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ABSTRACT: Protein lysine acetylation plays an important role in the normal functioning of cells, including gene expression regulation, protein stability and metabolism regulation. Although large amounts of lysine acetylation sites have been identified via large-scale mass spectrometry or traditional experimental methods, the lysine (K)-acetyl-transferase (KAT) responsible for the acetylation of a given protein or lysine site remains largely unknown due to the experimental limitations of KAT substrate identification. Hence, the in silico prediction of KAT-specific acetylation sites may provide direction for further experiments. In our previous study, we developed the acetylation set enrichment based (ASEB) computer program to predict which KAT-families are responsible for the acetylation of a given protein or lysine site. In this article, we provide KAT-specific acetylation site prediction as a web service. This web server not only provides the online tool and R package for the method in our previous study, but several useful services are also included, such as the integration of protein-protein interaction information to enhance prediction accuracy. This web server can be freely accessed at http://cmbi.bjmu.edu.cn/huac.
Nucleic Acids Research 05/2012; 40(Web Server issue):W376-9. · 8.03 Impact Factor
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ABSTRACT: Previous studies have indicated that ERp44 inhibits inositol 1,4,5-trisphosphate (IP(3))-induced Ca(2+) release (IICR) via IP(3)R(1), but the mechanism remains largely unexplored. Using extracellular ATP to induce intracellular calcium transient as an IICR model, Ca(2+) image, pull down assay, and Western blotting experiments were carried out in the present study. We found that extracellular ATP induced calcium transient via IP(3)Rs (IICR) and the IICR were markedly decreased in ERp44 overexpressed Hela cells. The inhibitory effect of C160S/C212S but not C29S/T396A/ΔT(331-377) mutants of ERp44 on IICR were significantly decreased compared with ERp44. However, the binding capacity of ERp44 to L3V domain of IP(3)R(1) (1L3V) was enhanced by ERp44 C160S/C212S mutation. Taken together, these results suggest that the mutants of ERp44, C160/C212, can more tightly bind to IP(3)R(1) but exhibit a weak inhibition of IP(3)R(1) channel activity in Hela cells.
Protein & Cell 12/2011; 2(12):990-6.
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ABSTRACT: Lysine acetylation is a well-studied post-translational modification on both histone and nonhistone proteins. More than 2000 acetylated proteins and 4000 lysine acetylation sites have been identified by large scale mass spectrometry or traditional experimental methods. Although over 20 lysine (K)-acetyl-transferases (KATs) have been characterized, which KAT is responsible for a given protein or lysine site acetylation is mostly unknown. In this work, we collected KAT-specific acetylation sites manually and analyzed sequence features surrounding the acetylated lysine of substrates from three main KAT families (CBP/p300, GCN5/PCAF, and the MYST family). We found that each of the three KAT families acetylates lysines with different sequence features. Based on these differences, we developed a computer program, Acetylation Set Enrichment Based method to predict which KAT-families are responsible for acetylation of a given protein or lysine site. Finally, we evaluated the efficiency of our method, and experimentally detected four proteins that were predicted to be acetylated by two KAT families when one representative member of the KAT family is over expressed. We conclude that our approach, combined with more traditional experimental methods, may be useful for identifying KAT families responsible for acetylated substrates proteome-wide.
Molecular & Cellular Proteomics 09/2011; 11(1):M111.011080. · 7.40 Impact Factor
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ABSTRACT: Prx4 (peroxiredoxin 4) is the only peroxiredoxin located in the ER (endoplasmic reticulum) and a proposed scavenger for H2O2. In the present study, we solved crystal structures of human Prx4 in three different redox forms and characterized the reaction features of Prx4 with H2O2. Prx4 exhibits a toroid-shaped decamer constructed of five catalytic dimers. Structural analysis revealed conformational changes around helix α2 and the C-terminal reigon with a YF (Tyr-Phe) motif from the partner subunit, which are required for interchain disulfide formation between Cys87 and Cys208, a critical step of the catalysis. The structural explanation for the restricting role of the YF motif on the active site dynamics is provided in detail. Prx4 has a high reactivity with H2O2, but is susceptible to overoxidation and consequent inactivation by H2O2. Either deletion of the YF motif or dissociation into dimers decreased the susceptibility of Prx4 to overoxidation by increasing the flexibility of Cys87.
