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Journal articles on the topic 'Post translational modification (PTM)'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Kim, Doo Nam, Tianzhixi Yin, Tong Zhang, et al. "Artificial Intelligence Transforming Post-Translational Modification Research." Bioengineering 12, no. 1 (2024): 26. https://doi.org/10.3390/bioengineering12010026.

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Post-Translational Modifications (PTMs) are covalent changes to amino acids that occur after protein synthesis, including covalent modifications on side chains and peptide backbones. Many PTMs profoundly impact cellular and molecular functions and structures, and their significance extends to evolutionary studies as well. In light of these implications, we have explored how artificial intelligence (AI) can be utilized in researching PTMs. Initially, rationales for adopting AI and its advantages in understanding the functions of PTMs are discussed. Then, various deep learning architectures and

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Park, Mi Kyung, Ho Lee, and Chang Hoon Lee. "Post-Translational Modification of ZEB Family Members in Cancer Progression." International Journal of Molecular Sciences 23, no. 23 (2022): 15127. http://dx.doi.org/10.3390/ijms232315127.

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Post-translational modification (PTM), the essential regulatory mechanisms of proteins, play essential roles in physiological and pathological processes. In addition, PTM functions in tumour development and progression. Zinc finger E-box binding homeobox (ZEB) family homeodomain transcription factors, such as ZEB1 and ZEB2, play a pivotal role in tumour progression and metastasis by induction epithelial-mesenchymal transition (EMT), with activation of stem cell traits, immune evasion and epigenetic reprogramming. However, the relationship between ZEB family members’ post-translational modifica

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Urasaki, Yasuyo, and Thuc T. Le. "Differentiation of Essential Oils Using Nanofluidic Protein Post-Translational Modification Profiling." Molecules 24, no. 13 (2019): 2383. http://dx.doi.org/10.3390/molecules24132383.

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Current methods for the authentication of essential oils focus on analyzing their chemical composition. This study describes the use of nanofluidic protein post-translational modification (PTM) profiling to differentiate essential oils by analyzing their biochemical effects. Protein PTM profiling was used to measure the effects of four essential oils, copaiba, mandarin, Melissa, and turmeric, on the phosphorylation of MEK1, MEK2, and ERK1/2 in the MAPK signaling pathway; Akt and 4EBP1 in the pI3K/Akt/mTOR signaling pathway; and STAT3 in the JAK/STAT signaling pathway in cultured HepG2 cells. T

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Xi, Xiaoming, and Wuli Zhao. "Anti-Tumor Potential of Post-Translational Modifications of PD-1." Current Issues in Molecular Biology 46, no. 3 (2024): 2119–32. http://dx.doi.org/10.3390/cimb46030136.

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Programmed cell death protein-1 (PD-1) is a vital immune checkpoint molecule. The location, stability, and protein–protein interaction of PD-1 are significantly influenced by post-translational modification (PTM) of proteins. The biological information of PD-1, including its gene and protein structures and the PD-1/PD-L1 signaling pathway, was briefly reviewed in this review. Additionally, recent research on PD-1 post-translational modification, including the study of ubiquitination, glycosylation, phosphorylation, and palmitoylation, was summarized, and research strategies for PD-1 PTM drugs

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Wang, Duolin, Yanchun Liang, and Dong Xu. "Capsule network for protein post-translational modification site prediction." Bioinformatics 35, no. 14 (2018): 2386–94. http://dx.doi.org/10.1093/bioinformatics/bty977.

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Abstract Motivation Computational methods for protein post-translational modification (PTM) site prediction provide a useful approach for studying protein functions. The prediction accuracy of the existing methods has significant room for improvement. A recent deep-learning architecture, Capsule Network (CapsNet), which can characterize the internal hierarchical representation of input data, presents a great opportunity to solve this problem, especially using small training data. Results We proposed a CapsNet for predicting protein PTM sites, including phosphorylation, N-linked glycosylation,

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Đukić, Teodora, Katarina Smiljanić, Jelena Mihailović, et al. "Proteomic Profiling of Major Peanut Allergens and Their Post-Translational Modifications Affected by Roasting." Foods 11, no. 24 (2022): 3993. http://dx.doi.org/10.3390/foods11243993.

