SVMyr: A Web Server Detecting Co- and Post-translational Myristoylation in Proteins

Myristoylation (MYR) is a protein modification where a myristoyl group is covalently attached to an exposed (N-terminal) glycine residue. Glycine myristoylation occurs during protein translation (co-translation) or after (post-translation). Myristoylated proteins have a role in signal transduction, apoptosis, and pathogen-mediated processes and their prediction can help in functionally annotating the fraction of proteins undergoing MYR in different proteomes.Here we present SVMyr, a web server allowing the detection of both co- and post-translational myristoylation sites, based on Support Vector Machines (SVM). The input encodes composition and physicochemical features of the octapeptides, known to act as substrates and to physically interact with N-myristoyltransferases (NMTs), the enzymes catalyzing the myristoylation reaction.The method, adopting a cross validation procedure, scores with values of Area Under the Curve (AUC) and Matthews Correlation Coefficient (MCC) of 0.92 and 0.61, respectively. When benchmarked on an independent dataset including experimentally detected 88 medium/high confidence co-translational myristoylation sites and 528 negative examples, SVMyr outperforms available methods, with AUC and MCC equal to 0.91 and 0.58, respectively.A unique feature of SVMyr is the ability to predict post-translational myristoylation sites by coupling the trained SVMs with the detection of caspase cleavage sites, identified by searching regular motifs matching upstream caspase cleavage sites, as reported in literature.Finally, SVMyr confirms 96% of the UniProt set of the electronically annotated myristoylated proteins (31,048) and identifies putative myristoylomes in eight different proteomes, highlighting also new putative NMT substrates.SVMyr is freely available through a user-friendly web server at https://busca.biocomp.unibo.it/lipipred.     

Lysine long-chain fatty acylation regulates the TEAD transcription factor

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Comprehensive Analysis of the Lysine Succinylome and Protein Co-modifications in Developing Rice Seeds

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Highlights

• •Nonenzymatically Ksu proteins shown different pattern from native cell Ksu proteins.
• •Motif preference of Ksu proteins was associated with different biological processes.
• •Up to 67 developing rice seeds proteins contain PTMs of Kac, Ksu, Kcr, Kmal, and Khib.
• •Some lysine residues of the key pathway enzymes are modified by succinylation.

     

植物组蛋白赖氨酸甲基化建立过程及其遗传性研究进展

表观遗传学主要包括DNA甲基化、组蛋白修饰和非编码RNA,组蛋白甲基化作为组蛋白修饰中的一种重要修饰,在植物体的发育和环境适应中发挥着重要作用。组蛋白甲基化主要发生在赖氨酸残基上,同时根据不同的赖氨酸位点和每个赖氨酸位点甲基化程度的不同,形成了不同的赖氨酸甲基化修饰。根据对基因的不同功能,通常将组蛋白赖氨酸甲基化修饰分为2大类:(1)能够促进基因表达的,如H3K4me3和H3K36me3;(2)能够抑制基因表达的,如H3K9me2和H3K27me3。不同的组蛋白赖氨酸甲基化去甲基化过程需要相应的阅读(reader)、书写(writer)和擦除(eraser)3种蛋白。同时,组蛋白赖氨酸甲基化的遗传性质目前还不是很清楚。综述了植物中组蛋白赖氨酸甲基化建立与去除过程,以及对组蛋白赖氨酸甲基化可遗传性的探讨。     

黄芩素的结构修饰以及抗肿瘤活性研究

为了改善黄芩素的抗肿瘤活性。本实验以黄芩素为原料,对其进行结构修饰。首先通过mannich反应,在8位引入胺亚甲基,然后通过酰基化反应在7位(6位)酚羟基上引入不同的疏水性基团。并利用CCK-8法对目标化合物进行抗MCF-7肿瘤细胞的活性评价。结果合成得到了6个目标化合物,通过1HNMR、13CNMR、MS和化学手段相结合的方法确定了其结构,其中化合物2~6为新化合物。实验利用黄酮类邻二酚羟基的特性,通过与氯化锶的络合反应,巧妙而简单的确证了所得目标化合物的酯键是在化合物的7位羟基上。抗MCF-7肿瘤活性实验表明,在黄芩素8位上引入含氮原子的胺亚甲基后活性比先导化合物黄芩素强,在其7位上再引入酯键后3个化合物活性比先导化合物强。     