Biochemical Journal 09/2011; 441(1):113-8. · 4.90 Impact Factor
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ABSTRACT: High-throughput RNA sequencing (RNA-seq) technology provides a revolutionary approach to studying splicing events de novo. However, identifying splice junctions with high sensitivity and specificity remains a challenge. In the present study, we proposed a new tool named SeqSaw to detect splice junctions with or without the canonical GT-AG splicing signal. SeqSaw was applied to two ENCODE RNA-seq datasets and also compared with two existing methods. It was shown that the proposed method obtained better results on finding novel splice junctions. Experiments also revealed that the current sequencing depth has not yet reached saturation to detect novel transcripts. Moreover, by comparing the number of supporting reads, we demonstrated that many un-annotated splicing events can be tissue specific.
Biochemical and Biophysical Research Communications 06/2011; 409(2):299-303. · 2.48 Impact Factor
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04/2011;
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ABSTRACT: Cubic Mg0.58Zn0.42O thin films with (100) orientation were grown on cubic MgO substrates. The band gap of the alloy films corresponds to solar blind band. In the case that a MgO buffer layer was employed, the surface roughness was decreased from 38 to 1.6 nm under the same growth conditions. A metal−semiconductor−metal photodetector based on this MgZnO film was fabricated, which showed a low dark current of 0.16 pA and lower sub-bandgap photoresponse than the ones with rougher surface in our early reports.Keywords: high smooth; MgZnO; MOCVD; UV photodetector
07/2010;
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ABSTRACT: Cubic Mg(0.58)Zn(0.42)O thin films with (100) orientation were grown on cubic MgO substrates. The band gap of the alloy films corresponds to solar blind band. In the case that a MgO buffer layer was employed, the surface roughness was decreased from 38 to 1.6 nm under the same growth conditions. A metal-semiconductor-metal photodetector based on this MgZnO film was fabricated, which showed a low dark current of 0.16 pA and lower sub-bandgap photoresponse than the ones with rougher surface in our early reports.
ACS Applied Materials & Interfaces 07/2010; 2(7):1918-21. · 4.53 Impact Factor
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ABSTRACT: High-throughput RNA sequencing (RNA-seq) is rapidly emerging as a major quantitative transcriptome profiling platform. Here, we present DEGseq, an R package to identify differentially expressed genes or isoforms for RNA-seq data from different samples. In this package, we integrated three existing methods, and introduced two novel methods based on MA-plot to detect and visualize gene expression difference. AVAILABILITY: The R package and a quick-start vignette is available at http://bioinfo.au.tsinghua.edu.cn/software/degseq
Bioinformatics 10/2009; 26(1):136-8. · 5.47 Impact Factor
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Likun Wang,
Lei Wang,
Stefano Vavassori,
Shengjian Li,
Huimin Ke,
Tiziana Anelli,
Massimo Degano,
Riccardo Ronzoni,
Roberto Sitia,
Fei Sun,
Chih-Chen Wang
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ABSTRACT: ERp44 mediates thiol-dependent retention in the early secretory pathway, forming mixed disulphides with substrate proteins through its conserved CRFS motif. Here, we present its crystal structure at a resolution of 2.6 A. Three thioredoxin domains-a, b and b'-are arranged in a clover-like structure. A flexible carboxy-terminal tail turns back to the b' and a domains, shielding a hydrophobic pocket in domain b' and a hydrophobic patch around the CRFS motif in domain a. Mutational and functional studies indicate that the C-terminal tail gates the CRFS area and the adjacent hydrophobic pocket, dynamically regulating protein quality control.
EMBO Reports 08/2008; 9(7):642-7. · 7.36 Impact Factor