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Post-translational modifications (PTMs) are covalent changes occurring on amino acid side chains of proteins and yet are neglected structural and functional aspects of protein architecture. The objective was to detect differences in PTM profiles that take place after roasting using open PTM search. We conducted a bottom-up proteomic study to investigate the impact of peanut roasting on readily soluble allergens and their PTM profiles. Proteomic PTM profiling of certain modifications was confirmed by Western blotting with a series of PTM-specific antibodies. In addition to inducing protein aggr

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7

Kitamura, Naoya, and James J. Galligan. "A global view of the human post-translational modification landscape." Biochemical Journal 480, no. 16 (2023): 1241–65. http://dx.doi.org/10.1042/bcj20220251.

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Post-translational modifications (PTMs) provide a rapid response to stimuli, finely tuning metabolism and gene expression and maintain homeostasis. Advances in mass spectrometry over the past two decades have significantly expanded the list of known PTMs in biology and as instrumentation continues to improve, this list will surely grow. While many PTMs have been studied in detail (e.g. phosphorylation, acetylation), the vast majority lack defined mechanisms for their regulation and impact on cell fate. In this review, we will highlight the field of PTM research as it currently stands, discussi

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Hernandez-Valladares, Maria, Rebecca Wangen, Frode S. Berven, and Astrid Guldbrandsen. "Protein Post-Translational Modification Crosstalk in Acute Myeloid Leukemia Calls for Action." Current Medicinal Chemistry 26, no. 28 (2019): 5317–37. http://dx.doi.org/10.2174/0929867326666190503164004.

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Background: Post-translational modification (PTM) crosstalk is a young research field. However, there is now evidence of the extraordinary characterization of the different proteoforms and their interactions in a biological environment that PTM crosstalk studies can describe. Besides gene expression and phosphorylation profiling of acute myeloid leukemia (AML) samples, the functional combination of several PTMs that might contribute to a better understanding of the complexity of the AML proteome remains to be discovered. Objective: By reviewing current workflows for the simultaneous enrichment

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Dunphy, Katie, Paul Dowling, Despina Bazou, and Peter O’Gorman. "Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers." Cancers 13, no. 8 (2021): 1930. http://dx.doi.org/10.3390/cancers13081930.

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Post-translational modifications (PTMs) add a layer of complexity to the proteome through the addition of biochemical moieties to specific residues of proteins, altering their structure, function and/or localization. Mass spectrometry (MS)-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with a high level of sensitivity and specificity. The low stoichiometry of modified peptides means fractionation and enrichment techniques are often performed prior to MS to improve detection yields. Immuno-based techniques remain popular,

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10

Wang, BingHua, Minghui Wang, and Ao Li. "Prediction of post-translational modification sites using multiple kernel support vector machine." PeerJ 5 (April 27, 2017): e3261. http://dx.doi.org/10.7717/peerj.3261.

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Protein post-translational modification (PTM) is an important mechanism that is involved in the regulation of protein function. Considering the high-cost and labor-intensive of experimental identification, many computational prediction methods are currently available for the prediction of PTM sites by using protein local sequence information in the context of conserved motif. Here we proposed a novel computational method by using the combination of multiple kernel support vector machines (SVM) for predicting PTM sites including phosphorylation, O-linked glycosylation, acetylation, sulfation an

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11

Suraritdechachai, Surased, Benya Lakkanasirorat, and Chayasith Uttamapinant. "Molecular probes for cellular imaging of post-translational proteoforms." RSC Chemical Biology 3, no. 2 (2022): 201–19. http://dx.doi.org/10.1039/d1cb00190f.

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Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes.

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12

Pascovici, Dana, Jemma X. Wu, Matthew J. McKay, et al. "Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools." International Journal of Molecular Sciences 20, no. 1 (2018): 16. http://dx.doi.org/10.3390/ijms20010016.

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Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques, offering increasing coverage and new opportunities to study human health and disease. Techniques such as

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13

Han, Ye, Fei He, Qing Shao, Duolin Wang, and Dong Xu. "MTPrompt-PTM: A Multi-Task Method for Post-Translational Modification Prediction Using Prompt Tuning on a Structure-Aware Protein Language Model." Biomolecules 15, no. 6 (2025): 843. https://doi.org/10.3390/biom15060843.