Structural relationship between tRNA2 Lys and tRNA4 Lys from mouse lymphoma cells

Summary Mouse lymphoma cells have three major isoaccepting lysine tRNAs. Two of these isoacceptors, tRNA₂ ^Lys and tRNA₄ ^Lys, were sequenced by rapid gel or chromatogram readout methods. They have the same primary sequence but differ in two modified nucleotides. tRNA₄ ^Lys has an unmodified uridine replacing one dihydrouridine and an unidentified nucleotide, t⁶A^*, replacing t⁶A. This unidentified nucleotide is not a hypomodified form of t⁶A. Thus, tRNA4ys is not a simple precursor of tRNA₂ ^Lys. Both tRNAs have an unidentified nucleotide, U^**, in the third position of the anticodon. Also, partial sequences of minor homologs of tRNA₂ ^Lys and tRNA₄ ^Lys were obtained. The distinctions between tRNA₂ ^Lys and tRNA₄ ^Lys may be part of significant cellular roles as illustrated by the differential effects of these isoacceptors on the synthesis by lysyl-tRNA synthetase of diadenosine-5,5-P₁,P₄-tetraphosphate, a putative signal in DNA replication.     

Oligomerization and Auto-methylation of the Human Lysine Methyltransferase SETD6

Signaling via lysine methylation by protein lysine methyltransferases (PKMTs), has been linked to diverse biological and disease processes. The mono-methyltransferase SETD6 (SET-domain-containing protein 6) is a member of the PKMT family and was previously shown to regulate essential cellular processes such as the NF-κB, WNT and the oxidative stress pathways. However, on the biochemical level, little is known about the enzymatic mode of action of SETD6. Here we provide evidence that SETD6 forms high-molecular-weight structures. Specifically, we demonstrate that SETD6 monomeric, dimeric and trimeric forms are stabilized by the methyl donor, S-adenosyl-l-methionine. We then show that SETD6 has auto-methylation activity at K39 and K179, which serves as the major auto-methylation sites with a moderate auto-methylation activity toward K372. A point mutation at K179 but not at K39 and K372, located at the SET domain of SETD6, impaired SETD6 ability to form a trimer, strongly implying a link between the auto-methylation and the oligomerization state. Finally, by radioactive in vitro methylation experiments and biochemical kinetics analysis, we show that the auto-methylation at K39 and K179 increases the catalytic rate of SETD6. Collectively, our data support a model by which SETD6 auto-methylation and self-interaction positively regulate its enzymatic activity in vitro and may suggest that other PKMTs are regulated in the same manner.     

Lysine transport across the small intestine. Stimulating and inhibitory effects of neutral amino acids

Summary The ordinary aliphatic, neutral amino acids and phenylalanine have been examined for cis-inhibition of influx of alanine (J _mc ^ala ) and lysine (J _mc ^lys ) and trans-stimulation ofJ _mc ^lys across the brush border membrane of rat small intestines: and their effects on the unidirectional mucosa-to-serosa flux (J _ms ^lys ) across the short circuited intestine have been studied. The effects of alanine, -amino-n-butyric acid, leucine, and methionine on the steady-state epithelial uptake of lysine [Lys] _c have also been measured. In addition the trans-effects of alanine and leucine have been examined for sodium-dependence, and alanine was tested as trans-stimulator of influx of galactose across the brush border membrane (J _mc ^gal ).All the neutral amino acids were found to be competitive cis-inhibitors ofJ _mc ^lys , and all, except isoleucine, were trans-stimulators ofJ _mc ^lys . The magnitude of the trans-effect was unrelated to the efficiency of the amino acid as cis-inhibitor. As illustrated by alanine, the trans-effects are probably completely sodium-dependent. Alanine was also effective as trans-stimulator ofJ _mc ^gal . With respect to effects on [Lys] _c andJ _ms ^lys the neutral amino acids fall into two groups: One which reduces [Lys] _c and stimulatesJ _ms ^lys , and one which increases [Lys] _c and relatively inhibitsJ _ms ^lys . These effects are not correlated with the affinities of the neutral amino acids for the two carriers involved.It is proposed that the trans-effects onJ _mc ^lys are induced by an electrogenic, sodium-coupled efflux of the neutral amino acid across the brush border membrane, that the stimulation ofJ _ms ^lys is brought about by a selective stimulation (of unknown nature) of efflux of lysine across the basolateral membrane (J _cs ^lys ), assisted by competitive inhibition of lysine efflux across the brush border membrane (J _cm ^lys ), and that the amino acids which do not stimulateJ _cm ^lys increase [Lys] _c by competitively inhibitingJ _cs ^lys andJ _cm ^lys .The inhibitory effect of the neutral amino acids onJ _mc ^lys support the view that the carrier of basic amino acids serves as a second carrier of these amino acids.     

