The ABCs of PTMs

Barber, Karl W.; Rinehart, Jesse

doi:10.1038/nchembio.2572

Cited by 79 publications

(70 citation statements)

References 25 publications

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“…Access to posttranslationally modified proteins is now facilitated by recent developments in protein chemical synthesis (Conibear et al 2018), genetic code engineering (Liu and Schultz 2010; Lang and Chin 2014) and enzymatic protein modification (Zhang et al 2018), enabling studies of the role of PTMs in protein structure and function. Furthermore, increased commercial availability of the requisite building blocks for solid phase peptide synthesis (SPPS) means that peptides and proteins bearing PTMs are finding application in the pharmaceutical industry, chemical biology and peptide-based materials (Barber and Rinehart 2018).…”

Section: Introductionmentioning

confidence: 99%

Random coil shifts of posttranslationally modified amino acids

et al. 2019

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Most eukaryotic proteins are modified during and/or after translation, regulating their structure, function and localisation. The role of posttranslational modifications (PTMs) in both normal cellular processes and in diseases is already well recognised and methods for detection of PTMs and generation of specifically modified proteins have developed rapidly over the last decade. However, structural consequences of PTMs and their specific effects on protein dynamics and function are not well understood. Furthermore, while random coil NMR chemical shifts of the 20 standard amino acids are available and widely used for residue assignment, dihedral angle predictions and identification of structural elements or propensity, they are not available for most posttranslationally modified amino acids. Here, we synthesised a set of random coil peptides containing common naturally occurring PTMs and determined their random coil NMR chemical shifts under standardised conditions. We highlight unique NMR signatures of posttranslationally modified residues and their effects on neighbouring residues. This comprehensive dataset complements established random coil shift datasets of the 20 standard amino acids and will facilitate identification and assignment of posttranslationally modified residues. The random coil shifts will also aid in determination of secondary structure elements and prediction of structural parameters of proteins and peptides containing PTMs.

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Section: Introductionmentioning

confidence: 99%

Random coil shifts of posttranslationally modified amino acids

et al. 2019

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“…In proteinopathy, hydrophobic interaction in-between the aggregation-prone proteins lead to the formation of aggregates. In general, the amino acid sequence of a protein determines its post-translational modifications [20]. Post-translational modifications, such as protein folding, not only regulate the protein function but also mask the hydrophobic regions in the newly synthesized protein [20,21].…”

mentioning

confidence: 99%

“…In general, the amino acid sequence of a protein determines its post-translational modifications [20]. Post-translational modifications, such as protein folding, not only regulate the protein function but also mask the hydrophobic regions in the newly synthesized protein [20,21]. However, events such as intense protein overexpression, gene missense mutation, incomplete protein synthesis, endoplasmic reticulum stress, and protein folding co-factors shortages may cause unmasking of these hydrophobic protein regions [22].…”

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confidence: 99%

Targeting Aggrephagy for the Treatment of Alzheimer’s Disease

Malampati

Song

Tong

et al. 2020

Cells

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Alzheimer’s disease (AD) is one of the most common neurodegenerative diseases in older individuals with specific neuropsychiatric symptoms. It is a proteinopathy, pathologically characterized by the presence of misfolded protein (Aβ and Tau) aggregates in the brain, causing progressive dementia. Increasing studies have provided evidence that the defect in protein-degrading systems, especially the autophagy-lysosome pathway (ALP), plays an important role in the pathogenesis of AD. Recent studies have demonstrated that AD-associated protein aggregates can be selectively recognized by some receptors and then be degraded by ALP, a process termed aggrephagy. In this study, we reviewed the role of aggrephagy in AD development and discussed the strategy of promoting aggrephagy using small molecules for the treatment of AD.

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“…Furthermore, N258S substitution was predicted to enhance the probability of ubiquitination of lysine residue at position 255 and L94F alteration increased the sumoylation probability of lysine 92 (Table 2). It is known that post-translational modifications are involved in the process of activation or suppression of the protein's activity (Friso and Wijk, 2015;Barber and Rinehart, 2018). The post-translational modifications are important factors that can be regulated to influence salinity tolerance in plants (Roy et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

ANALYSIS OF NATURAL VARIATION IN OsHKT1;1 GENE SEQUENCE AND GENE EXPRESSION IN RELATION TO SALINITY IN RICE (Oryza sativa L.)

do¹,

Nguyen²,

Tang³

2020

THE JAPS

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Rice is a main food crop, but sensitive to salinity. The high affinity K + transporters (HKTs) have been proven to be important to salt tolerance in plants. In the current study, the natural variations in gene sequence of OsHKT1;1 were investigated for uncovering the potential allelic variants in salt tolerance in rice. Sequence analysis of OsHKT1;1 gene was conducted in the coding and promoter regions of all investigated rice cultivars. There were nine SNPs in the coding sequences and ten SNPs in the promoter sequences. Amongst nine SNPs found in the coding sequences, four were nonsynonymous (C89T, C280T, T536C, A773G) leading to four substituted amino acids P30L, L94F, F179S, and N258S. In silico analysis revealed no potential effects of the substituted amino acids to protein structure, but caused changes in post-translational modifications. In the promoter sequences, eight out of ten SNPs caused to five additions and six deletions of the cis-regulatory elements, in which some of them were shown to be involved in stress responses. OsHKT1;1 gene expression was analyzed in the roots and leaves in response to different salt concentrations. While the expression of OsHKT1;1 was induced in the leaves at the beginning of salt treatment (day 1 and day 2), it was decreased or unchanged in the roots.

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The ABCs of PTMs

Cited by 79 publications

References 25 publications

Random coil shifts of posttranslationally modified amino acids

Random coil shifts of posttranslationally modified amino acids

Targeting Aggrephagy for the Treatment of Alzheimer’s Disease

ANALYSIS OF NATURAL VARIATION IN OsHKT1;1 GENE SEQUENCE AND GENE EXPRESSION IN RELATION TO SALINITY IN RICE (Oryza sativa L.)

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