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Post-translational modifications (PTMs) regulate protein function, stability, and interactions, playing essential roles in cellular signaling, localization, and disease mechanisms. Computational approaches enable scalable PTM site prediction; however, traditional models focus only on local sequence features from fragments around potential modification sites, limiting the scope of their predictions. Recently, pre-trained protein language models (PLMs) have improved PTM prediction by leveraging biological knowledge derived from extensive protein databases. However, most PLMs used for PTM site pr

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14

Yang, Tangpo, Zheng Liu, and Xiang David Li. "Developing diazirine-based chemical probes to identify histone modification ‘readers’ and ‘erasers’." Chemical Science 6, no. 2 (2015): 1011–17. http://dx.doi.org/10.1039/c4sc02328e.

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15

Chen, Zhen, Xuhan Liu, Fuyi Li, et al. "Large-scale comparative assessment of computational predictors for lysine post-translational modification sites." Briefings in Bioinformatics 20, no. 6 (2018): 2267–90. http://dx.doi.org/10.1093/bib/bby089.

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Abstract Lysine post-translational modifications (PTMs) play a crucial role in regulating diverse functions and biological processes of proteins. However, because of the large volumes of sequencing data generated from genome-sequencing projects, systematic identification of different types of lysine PTM substrates and PTM sites in the entire proteome remains a major challenge. In recent years, a number of computational methods for lysine PTM identification have been developed. These methods show high diversity in their core algorithms, features extracted and feature selection techniques and ev

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16

Ito, K. "Impact of post-translational modifications of proteins on the inflammatory process." Biochemical Society Transactions 35, no. 2 (2007): 281–83. http://dx.doi.org/10.1042/bst0350281.

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PTM (post-translational modification) is the chemical modification of a protein after its translation. The well-studied PTM is phosphorylation, but, recently, PTMs have been re-focused by extensive studies on histone modifications and the discovery of the ubiquitin system. Histone acetylation is the well-established epigenetic regulator for gene expression. Recent studies show that different patterns of PTMs and cross-talk of individual modifications (acetylation, methylation, phosphorylation) are keys of gene regulation (known as the ‘histone code’). As well as histone, non-histone proteins a

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17

Malik, Arshi, Sarah Afaq, Afaf S. Alwabli, and Khalid Al-ghmady. "Networking of predicted post-translational modification (PTM) sites in human EGFR." Bioinformation 15, no. 7 (2019): 448–54. http://dx.doi.org/10.6026/97320630015448.

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18

Arntzen, Magnus Ø., Christoffer Leif Osland, Christopher Rasch-Olsen Raa, et al. "POSTMan (POST-translational modification analysis), a software application for PTM discovery." PROTEOMICS 9, no. 5 (2009): 1400–1406. http://dx.doi.org/10.1002/pmic.200800500.

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19

Duong, Van-An, Onyou Nam, EonSeon Jin, Jong-Moon Park, and Hookeun Lee. "Discovery of Post-Translational Modifications in Emiliania huxleyi." Molecules 26, no. 7 (2021): 2027. http://dx.doi.org/10.3390/molecules26072027.

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Emiliania huxleyi is a cosmopolitan coccolithophore that plays an essential role in global carbon and sulfur cycling, and contributes to marine cloud formation and climate regulation. Previously, the proteomic profile of Emiliania huxleyi was investigated using a three-dimensional separation strategy combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS). The current study reuses the MS/MS spectra obtained, for the global discovery of post-translational modifications (PTMs) in this species without specific enrichment methods. Twenty-five different PTM types were examined using

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20

Wang, Duolin, Dongpeng Liu, Jiakang Yuchi, et al. "MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization." Nucleic Acids Research 48, W1 (2020): W140—W146. http://dx.doi.org/10.1093/nar/gkaa275.

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Abstract MusiteDeep is an online resource providing a deep-learning framework for protein post-translational modification (PTM) site prediction and visualization. The predictor only uses protein sequences as input and no complex features are needed, which results in a real-time prediction for a large number of proteins. It takes less than three minutes to predict for 1000 sequences per PTM type. The output is presented at the amino acid level for the user-selected PTM types. The framework has been benchmarked and has demonstrated competitive performance in PTM site predictions by other researc

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Tromp, Angelino T., Michiel Van Gent, Joris P. Jansen, et al. "Host–Receptor Post-Translational Modifications Refine Staphylococcal Leukocidin Cytotoxicity." Toxins 12, no. 2 (2020): 106. http://dx.doi.org/10.3390/toxins12020106.