Identification,Quantification, and System Analysis of Protein N‐ε Lysine Methylation in Anucleate Blood Platelets

Protein posttranslational modifications critically regulate a range of physiological and disease processes. In addition to tyrosine, serine, and threonine phosphorylation, reversible N‐ε acylation and alkylation of protein lysine residues also modulate diverse aspects of cellular function. Studies of lysine acyl and alkyl modifications have focused on nuclear proteins in epigenetic regulation; however, lysine modifications are also prevalent on cytosolic proteins to serve increasingly apparent, although less understood roles in cell regulation. Here, the methyl‐lysine (meK) proteome of anucleate blood platelets is characterized. With high‐resolution, multiplex MS methods, 190 mono‐, di‐, and tri‐meK modifications are identified on 150 different platelet proteins—including 28 meK modifications quantified by tandem mass tag (TMT) labeling. In addition to identifying meK modifications on calmodulin (CaM), GRP78 (HSPA5, BiP), and EF1A1 that have been previously characterized in other cell types, more novel modifications are also uncovered on cofilin, drebin‐like protein (DBNL, Hip‐55), DOCK8, TRIM25, and numerous other cytoplasmic proteins. Together, the results and analyses support roles for lysine methylation in mediating cytoskeletal, translational, secretory, and other cellular processes. MS data for this study have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD012217.     

Prion Protein Prolines 102 and 105 and the Surrounding Lysine Cluster Impede Amyloid Formation

Human prion diseases can have acquired, sporadic, or genetic origins, each of which results in the conversion of prion protein (PrP) to transmissible, pathological forms. The genetic prion disease Gerstmann-Straussler-Scheinker syndrome can arise from point mutations of prolines 102 or 105. However, the structural effects of these two prolines, and mutations thereof, on PrP misfolding are not well understood. Here, we provide evidence that individual mutations of Pro-102 or Pro-105 to noncyclic aliphatic residues such as the Gerstmann-Straussler-Scheinker-linked leucines can promote the in vitro formation of PrP amyloid with extended protease-resistant cores reminiscent of infectious prions. This effect was enhanced by additional charge-neutralizing mutations of four nearby lysine residues comprising the so-called central lysine cluster. Substitution of these proline and lysine residues accelerated PrP conversion such that spontaneous amyloid formation was no longer slower than scrapie-seeded amyloid formation. Thus, Pro-102 and Pro-105, as well as the lysines in the central lysine cluster, impede amyloid formation by PrP, implicating these residues as key structural modulators in the conversion of PrP to disease-associated types of amyloid.     

Quantitative Global Proteome and Lysine Succinylome Analyses Reveal the Effects of Energy Metabolism in Renal Cell Carcinoma

In light of the increasing incidence of renal cell carcinoma (RCC), its molecular mechanisms have been comprehensively explored in numerous recent studies. However, few studies focus on the influence of multi‐factor interactions during the occurrence and development of RCC. This study aims to investigate the quantitative global proteome and the changes in lysine succinylation in related proteins, seeking to facilitate a better understanding of the molecular mechanisms underlying RCC. LC‐MS/MS combined with bioinformatics analysis are used to quantitatively detect the perspectives at the global protein level. IP and WB analysis were conducted to further verify the alternations of related proteins and lysine succinylation. A total of 3,217 proteins and 1,238 lysine succinylation sites are quantified in RCC tissues, and 668 differentially expressed proteins and 161 differentially expressed lysine succinylation sites are identified. Besides, expressions of PGK1 and PKM2 at protein and lysine, succinylation levels are significantly altered in RCC tissues. Bioinformatics analysis indicates that the glycolysis pathway is a potential mechanism of RCC progression and lysine succinylation may plays a potential role in energy metabolism. These results can provide a new direction for exploring the molecular mechanism of RCC tumorigenesis.     

