Tissue-specific sequence and structural environments of lysine acetylation sites

Karabulut, Nermin Pinar; Frishman, Dmitrij

doi:10.1016/j.jsb.2015.06.001

Cited by 6 publications

(17 citation statements)

References 48 publications

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“…Consistent with enhanced acetylation at lysine-rich motifs, recent studies indicate that lysine acetylation preferentially occurs in a general lysine-rich local environment, in which neighboring lysines facilitate primary lysine acetylation [27, 29]. Secondly, the acetylated lysines identified in our study often contain I/V residues at positions P +2 or P -2 (e.g.…”

Section: Discussionsupporting

confidence: 85%

Conserved Lysine Acetylation within the Microtubule-Binding Domain Regulates MAP2/Tau Family Members

et al. 2016

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Lysine acetylation has emerged as a dominant post-translational modification (PTM) regulating tau proteins in Alzheimer’s disease (AD) and related tauopathies. Mass spectrometry studies indicate that tau acetylation sites cluster within the microtubule-binding region (MTBR), a region that is highly conserved among tau, MAP2, and MAP4 family members, implying that acetylation could represent a conserved regulatory mechanism for MAPs beyond tau. Here, we combined mass spectrometry, biochemical assays, and cell-based approaches to demonstrate that the tau family members MAP2 and MAP4 are also subject to reversible acetylation. We identify a cluster of lysines in the MAP2 and MAP4 MTBR that undergo CBP-catalyzed acetylation, many of which are conserved in tau. Similar to tau, MAP2 acetylation can occur in a cysteine-dependent auto-regulatory manner in the presence of acetyl-CoA. Furthermore, tubulin reduced MAP2 acetylation, suggesting tubulin binding dictates MAP acetylation status. Taken together, these results uncover a striking conservation of MAP2/Tau family post-translational modifications that could expand our understanding of the dynamic mechanisms regulating microtubules.

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Section: Discussionsupporting

confidence: 85%

Conserved Lysine Acetylation within the Microtubule-Binding Domain Regulates MAP2/Tau Family Members

et al. 2016

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“…Acetylation is a reversible enzymatic process, where acetyl groups are added to free amines of lysine. Lysine acetylation is highly tissue specific and considered as a dynamic process that requires tight balance between acetylases and deacetylases 19 36. Acetylation of histones and transcription factors plays a key role in nuclear transcription regulation 37–39.…”

Section: Discussionmentioning

confidence: 99%

Antimodified protein antibody response pattern influences the risk for disease relapse in patients with rheumatoid arthritis tapering disease modifying antirheumatic drugs

Figueiredo

Bang²,

Cobra³

et al. 2016

Ann Rheum Dis

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“…For now, many PTM sites can mapped on known PDB structures, such as glycosylaiton, acetylation, methylation etc. Karabulut et al have used Spatial amino acid composition to identify tissue specific acetylation site and they also discovered that characteristic of 3D structure are different from the one of amino acid sequence [18]. To sum up, we proposed that spatial amino acid composition and side chain orientation methods can be used to enable the identification of PTM sites on protein 3D structure.…”

Section: Resultsmentioning

confidence: 99%

“…Durek and co-workers characterized phosphorylation sites by spatial amino acid propensity distributions to generate spatial signature motifs and the subsequent assessment of this information to improve the prediction of phosphorylation sites in proteins [17]. Karabulut et al present the first comprehensive analysis of global and tissue-specific sequence and structure properties of lysine acetylation sites based on recent experimental data [18]. The study of Marino et al have tried to observe characteristics of endogenously SNO modified in WT mouse liver on protein 3D structures, and concluded the endogenous S-nitrosoproteome in the liver has structural features that accommodate multiple mechanisms for selective site-directed S-nitrosylation [19].…”

Section: Introductionmentioning

confidence: 99%

Characterization and Identification of Protein S-Nitrosylation Sites Based on Tertiary Structures

Lee¹,

Hsu²,

Chang³

2020

IJBBB

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S-nitrosylation (SNO) is a sulfur atom occurring in cysteine amino acid in the protein connected to nitric oxide (NO), and it is one of the most important and universal Post-translational modifications. Nitroso modification will affect regulating cell function and information transfer. In recent years, there were many studies have developed the method of indentify S-nitrosylation substrate site in silicon. Unfortunately, people did not find significant characteristics for identification in protein sequence. Therefore, this study aims to explore structural characteristics on tertiary structures of S-nitrosylated proteins. As the number of the crystal structure in the PDB increases, also many SNO sites have been experimentally verified, we characterized these substrate sites containing 3D structures by structural analysis methods, such as Spatial amino acid composition, side chain orientation, and DSSP relative solvent accessible area. Besides, the support vector machine (SVM) was employed to generate the predictive model with the consideration of both sequential and spatial features. According to the evaluation of five-fold cross-validation, the spatial model could obtain a higher accuracy than the sequential model. Additionally, this work revealed that the model concerning multiple spatial features could achieve best performance in the prediction of SNO sites.

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Tissue-specific sequence and structural environments of lysine acetylation sites

Cited by 6 publications

References 48 publications

Conserved Lysine Acetylation within the Microtubule-Binding Domain Regulates MAP2/Tau Family Members

Conserved Lysine Acetylation within the Microtubule-Binding Domain Regulates MAP2/Tau Family Members

Antimodified protein antibody response pattern influences the risk for disease relapse in patients with rheumatoid arthritis tapering disease modifying antirheumatic drugs

Characterization and Identification of Protein S-Nitrosylation Sites Based on Tertiary Structures

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