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Staphylococcal bi-component pore-forming toxins, also known as leukocidins, target and lyse human phagocytes in a receptor-dependent manner. S-components of the leukocidins Panton-Valentine leukocidin (PVL), γ-haemolysin AB (HlgAB) and CB (HlgCB), and leukocidin ED (LukED) specifically employ receptors that belong to the class of G-protein coupled receptors (GPCRs). Although these receptors share a common structural architecture, little is known about the conserved characteristics of the interaction between leukocidins and GPCRs. In this study, we investigated host cellular pathways contributi

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Wang, Qi, Keyun Wang, and Mingliang Ye. "Strategies for large-scale analysis of non-histone protein methylation by LC-MS/MS." Analyst 142, no. 19 (2017): 3536–48. http://dx.doi.org/10.1039/c7an00954b.

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23

Dilweg, Ivar W., and Remus T. Dame. "Post-translational modification of nucleoid-associated proteins: an extra layer of functional modulation in bacteria?" Biochemical Society Transactions 46, no. 5 (2018): 1381–92. http://dx.doi.org/10.1042/bst20180488.

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Post-translational modification (PTM) of histones has been investigated in eukaryotes for years, revealing its widespread occurrence and functional importance. Many PTMs affect chromatin folding and gene activity. Only recently the occurrence of such modifications has been recognized in bacteria. However, it is unclear whether PTM of the bacterial counterparts of eukaryotic histones, nucleoid-associated proteins (NAPs), bears a comparable significance. Here, we scrutinize proteome mass spectrometry data for PTMs of the four most abundantly present NAPs in Escherichia coli (H-NS, HU, IHF and FI

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Holstein, Elisa, Annalena Dittmann, Anni Kääriäinen, et al. "The Burden of Post-Translational Modification (PTM)—Disrupting Mutations in the Tumor Matrisome." Cancers 13, no. 5 (2021): 1081. http://dx.doi.org/10.3390/cancers13051081.

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Background: To evaluate the occurrence of mutations affecting post-translational modification (PTM) sites in matrisome genes across different tumor types, in light of their genomic and functional contexts and in comparison with the rest of the genome. Methods: This study spans 9075 tumor samples and 32 tumor types from The Cancer Genome Atlas (TCGA) Pan-Cancer cohort and identifies 151,088 non-silent mutations in the coding regions of the matrisome, of which 1811 affecting known sites of hydroxylation, phosphorylation, N- and O-glycosylation, acetylation, ubiquitylation, sumoylation and methyl

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Dougherty, Shannon E., Austin O. Maduka, Toshifumi Inada, and Gustavo M. Silva. "Expanding Role of Ubiquitin in Translational Control." International Journal of Molecular Sciences 21, no. 3 (2020): 1151. http://dx.doi.org/10.3390/ijms21031151.

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The eukaryotic proteome has to be precisely regulated at multiple levels of gene expression, from transcription, translation, and degradation of RNA and protein to adjust to several cellular conditions. Particularly at the translational level, regulation is controlled by a variety of RNA binding proteins, translation and associated factors, numerous enzymes, and by post-translational modifications (PTM). Ubiquitination, a prominent PTM discovered as the signal for protein degradation, has newly emerged as a modulator of protein synthesis by controlling several processes in translation. Advance

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Cheng, Alice, Charles E. Grant, William S. Noble, and Timothy L. Bailey. "MoMo: discovery of statistically significant post-translational modification motifs." Bioinformatics 35, no. 16 (2018): 2774–82. http://dx.doi.org/10.1093/bioinformatics/bty1058.

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Abstract Motivation Post-translational modifications (PTMs) of proteins are associated with many significant biological functions and can be identified in high throughput using tandem mass spectrometry. Many PTMs are associated with short sequence patterns called ‘motifs’ that help localize the modifying enzyme. Accordingly, many algorithms have been designed to identify these motifs from mass spectrometry data. Accurate statistical confidence estimates for discovered motifs are critically important for proper interpretation and in the design of downstream experimental validation. Results We d

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Xue, Xiangfei, Xiao Zhang, Fenyong Sun, and Jiayi Wang. "Emerging Role of Protein Post-Translational Modification in the Potential Clinical Application of Cancer." Nano LIFE 10, no. 01n02 (2020): 2040008. http://dx.doi.org/10.1142/s1793984420400085.

