CPLM: a database of protein lysine modifications

Liu, Zexian; Wang, Yongbo; Gao, Tianshun; Pan, Zhicheng; Cheng, Han; Yang, Qing; Cheng, Zhongyi; Guo, An‐Yuan; Ren, Jian; Xue, Yu

doi:10.1093/nar/gkt1093

Cited by 159 publications

(116 citation statements)

References 40 publications

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“…In Mus musculus , the focus of the majority of acetyl-proteomics studies, 13,186 sites across 4,024 proteins have been identified and a full 63% of mitochondrially localized proteins contain acetylation sites. A comparable amount of sites have been found in human cell lines: ~11,000 sites [44–46]. The bulk of this data has been generated in the past four years.…”

Section: Probing the Extent Of The Mitochondrial Acetylomementioning

confidence: 85%

Mechanisms and Dynamics of Protein Acetylation in Mitochondria

Baeza

Smallegan

Denu

2016

Trends in Biochemical Sciences

271

237

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Reversible protein acetylation is a major regulatory mechanism for controlling protein function. Through genetic manipulations, dietary perturbations, and new proteomic technologies, the diverse functions of protein acetylation are coming into focus. Protein acetylation in mitochondria has taken center stage, revealing that 63% of mitochondrially localized proteins contain lysine acetylation sites. Here we summarize the field, and discuss salient topics that cover spurious versus targeted acetylation, the role of SIRT3 deacetylation, nonenzymatic acetylation, and molecular models for regulatory acetylations that display high and low stoichiometry.

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Section: Probing the Extent Of The Mitochondrial Acetylomementioning

confidence: 85%

Mechanisms and Dynamics of Protein Acetylation in Mitochondria

Baeza

Smallegan

Denu

2016

Trends in Biochemical Sciences

271

237

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“…For instance, an integrated database of Compendium of Protein Lysine Modifications reported that there are 7151 lysine acetylation sites in 3311 proteins (Liu et al, 2014). This is supported by experimentally that CBP/p300, PCAF, and HDACs have non-histone target proteins, such as transcription factors, transcription cofactors, and cytoskeleton (Brochier et al, 2013; Chen et al, 2005; Dompierre et al, 2007; Federman et al, 2013; Gaub et al, 2010).…”

Section: Epigenetic Mechanisms In Memory Formationmentioning

confidence: 99%

Epigenetic regulation of Fgf1 transcription by CRTC1 and memory enhancement

Uchida

Shumyatsky

2018

Brain Research Bulletin

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Recent evidence demonstrates that epigenetic regulation of gene transcription is critically involved in learning and memory. Here, we discuss the role of histone acetylation and DNA methylation, which are two best understood epigenetic processes in memory processes. More specifically, we focus on learning-strength-dependent changes in chromatin on the fibroblast growth factor 1 (Fgf1) gene and on the molecular events that modulate regulation of Fgf1 transcription, required for memory enhancement, with the specific focus on CREB-regulated transcription coactivator 1 (CRTC1).

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“…To construct a robust benchmark dataset, experimentally validated protein sequences with lysine succinylation site details were collected from SwissProt/UniProt (retrieved on 21 May 2017) [17] and Compendium of Protein Lysine Modifications database curated by CUCKOO Workgroup [18]. Initially, 897 proteins with 2523 verified succinylation site (i.e.…”

Section: Datasetsmentioning

confidence: 99%

DV-iSucLys: Decision Voting to Improve Protein Lysine Succinylation Site Identification from Sequence Data

Islam¹

2017

AJBLS

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Protein Post Translation Modification identification is one of the important steps in conducting disease-associated mutation studies. Though multiple chemical alterations happen in a protein after translation, the addition of succinyl group to lysine residue plays a vital role in regulating cellular metabolism and thus disease. Use of a classification algorithm on some features, driven either from protein structural, physicochemical or even biochemical information becomes a common approach that can yield a satisfactory result up to a certain level. Although, researchers already developed many computational methods to identify whether a lysine residue modified with succinyl group after translation, most of them focused on the improvement either on a single decision using a single method or feature enrichment or even development of a benchmark dataset. Therefore, there still exists scope for further improvement to characterise lysine residues of a protein sequence by considering multiple predictors at a time. In this study, an ensemble based approach called DV-iSucLys has been designed to characterise the lysine residue by adapting three well known and conceptually different classifiers and ensembling their decisions. Also, a benchmark succinylation dataset was extracted from existing benchmark datasets and recently updated succinylation data from UniProt consortium to investigate the performance of the proposed approach as well as contribute to further research. Analysing rigorous cross-validation results show that DV-iSucLys can characterise succinyl lysine residue better than the existing predictors.

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CPLM: a database of protein lysine modifications

Cited by 159 publications

References 40 publications

Mechanisms and Dynamics of Protein Acetylation in Mitochondria

Mechanisms and Dynamics of Protein Acetylation in Mitochondria

Epigenetic regulation of Fgf1 transcription by CRTC1 and memory enhancement

DV-iSucLys: Decision Voting to Improve Protein Lysine Succinylation Site Identification from Sequence Data

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