Position-Specific Analysis and Prediction for Protein Lysine Acetylation Based on Multiple Features

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Suo, Sheng Bao ^a   Qiu, Jian Ding ^a,b   Shi, Shao Ping ^a   Sun, Xing Yu ^a   Huang, Shu Yun ^a   Chen, Xiang ^a   Liang, Ru Ping ^a  

^a NANCHANG UNIVERSITY   (China)

^b Pingxiang University   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LYSINE;

ACETYLATION; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; COMPUTER INTERFACE; COMPUTER PROGRAM; CORRELATION COEFFICIENT; CYTOSKELETON; ENTROPY; MOLECULAR DYNAMICS; PHYSICAL CHEMISTRY; PROTEIN ANALYSIS; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY; SUPPORT VECTOR MACHINE; TRANSCRIPTION REGULATION;

ACETYLATION; AMINO ACID SEQUENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; LYSINE; PHYSICOCHEMICAL PROCESSES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; USER-COMPUTER INTERFACE;

EID: 84869217522     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0049108     Document Type: Article

References (62)

1. Chung C, Liu J, Emili A, Frey BJ, (2011) Computational refinement of post-translational modifications predicted from tandem mass spectrometry. Bioinformatics 27: 797-806.
2. Yang XJ, (2004) Lysine acetylation and the bromodomain: a new partnership for signaling. Bioessays 26: 1076-1087.
3. Vidali G, Gershey EL, Allfrey VG, (1968) Chemical studies of histone acetylation. The distribution of epsilon-N-acetyllysine in calf thymus histones. The Journal of biological chemistry 243: 6361-6366.
4. Sadoul K, Wang J, Diagouraga B, Khochbin S, (2011) The Tale of Protein Lysine Acetylation in the Cytoplasm. Journal of Biomedicine and Biotechnology 2011: 970382.
5. Marks PA, (2007) Discovery and development of SAHA as an anticancer agent. Oncogene 26: 1351-1356.
6. Grant PA, (2001) A tale of histone modifications. Genome Biology 2: REVIEWS0003.
7. Verreault A, Kaufman PD, Kobayashi R, Stillman B, (1998) Nucleosomal DNA regulates the core-histone-binding subunit of the human Hat1 acetyltransferase. Current Biology 8: 96-108.
8. Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ, (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nature Structural & Molecular Biology 14: 1025-1040.
9. Yang XJ, Seto E, (2008) Lysine acetylation: codified crosstalk with other post-translational modifications. Molecular Cell 31: 449-461.
10. Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, et al. (2009) Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions. Science 325: 834-840.
11. Medzihradszky KF (2005) Peptide sequence analysis. Biological Mass Spectrometry. San Diego: Elsevier Academic Press Inc. 209-244.
12. Welsch DJ, Nelsestuen GL, (1988) Amino-terminal alanine functions in a calcium-specific process essential for membrane-binding by prothrombin fragment-1. Biochemistry 27: 4939-4945.
13. Umlauf D, Goto Y, Feil R, (2004) Site-specific analysis of histone methylation and acetylation. Methods in Molecular Biology 287: 99-120.
14. Basu A, Rose KL, Zhang JM, Beavis RC, Ueberheide B, et al. (2009) Proteome-wide prediction of acetylation substrates. Proceedings of the National Academy of Sciences of the United States of America 106: 13785-13790.
15. Gnad F, Ren SB, Choudhary C, Cox J, Mann M, (2010) Predicting post-translational lysine acetylation using support vector machines. Bioinformatics 26: 1666-1668.
16. Cai YD, Lu L, (2008) Predicting N-terminal acetylation based on feature selection method. Biochemical and Biophysical Research Communications 372: 862-865.
17. Lee TY, Hsu JBK, Lin FM, Chang WC, Hsu PC, et al. (2010) N-Ace: Using Solvent Accessibility and Physicochemical Properties to Identify Protein N-Acetylation Sites. Journal of Computational Chemistry 31: 2759-2771.
18. Xu Y, Wang X-B, Ding J, Wu L-Y, Deng N-Y, (2010) Lysine acetylation sites prediction using an ensemble of support vector machine classifiers. Journal of Theoretical Biology 264: 130-135.
19. Li SL, Li H, Li MF, Shyr Y, Xie L, et al. (2009) Improved Prediction of Lysine Acetylation by Support Vector Machines. Protein and Peptide Letters 16: 977-983.
20. Li A, Xue Y, Jin CJ, Wang MH, Yao XB, (2006) Prediction of N-epsilon-acetylation on internal lysines implemented in Bayesian Discriminant Method. Biochemical and Biophysical Research Communications 350: 818-824.
21. Marmorstein R, (2001) Structure and function of histone acetyltransferases. Cellular and Molecular Life Sciences 58: 693-703.
22. Marmorstein R, (2001) Structure of histone acetyltransferases. Journal of Molecular Biology 311: 433-444.
23. Weinert BT, Wagner SA, Horn H, Henriksen P, Liu WSR, et al. (2011) Proteome-wide mapping of the drosophila acetylome demonstrates a high degree of conservation of lysine acetylation. Science Signaling 4.
24. Chen K, Kurgan LA, Ruan JS (2007) Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs. BMC Structural Biology 7.
25. Obenauer JC, Cantley LC, Yaffe MB, (2003) Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Research 31: 3635-3641.
26. Liu ZX, Cao J, Gao XJ, Zhou YH, Wen LP, et al. (2011) CPLA 1.0: an integrated database of protein lysine acetylation. Nucleic Acids Research 39: D1029-D1034.
27. Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, et al. (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Research 40: D261-D270.
28. Prasad TSK, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Research 37: D767-D772.