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Cancer, one of the largest public health problems in the world, greatly endangers human health. Every country in the world faces a significant burden due to cancer. Protein post-translational modification (PTM) plays a very important role in life. PTM makes the structure of proteins more complex and the functions more perfect. Common PTM processes include methylation, acetylation, phosphorylation, glycosylation and ubiquitination. In this paper, we introduce several common types of PTMs that were discovered in recent years in various cancer types, especially the early stages of cancer, and we

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Xu, Yongjie, Wei Wu, Qiu Han, et al. "Post-translational modification control of RNA-binding protein hnRNPK function." Open Biology 9, no. 3 (2019): 180239. http://dx.doi.org/10.1098/rsob.180239.

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Heterogeneous nuclear ribonucleoprotein K (hnRNPK), a ubiquitously occurring RNA-binding protein (RBP), can interact with numerous nucleic acids and various proteins and is involved in a number of cellular functions including transcription, translation, splicing, chromatin remodelling, etc. Through its abundant biological functions, hnRNPK has been implicated in cellular events including proliferation, differentiation, apoptosis, DNA damage repair and the stress and immune responses. Thus, it is critical to understand the mechanism of hnRNPK regulation and its downstream effects on cancer and

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Nie, Litong, Mingrui Zhu, Shengnan Sun, et al. "An optimization of the LC-MS/MS workflow for deep proteome profiling on an Orbitrap Fusion." Analytical Methods 8, no. 2 (2016): 425–34. http://dx.doi.org/10.1039/c5ay01900a.

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Deolankar, Sayali Chandrashekhar, Shashanka G. Koyangana, Arun H. Patil, Yashwanth Subbannayya, Prashant Kumar Modi, and T. S. Keshava Prasad. "Data on multiple post-translational modifications in Alzheimer's disease." Neuroscience Research Notes 5, no. 2 (2022): 153. http://dx.doi.org/10.31117/neuroscirn.v5i2.153.

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This article describes the data obtained for global post-translational modifications (PTMs) profiled for Alzheimer's Disease (AD) from two distinct human brain regions and one cerebrospinal fluid (CSF) sample. The PTM profiling was performed to identify phosphorylation, O-GluNAcetylation, methylation, acetylation and citrullination using three publicly available LC-MS/MS raw data sets (PRIDE ID: PXD004010, PXD002516, PXD004863). A total of 1,857 PTM harbouring proteins with 4,961 unique post-translationally modified peptides were identified. Among the modified peptides, 75 corresponded uniquel

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Taylor, Bethany C., and Nicolas L. Young. "Combinations of histone post-translational modifications." Biochemical Journal 478, no. 3 (2021): 511–32. http://dx.doi.org/10.1042/bcj20200170.

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Histones are essential proteins that package the eukaryotic genome into its physiological state of nucleosomes, chromatin, and chromosomes. Post-translational modifications (PTMs) of histones are crucial to both the dynamic and persistent regulation of the genome. Histone PTMs store and convey complex signals about the state of the genome. This is often achieved by multiple variable PTM sites, occupied or unoccupied, on the same histone molecule or nucleosome functioning in concert. These mechanisms are supported by the structures of ‘readers’ that transduce the signal from the presence or abs

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Li, Xu, Pingdong Cai, Xinyuan Tang, Yingzi Wu, Yue Zhang, and Xianglu Rong. "Lactylation Modification in Cardiometabolic Disorders: Function and Mechanism." Metabolites 14, no. 4 (2024): 217. http://dx.doi.org/10.3390/metabo14040217.

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Cardiovascular disease (CVD) is recognized as the primary cause of mortality and morbidity on a global scale, and developing a clear treatment is an important tool for improving it. Cardiometabolic disorder (CMD) is a syndrome resulting from the combination of cardiovascular, endocrine, pro-thrombotic, and inflammatory health hazards. Due to their complex pathological mechanisms, there is a lack of effective diagnostic and treatment methods for cardiac metabolic disorders. Lactylation is a type of post-translational modification (PTM) that plays a regulatory role in various cellular physiologi

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Kumar, Ramesh, Divya Mehta, Nimisha Mishra, Debasis Nayak, and Sujatha Sunil. "Role of Host-Mediated Post-Translational Modifications (PTMs) in RNA Virus Pathogenesis." International Journal of Molecular Sciences 22, no. 1 (2020): 323. http://dx.doi.org/10.3390/ijms22010323.