Molecular role of NAA38 in thermostability and catalytic activity of the human NatC N-terminal acetyltransferase

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Structural biology of the chromodomain: form and function

The chromodomain motif is found among certain chromosomal proteins of all eukaryotes. The chromodomain fold - three beta strands packed against a C-terminal alpha helix - mediates protein-protein and/or protein-nucleic acid interactions. In some cases, the affinity of chromodomain binding is regulated by lysine methylation, which appears to target chromodomain proteins and associated complexes to specific sites in chromatin. In this review, our current knowledge of chromodomain structure and function is summarized.     

Compensatory Growth of C2C12 Myotubes Induced by the Combined Effect of Lysine Sufficiency and Modulation of IGF-I and Glucocorticoid Levels

We have reported that a change from a lysine-deficient diet to a lysine-sufficient diet induced compensatory growth in rats and pigs. The aim of the present study was to determine whether compensatory growth of C2C12 myotubes occurs only by sufficiency of lysine or also by the synergic effect of sufficiency of lysine and modulation of the levels of insulin-like growth factor-I (IGF-I) and glucocorticoid in a medium. The results provide the first evidence of compensatory growth of C2C12 myotubes induced by sufficiency of a single amino acid in combination with modulation of the levels of IGF-I and glucocorticoid.     

Applying the tools of chemistry (mass spectrometry and covalent modification by small molecule reagents) to the detection of prions and the study of their structure

Prions are molecular pathogens, able to convert a normal cellular prion protein (PrP^C) into a prion (PrP^Sc). The information necessary for this conversion is contained in the conformation of PrP^Sc. Mass spectrometry (MS) and small-molecule covalent reactions have been used to study prions. Mass spectrometry has been used to detect and quantitate prions in the attomole range (10^?18 mole). MS-based analysis showed that both possess identical amino acid sequences, one disulfide bond, a GPI anchor, asparagine-linked sugar antennae, and unoxidized methionines. Mass spectrometry has been used to define elements of the secondary and tertiary structure of wild-type PrP^Sc and GPI-anchorless PrP^Sc. It has also been used to study the quaternary structure of the PrP^Sc multimer. Small molecule reagents react differently with the same lysine in the PrP^C conformation than in the PrP^Sc conformation. Such differences can be detected by Western blot using mAbs with lysine-containing epitopes, such as 3F4 and 6D11. This permits the detection of PrP^Sc without the need for proteinase K pretreatment and can be used to distinguish among prion strains. These results illustrate how two important chemical tools, mass spectrometry and covalent modification by small molecules, are being applied to the detection and structural study of prions. Furthermore these tools are or can be applied to the study of the other protein misfolding diseases such as Alzheimer Disease, Parkinson Disease, or ALS.     

反相高效液相层析在糖化白蛋白肽段分离纯化中的应用

采用一种简单的“甲醇-水-三氟醋酸”作为洗脱体系的反相高效液相层析（简称RP-HPLC）对通过固相合成方法合成的糖化白蛋白肽段进行了分析鉴定和分离纯化.使用酸敏性PEG载体,Fmoc保护化学法合成了白蛋白八肽NH₂-Lys-Gln-Thr-Ala-Leu-Tyr-Tyr-Cys-COOH.对其N端Lys进行糖化反应后,经Sephadex G-10柱色谱纯化后,通过RP-HPLC分析,证明得到了糖化八肽的单一峰.使用Merrifield树脂,Boc保护化学法合成了白蛋白七肽NH₂-Gln-Thr-Ala-Leu-Tyr-Tyr-Cys-COOH.通过RP-HPLC半制备分离提纯后,得到了所需的肽段.对N^α-Boc-Lys的ε氨基进行糖化反应后,经RP-HPLC分析,证明得到了比较纯的糖化赖氨酸,与纯化后的白蛋白七肽偶联后,通过RP-HPLC分析,得到了偶联产物——糖化八肽的单一峰.