMB9 expression is dependent on the translation elongation factor EEF1A2. These mechanisms constitute a defense response to preserve cellular proteostasis under mitochondrial stress. Our findings define a mode of proteasomal activation through the change in proteasome composition driven by EEF1A2 and its spatial regulation, and are useful to formulate therapies to prevent neurodegenerative diseases.
Defects in mitochondrial function activate compensatory responses in the cell. Mitochondrial stress that is caused by unfolded proteins inside the organelle induces a transcriptional response (termed ...the "mitochondrial unfolded protein response" UPRmt) that is mediated by activating transcription factor associated with stress 1 (ATFS-1). The UPRmt increases mitochondrial protein quality control. Mitochondrial dysfunction frequently causes defects in the import of proteins, resulting in the accumulation of mitochondrial proteins outside the organelle. In yeast, cells respond to mistargeted mitochondrial proteins by increasing activity of the proteasome in the cytosol (termed the "unfolded protein response activated by mistargeting of proteins" UPRam). The presence and relevance of this response in higher eukaryotes is unclear. Here, we demonstrate that defects in mitochondrial protein import in Caenorhabditis elegans lead to proteasome activation and life span extension. Both proteasome activation and life span prolongation partially depend on ATFS-1, despite its lack of influence on proteasomal gene transcription. Importantly, life span prolongation depends on the fully assembled proteasome. Our data provide a link between mitochondrial dysfunction and proteasomal activity and demonstrate its direct relevance to mechanisms that promote longevity.
Malaria is an infectious disease caused by parasites of the genus Plasmodium, which leads to approximately one million deaths per annum worldwide. Chemical validation of new antimalarial targets is ...urgently required in view of rising resistance to current drugs. One such putative target is the enzyme N-myristoyltransferase, which catalyses the attachment of the fatty acid myristate to protein substrates (N-myristoylation). Here, we report an integrated chemical biology approach to explore protein myristoylation in the major human parasite P. falciparum, combining chemical proteomic tools for identification of the myristoylated and glycosylphosphatidylinositol-anchored proteome with selective small-molecule N-myristoyltransferase inhibitors. We demonstrate that N-myristoyltransferase is an essential and chemically tractable target in malaria parasites both in vitro and in vivo, and show that selective inhibition of N-myristoylation leads to catastrophic and irreversible failure to assemble the inner membrane complex, a critical subcellular organelle in the parasite life cycle. Our studies provide the basis for the development of new antimalarials targeting N-myristoyltransferase.
Novel multifunctional reagents were applied in combination with a lipid probe for affinity enrichment of myristoylated proteins and direct detection of lipid‐modified tryptic peptides by mass ...spectrometry. This method enables high‐confidence identification of the myristoylated proteome on an unprecedented scale in cell culture, and allowed the first quantitative analysis of dynamic changes in protein lipidation during vertebrate embryonic development.
Catch and release: Multifunctional capture reagents were developed that enable enzymatically‐triggered release and direct detection of lipid‐modified peptides by mass spectrometry. Dynamic proteome lipidation was visualized, enriched, and identified on an unprecedented scale, both in cells and in a developing zebrafish embryo.
Site-specifically phosphorylated lysine peptides Bertran-Vicente, Jordi; Serwa, Remigiusz A; Schümann, Michael ...
Journal of the American Chemical Society,
10/2014, Letnik:
136, Številka:
39
Journal Article
Recenzirano
Protein phosphorylation controls major processes in cells. Although phosphorylation of serine, threonine, and tyrosine and also recently histidine and arginine are well-established, the extent and ...biological significance of lysine phosphorylation has remained elusive. Research in this area has been particularly limited by the inaccessibility of peptides and proteins that are phosphorylated at specific lysine residues, which are incompatible with solid-phase peptide synthesis (SPPS) due to the intrinsic acid lability of the P(═O)-N phosphoramidate bond. To address this issue, we have developed a new synthetic route for the synthesis of site-specifically phospholysine (pLys)-containing peptides by employing the chemoselectivity of the Staudinger-phosphite reaction. Our synthetic approach relies on the SPPS of unprotected ε-azido lysine-containing peptides and their subsequent reaction to phosphoramidates with phosphite esters before they are converted into the natural modification via UV irradiation or basic deprotection. With these peptides in hand, we demonstrate that electron-transfer dissociation tandem mass spectrometry can be used for unambiguous assignment of phosphorylated-lysine residues within histone peptides and that these peptides can be detected in cell lysates using a bottom-up proteomic approach. This new tagging method is expected to be an essential tool for evaluating the biological relevance of lysine phosphorylation.
Modelling of bridge structures is an important topic due to the increasing need to get accurate information in a visual way. Registration between as-built laser data and global design reference one ...is necessary to guarantee the validity and dependency of the proposed model. This research presents a new registration method based on artificial neural networks (ANN) methodology. A developed software is implemented to apply ANN and to achieve the research objective. A steel structure bridge is chosen for the application of the proposed system. A point cloud laser data (as built) of the bridge is registered to the design model. The results show that the developed registration method is potential and reliable due to the insignificance of the error between both as-built model and the design model. The assumed level of significance is 95% and the error between as-built model and the design model after the registration process is found to be less than 5%. So, one concludes that the developed method can be used as a registration method for the laser scanning bridge structures. Some recommendations are presented to the future study concerned with using deep learning (DL) to apply the registration process to get better results.
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