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Being opportunistic intracellular pathogens, viruses are dependent on the host for their replication. They hijack host cellular machinery for their replication and survival by targeting crucial cellular physiological pathways, including transcription, translation, immune pathways, and apoptosis. Immediately after translation, the host and viral proteins undergo a process called post-translational modification (PTM). PTMs of proteins involves the attachment of small proteins, carbohydrates/lipids, or chemical groups to the proteins and are crucial for the proteins’ functioning. During viral inf

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Wang, Minghui, Yujie Jiang, and Xiaoyi Xu. "A novel method for predicting post-translational modifications on serine and threonine sites by using site-modification network profiles." Molecular BioSystems 11, no. 11 (2015): 3092–100. http://dx.doi.org/10.1039/c5mb00384a.

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HE, LIN, XI HAN, and BIN MA. "DE NOVO SEQUENCING WITH LIMITED NUMBER OF POST-TRANSLATIONAL MODIFICATIONS PER PEPTIDE." Journal of Bioinformatics and Computational Biology 11, no. 04 (2013): 1350007. http://dx.doi.org/10.1142/s0219720013500078.

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De novo sequencing derives the peptide sequence from a tandem mass spectrum without the assistance of protein databases. This analysis has been indispensable for the identification of novel or modified peptides in a biological sample. Currently, the speed of de novo sequencing algorithms is not heavily affected by the number of post-translational modification (PTM) types in consideration. However, the accuracy of the algorithms can be degraded due to the increased search space. Most peptides in a proteomics research contain only a small number of PTMs per peptide, yet the types of PTMs can com

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Linthwaite, Victoria L., and Martin J. Cann. "A methodology for carbamate post-translational modification discovery and its application in Escherichia coli." Interface Focus 11, no. 2 (2021): 20200028. http://dx.doi.org/10.1098/rsfs.2020.0028.

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Carbon dioxide can influence cell phenotypes through the modulation of signalling pathways. CO 2 regulates cellular processes as diverse as metabolism, cellular homeostasis, chemosensing and pathogenesis. This diversity of regulated processes suggests a broadly conserved mechanism for CO 2 interactions with diverse cellular targets. CO 2 is generally unreactive but can interact with neutral amines on protein under normal intracellular conditions to form a carbamate post-translational modification (PTM). We have previously demonstrated the presence of this PTM in a subset of protein produced by

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Blee, Tajekesa K. P., Nicola K. Gray, and Matthew Brook. "Modulation of the cytoplasmic functions of mammalian post-transcriptional regulatory proteins by methylation and acetylation: a key layer of regulation waiting to be uncovered?" Biochemical Society Transactions 43, no. 6 (2015): 1285–95. http://dx.doi.org/10.1042/bst20150172.

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Post-transcriptional control of gene expression is critical for normal cellular function and viability and many of the proteins that mediate post-transcriptional control are themselves subject to regulation by post-translational modification (PTM), e.g. phosphorylation. However, proteome-wide studies are revealing new complexities in the PTM status of mammalian proteins, in particular large numbers of novel methylated and acetylated residues are being identified. Here we review studied examples of methylation/acetylation-dependent regulation of post-transcriptional regulatory protein (PTRP) fu

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Gannon, Harry G., Amber Riaz-Bradley, and Martin J. Cann. "A Non-Functional Carbon Dioxide-Mediated Post-Translational Modification on Nucleoside Diphosphate Kinase of Arabidopsis thaliana." International Journal of Molecular Sciences 25, no. 2 (2024): 898. http://dx.doi.org/10.3390/ijms25020898.

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The carbamate post-translational modification (PTM), formed by the nucleophilic attack of carbon dioxide by a dissociated lysine epsilon-amino group, is proposed as a widespread mechanism for sensing this biologically important bioactive gas. Here, we demonstrate the discovery and in vitro characterization of a carbamate PTM on K9 of Arabidopsis nucleoside diphosphate kinase (AtNDK1). We demonstrate that altered side chain reactivity at K9 is deleterious for AtNDK1 structure and catalytic function, but that CO2 does not impact catalysis. We show that nucleotide substrate removes CO2 from AtNDK

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Liu, Hui-Fang, and Rong Liu. "Structure-based prediction of post-translational modification cross-talk within proteins using complementary residue- and residue pair-based features." Briefings in Bioinformatics 21, no. 2 (2019): 609–20. http://dx.doi.org/10.1093/bib/bby123.