29. Li H, Xing XB, Ding GH, Li QR, Wang C, et al. (2009) SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications. Molecular & Cellular Proteomics 8: 1839-1849.
30. Li WZ, Godzik A, (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
31. Shannon CE, (1997) The mathematical theory of communication (Reprinted). M D Computing 14: 306-317.
32. Feng J, Yuefei S, Cungen C, (2010) An information entropy-based approach to outlier detection in rough sets. Expert Systems with Applications 37: 6338-6344.
33. Ke C, Yingfu J, Li D, Kurgan L, (2009) Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs. Journal of Computational Chemistry 30: 163-172172.
34. Shen HB, Yang J, Chou KC, (2006) Fuzzy KNN for predicting membrane protein types from pseudo-amino acid composition. Journal of Theoretical Biology 240: 9-13.
35. Tan SB, (2006) An effective refinement strategy for KNN text classifier. Expert Systems with Applications 30: 290-298.
36. Gao JJ, Thelen JJ, Dunker AK, Xu D, (2010) Musite, a Tool for Global Prediction of General and Kinase-specific Phosphorylation Sites. Molecular & Cellular Proteomics 9: 2586-2600.
37. Tung CW, Ho SY (2008) Computational identification of ubiquitylation sites from protein sequences. BMC Bioinformatics 9.
38. Tomii K, Kanehisa M, (1996) Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Engineering 9: 27-36.
39. Nakai K, Kidera A, Kanehisa M, (1988) Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Engineering 2: 93-100.
40. Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, et al. (2008) AAindex: amino acid index database, progress report 2008. Nucleic Acids Research 36: D202-D205.
41. Janin J, Wodak S, (1978) Conformation of amino acid side-chains in proteins. Journal Of Molecular Biology 125: 357-386.
42. Chou KC, Shen HB, (2007) Recent progress in protein subcellular location prediction. Analytical Biochemistry 370: 1-16.
43. Chou KC, Zhang CT, (1995) Prediction of protein structural classes. Critical Reviews in Biochemistry and Molecular Biology 30: 275-349.
44. Sohn J, Rudolph J, (2007) Temperature dependence of binding and catalysis for the Cdc25B phosphatase. Biophysical Chemistry 125: 549-555.
45. Neuwirth M, Flicker K, Strohmeier M, Tews I, Macheroux P, (2007) Thermodynamic characterization of the protein-protein interaction in the heteromeric Bacillus subtilis pyridoxalphosphate synthase. Biochemistry 46: 5131-5139.
46. Georges E, (2007) The P-glycoprotein (ABCB1) linker domain encodes high-affinity binding sequences to alpha- and beta-tubulins. Biochemistry 46: 7337-7342.
47. Nomura T, Sokabe M, Yoshimura K, (2006) Lipid-protein interaction of the MscS mechanosensitive channel examined by scanning mutagenesis. Biophysical Journal 91: 2874-2881.
48. Urry DW, (2004) The change in Gibbs free energy for hydrophobic association- Derivation and evaluation by means of inverse temperature transitions. Chemical Physics Letters 399: 177-183.
49. Vacic V, Iakoucheva LM, Radivojac P, (2006) Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics 22: 1536-1537.
50. Pang CNI, Hayen A, Wilkins MR, (2007) Surface accessibility of protein post-translational modifications. Journal of Proteome Research 6: 1833-1845.
51. Chou MF, Schwartz D, (2011) Biological Sequence Motif Discovery Using motif-x. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis [et al] Chapter 13: Unit13.15.
52. Hutti JE, Jarrell ET, Chang JD, Abbott DW, Storz P, et al. (2004) A rapid method for determining protein kinase phosphorylation specificity. Nature Methods 1: 27-29.
53. Lu ZK, Cheng ZY, Zhao YM, Volchenboum SL (2011) Bioinformatic Analysis and Post-Translational Modification Crosstalk Prediction of Lysine Acetylation. Plos One 6.
54. Zhao SM, Xu W, Jiang WQ, Yu W, Lin Y, et al. (2010) Regulation of Cellular Metabolism by Protein Lysine Acetylation. Science 327: 1000-1004.
55. Yan Y, Barlev NA, Haley RH, Berger SL, Marmorstein R, (2000) Crystal structure of yeast Esa1 suggests a unified mechanism for catalysis and substrate binding by histone acetyltransferases. Molecular Cell 6: 1195-1205.
56. Neuwald AF, Landsman D, (1997) GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein. Trends In Biochemical Sciences 22: 154-155.
57. Kim SC, Sprung R, Chen Y, Xu YD, Ball H, et al. (2006) Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Molecular Cell 23: 607-618.
58. Trievel RC, Rojas JR, Sterner DE, Venkataramani RN, Wang L, et al. (1999) Crystal structure and mechanism of histone acetylation of the yeast GCN5 transcriptional coactivator. Proceedings of the National Academy of Sciences of the United States of America 96: 8931-8936.
59. Sternglanz R, Schindelin H, (1999) Structure and mechanism of action of the histone acetyltransferase Gcn5 and similarity to other N-acetyltransferases. Proceedings of the National Academy of Sciences of the United States of America 96: 8807-8808.
60. Rojas JR, Trievel RC, Zhou JX, Mo Y, Li XM, et al. (1999) Structure of Tetrahymena GCN5 bound to coenzyme A and a histone H3 peptide. Nature 401: 93-98.
61. Buchan DWA, Ward SM, Lobley AE, Nugent TCO, Bryson K, et al. (2010) Protein annotation and modelling servers at University College London. Nucleic Acids Research 38: W563-W568.
62. Bryson K, McGuffin LJ, Marsden RL, Ward JJ, Sodhi JS, et al. (2005) Protein structure prediction servers at University College London. Nucleic Acids Research 33: W36-W38.