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Abstract Post-translational modification (PTM)-based regulation can be mediated not only by the modification of a single residue but also by the interplay of different modifications. Accurate prediction of PTM cross-talk is a highly challenging issue and is in its infant stage. Especially, less attention has been paid to the structural preferences (except intrinsic disorder and spatial proximity) of cross-talk pairs and the characteristics of individual residues involved in cross-talk, which may restrict the improvement of the prediction accuracy. Here we report a structure-based algorithm cal

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Tikhonov, Dmitry, Liudmila Kulikova, Vladimir Rudnev, et al. "Changes in Protein Structural Motifs upon Post-Translational Modification in Kidney Cancer." Diagnostics 11, no. 10 (2021): 1836. http://dx.doi.org/10.3390/diagnostics11101836.

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Post-translational modification (PTM) leads to conformational changes in protein structure, modulates the biological function of proteins, and, consequently, changes the signature of metabolic transformations and the immune response in the body. Common PTMs are reversible and serve as a mechanism for modulating metabolic trans-formations in cells. It is likely that dysregulation of post-translational cellular signaling leads to abnormal proliferation and oncogenesis. We examined protein PTMs in the blood samples from patients with kidney cancer. Conformational changes in proteins after modific

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Xue, Han, Qingfeng Zhang, Panqin Wang, et al. "qPTMplants: an integrative database of quantitative post-translational modifications in plants." Nucleic Acids Research 50, no. D1 (2021): D1491—D1499. http://dx.doi.org/10.1093/nar/gkab945.

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Abstract As a crucial molecular mechanism, post-translational modifications (PTMs) play critical roles in a wide range of biological processes in plants. Recent advances in mass spectrometry-based proteomic technologies have greatly accelerated the profiling and quantification of plant PTM events. Although several databases have been constructed to store plant PTM data, a resource including more plant species and more PTM types with quantitative dynamics still remains to be developed. In this paper, we present an integrative database of quantitative PTMs in plants named qPTMplants (http://qptm

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Kissel, T., S. Reijm, LM Slot, et al. "Antibodies and B cells recognising citrullinated proteins display a broad cross-reactivity towards other post-translational modifications." Annals of the Rheumatic Diseases 79, no. 4 (2020): 472–80. http://dx.doi.org/10.1136/annrheumdis-2019-216499.

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ObjectiveAutoantibodies against antigens carrying distinct post-translational modifications (PTMs), such as citrulline, homocitrulline or acetyllysine, are hallmarks of rheumatoid arthritis (RA). The relation between these anti-modified protein antibody (AMPA)-classes is poorly understood as is the ability of different PTM-antigens to activate B-cell receptors (BCRs) directed against citrullinated proteins (CP). Insights into the nature of PTMs able to activate such B cells are pivotal to understand the ‘evolution’ of the autoimmune response conceivable underlying the disease. Here, we investi

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Taldaev, Amir, Vladimir Rudnev, Liudmila Kulikova, et al. "Molecular Dynamics Study of Citrullinated Proteins Associated with the Development of Rheumatoid Arthritis." Proteomes 10, no. 1 (2022): 8. http://dx.doi.org/10.3390/proteomes10010008.

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Biological activity regulation by protein post-translational modification (PTM) is critical for cell function, development, differentiation, and survival. Dysregulation of PTM proteins is present in various pathological conditions, including rheumatoid arthritis (RA). RA is a systemic autoimmune disease that primarily affects joints, and there are three main types of protein PTMs associated with the development of this disease, namely, glycosylation, citrullination, and carbamylation. Glycosylation is important for the processing and presentation of antigen fragments on the cell surface and ca

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Poltronieri, Palmiro, Masanao Miwa, and Mitsuko Masutani. "ADP-Ribosylation as Post-Translational Modification of Proteins: Use of Inhibitors in Cancer Control." International Journal of Molecular Sciences 22, no. 19 (2021): 10829. http://dx.doi.org/10.3390/ijms221910829.

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Among the post-translational modifications of proteins, ADP-ribosylation has been studied for over fifty years, and a large set of functions, including DNA repair, transcription, and cell signaling, have been assigned to this post-translational modification (PTM). This review presents an update on the function of a large set of enzyme writers, the readers that are recruited by the modified targets, and the erasers that reverse the modification to the original amino acid residue, removing the covalent bonds formed. In particular, the review provides details on the involvement of the enzymes per

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Corpas, Francisco J., Salvador González-Gordo, María A. Muñoz-Vargas, Marta Rodríguez-Ruiz, and José M. Palma. "The Modus Operandi of Hydrogen Sulfide(H2S)-Dependent Protein Persulfidation in Higher Plants." Antioxidants 10, no. 11 (2021): 1686. http://dx.doi.org/10.3390/antiox10111686.

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Protein persulfidation is a post-translational modification (PTM) mediated by hydrogen sulfide (H2S), which affects the thiol group of cysteine residues from target proteins and can have a positive, negative or zero impact on protein function. Due to advances in proteomic techniques, the number of potential protein targets identified in higher plants, which are affected by this PTM, has increased considerably. However, its precise impact on biological function needs to be evaluated at the experimental level in purified proteins in order to identify the specific cysteine(s) residue(s) affected.

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Xiao, Hao, Zeping Han, Min Xu, et al. "The Role of Post-Translational Modifications in Necroptosis." Biomolecules 15, no. 4 (2025): 549. https://doi.org/10.3390/biom15040549.

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Necroptosis, a distinct form of regulated necrosis implicated in various human pathologies, is orchestrated through sophisticated signaling pathways. During this process, cells undergoing necroptosis exhibit characteristic necrotic morphology and provoke substantial inflammatory responses. Post-translational modifications (PTMs)—chemical alterations occurring after protein synthesis that critically regulate protein functionality—constitute essential regulatory components within these complex signaling cascades. This intricate crosstalk between necroptotic pathways and PTM networks presents pro

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Song, Lei, and Zhao-Qing Luo. "Post-translational regulation of ubiquitin signaling." Journal of Cell Biology 218, no. 6 (2019): 1776–86. http://dx.doi.org/10.1083/jcb.201902074.

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Ubiquitination regulates many essential cellular processes in eukaryotes. This post-translational modification (PTM) is typically achieved by E1, E2, and E3 enzymes that sequentially catalyze activation, conjugation, and ligation reactions, respectively, leading to covalent attachment of ubiquitin, usually to lysine residues of substrate proteins. Ubiquitin can also be successively linked to one of the seven lysine residues on ubiquitin to form distinctive forms of polyubiquitin chains, which, depending upon the lysine used and the length of the chains, dictate the fate of substrate proteins.

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Chato-Astrain, Isabel, Marie Pronot, Thierry Coppola, and Stéphane Martin. "Molecular Organization and Regulation of the Mammalian Synapse by the Post-Translational Modification SUMOylation." Cells 13, no. 5 (2024): 420. http://dx.doi.org/10.3390/cells13050420.

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Neurotransmission occurs within highly specialized compartments forming the active synapse where the complex organization and dynamics of the interactions are tightly orchestrated both in time and space. Post-translational modifications (PTMs) are central to these spatiotemporal regulations to ensure an efficient synaptic transmission. SUMOylation is a dynamic PTM that modulates the interactions between proteins and consequently regulates the conformation, the distribution and the trafficking of the SUMO-target proteins. SUMOylation plays a crucial role in synapse formation and stabilization,

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Brewster, Richard C., and Alison N. Hulme. "Halomethyl-Triazoles for Rapid, Site-Selective Protein Modification." Molecules 26, no. 18 (2021): 5461. http://dx.doi.org/10.3390/molecules26185461.

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Post-translational modifications (PTMs) are used by organisms to control protein structure and function after protein translation, but their study is complicated and their roles are not often well understood as PTMs are difficult to introduce onto proteins selectively. Designing reagents that are both good mimics of PTMs, but also only modify select amino acid residues in proteins is challenging. Frequently, both a chemical warhead and linker are used, creating a product that is a misrepresentation of the natural modification. We have previously shown that biotin-chloromethyl-triazole is an ef

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Han, Danlu, Zhibo Yu, Jianbin Lai, and Chengwei Yang. "Post-translational modification: a strategic response to high temperature in plants." aBIOTECH 3, no. 1 (2022): 49–64. http://dx.doi.org/10.1007/s42994-021-00067-w.

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AbstractWith the increasing global warming, high-temperature stress is affecting plant growth and development with greater frequency. Therefore, an increasing number of studies examining the mechanism of temperature response contribute to a more optimal understanding of plant growth under environmental pressure. Post-translational modification (PTM) provides the rapid reconnection of transcriptional programs including transcription factors and signaling proteins. It is vital that plants quickly respond to changes in the environment in order to survive under stressful situations. Herein, we dis

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