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Information System for Post-translational Modifications Murali Mohan Podicheti School of Informatics Master of Science in Bioinformatics Final capstone project 16 December 2005, 3:30 PM Indiana University Bloomington, IN Agenda •Agenda < •Introduction to PTM •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future •References •Acknowledgements Post-translational modifications - Introduction Existing databases for hosting PTM information Why ISPTM? Features of ISPTM Implementations for future References Acknowledgements Approximate time left: 20 minutes December 16, 2005 Information System for Post-translational Modifications 2 Post-translational Modifications •Agenda •Introduction to PTM < •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future •References •Acknowledgements Translation is the process of synthesizing the peptide chain of amino acids specified by the nucleotide sequence on the mRNA. Approximate time left: 19 minutes December 16, 2005 Information System for Post-translational Modifications 3 The central Dogma •Agenda •Introduction to PTM < •Existing Databases •Why ISPTM? •Transcription •Feautures of ISPTM •Translation •Targets for Future •References •Acknowledgements It is not necessary that the final product of translation should be the final product of protein synthesis. Approximate time left: 18 minutes December 16, 2005 Information System for Post-translational Modifications 4 Changes after Translation •Agenda •Introduction to PTM < •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future •References •Acknowledgements Peptide chain undergoes folding Some amino acids might be changed Carbohydrates or lipids can be added Peptide can be activated by addition or removal of some residue (acetate, phosphate, methyl etc.) Changes in the Hydrogen bond proclivity which results in secondary and tertiary structures Some of the proteins might remain in cytosol while others are transported across the membrane or even imported into cellular organelles (mitochondria or chloroplasts) to accomplish their functions Approximate time left: 18 minutes December 16, 2005 Information System for Post-translational Modifications 5 Changes after Translation •Agenda •Introduction to PTM < •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future •References •Acknowledgements Post-translational Modifications Approximate time left: 17 minutes December 16, 2005 Information System for Post-translational Modifications 6 Types of Post-translational modifications •Agenda •Introduction to PTM -PTM Types < -Significance Several types of PTMs characterized. Some of them: Proteolytic cleavage Glycosylation -PTMs and Cancer -Identification and Prediction •Existing Databases •Why ISPTM? Methylation Hydroxylation Phosphorylation •Feautures of ISPTM Sulfation •Targets for Future Acylation •References •Acknowledgements Carboxylation Prenylation Selenation Formylation Approximate time left: 17 minutes Disulfide bond formation December 16, 2005 Information System for Post-translational Modifications 7 Phosphorylation •Agenda •Introduction to PTM -PTM Types < -Significance Phosphorylation is the addition of a phosphate (PO4) group to a protein or a small molecule -PTMs and Cancer -Identification and Prediction •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future •References •Acknowledgements Phosphorylation and dephosphorylation responsible for activating or deactivation many enzymes and receptors Phosphorylation catalyzed by various specific protein kinases, dephosphorylation by phosphatases Can occur on Serine, Threonine, Tyrosine Approximate time left: 16 minutes December 16, 2005 Information System for Post-translational Modifications 8 Glycosylation •Agenda •Introduction to PTM -PTM Types < -Significance -PTMs and Cancer Glycosylation is the addition of saccharide to a protein or a lipid molecule -Identification and Prediction •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future •References •Acknowledgements • N-Linked Glycosylation -Amide nitrogen of Asparagine •O-Linked Glycosylation - Hydroxy oxygen of Serine and Threonine Approximate time left: 14 minutes December 16, 2005 Information System for Post-translational Modifications 9 PTMs have significant biological functions •Agenda •Introduction to PTM -PTM Types -Significance < -PTMs and Cancer -Identification and Prediction •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future Extend the range of possible functions that can be exhibited by a protein by introducing new chemical groups. Alter the hydrophobicity of a protein (synthesis of membrane proteins). Activating or inactivating an enzyme. Energy metabolism Oxidative phosphorylation in respiration Photophosphorylation in protein synthesis •References Signal transduction •Acknowledgements Protein degradation Blood coagulation Immune system Approximate time left: 13 minutes December 16, 2005 Information System for Post-translational Modifications 10 PTMs and Cancer •Agenda •Introduction to PTM -PTM Types -Significance -PTMs and Cancer < -Identification and Prediction •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future •References Specific forms of post-translational modifications of histones (H3 and H4) can be used as tumor associated antigens for diagnosing prostate cancer Study of the role of p53 post-translational modifications in carcinogenesis and cancer prevention is useful in the development of new strategies for treating and preventing cancer. Development of new biomarkers and therapeutics Role of glycosylation in mediating the toxicity of hyperglycemia and in the control of the insulin gene expression •Acknowledgements Approximate time left: 13 minutes December 16, 2005 Information System for Post-translational Modifications 11 PTMs can be characterized or predicted •Agenda •Introduction to PTM -PTM Types -Significance Experimental methods Crystallography Mass Spectrometry -PTMs and Cancer -Identification and Prediction < •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future •References PTM Prediction tools Auto-motif server Sulfinator NetPhos server Predphospho server eMOTIF PROSITE •Acknowledgements Approximate time left: 12 minutes December 16, 2005 Information System for Post-translational Modifications 12 PTM Databases •Agenda •Introduction to PTM •Existing Databases < •Why ISPTM? •Feautures of ISPTM General PTM Databases RESID Unimod Delta Mass •Targets for Future •References •Acknowledgements PTM Databases for Specific Proteins Histone sequence database Human Protein Reference Database Plasma Proteome Database Databases for Specific PTMs Phospho.ELM – Phosphorylation GlycoSuiteDB, SweetDB – Glycosylation Approximate time left: 10 minutes December 16, 2005 Information System for Post-translational Modifications 13 Limitations of current PTM databases •Agenda •Introduction to PTM •Existing Databases < •Why ISPTM? •Feautures of ISPTM •Targets for Future •References •Acknowledgements The PTMs are mostly annotated in a static fashion, i.e. an amino acid is denoted as either modified or unmodified. In reality, some amino acids are modified under one condition, and return to their initial state when the condition changes. The status of a specific amino acid site with respect to a modification is highly associated with biological functionality of the protein. But this association is often not annotated in the database. Phosphorylation vs. signal transduction Glycosylation vs. cell-cell interaction Different PTMs on the same protein may be associated with each other. These associations are not annotated in the current databases either. Approximate time left: 9 minutes December 16, 2005 Information System for Post-translational Modifications 14 The Information System •Agenda •Introduction to PTM •Existing Databases •Why ISPTM? < •Feautures of ISPTM •Targets for Future •References •Acknowledgements Annotation of PTMs as well as their associations with Cell status Environmental conditions Biological functions Each other A public database that allows the submission of the PTM information with reference to the factors affecting them A web based interface that provides flexibility in querying the database A tool to visualize all PTMs in one protein under a given set of conditions Approximate time left: 7 minutes December 16, 2005 Information System for Post-translational Modifications 15 ER Model •Agenda •Introduction to PTM •Existing Databases •Why ISPTM? •Feautures of ISPTM < •Targets for Future •References •Acknowledgements Approximate time left: 6 minutes December 16, 2005 Information System for Post-translational Modifications 16 Database •Agenda •Introduction to PTM •Existing Databases •Why ISPTM? •Feautures of ISPTM < •Targets for Future •References •Acknowledgements Approximate time left: 6 minutes December 16, 2005 Information System for Post-translational Modifications 17 The Information System •Agenda •Introduction to PTM •Existing Databases •Why ISPTM? •Feautures of ISPTM < •Targets for Future •References •Acknowledgements Approximate time left: 6 minutes December 16, 2005 Information System for Post-translational Modifications 18 The Information System •Agenda •Introduction to PTM •Existing Databases •Why ISPTM? •Feautures of ISPTM < •Targets for Future •References •Acknowledgements Approximate time left: 6 minutes December 16, 2005 Information System for Post-translational Modifications 19 The Information System •Agenda •Introduction to PTM •Existing Databases •Why ISPTM? •Feautures of ISPTM < •Targets for Future URL: http://discover.uits.indiana.edu:8410 •References •Acknowledgements Approximate time left: 6 minutes December 16, 2005 Information System for Post-translational Modifications 20 Implementations for future •Agenda •Introduction to PTM •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future < •References •Acknowledgements Implement a middle layer between the database and the outside world to moderate the data submitted Allow data submissions through uploading of structured text content Implement the visualization using GD package so as the allow the user to save the output into an image file (eg: .png) Integrate the system with Curation and Alignment Tool for Protein Analysis (CATPA) Transfer the database to a development server and make it officially public Approximate time left: 1 minute December 16, 2005 Information System for Post-translational Modifications 21 References •Agenda •Introduction to PTM •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future •References < •Acknowledgements Approximate time left: 1 minute Caraglia, M., Tagliaferri, P., Budillon, A., and Abbruzzese, A. (1999). Posttranslational modifications of eukaryotic initiation factor-5A (eIF-5A) as a new target for anti-cancer therapy. Adv Exp Med Biol 472, 187-198. Demirev, P.A., Lin, J.S., Pineda, F.J., and Fenselaut, C. (2001). Bioinformatics and mass spectrometry for microorganism identification: proteome-wide posttranslational modifications and database search algorithms for characterization of intact H. pylori. Anal Chem 73, 4566-4573. Dwek, M.V., Ross, H.A., and Leathem, A.J. (2001). Proteome and glycosylation mapping identifies post-translational modifications associated with aggressive breast cancer. Proteomics 1, 756-762. Gong, C.X., Liu, F., Grundke-Iqbal, I., and Iqbal, K. (2005). Post-translational modifications of tau protein in Alzheimer's disease. J Neural Transm 112, 813838. Han, K.K., and Martinage, A. (1992). Post-translational chemical modification(s) of proteins. Int J Biochem 24, 19-28. Jung, E., Veuthey, A.L., Gasteiger, E., and Bairoch, A. (2001). Annotation of glycoproteins in the SWISS-PROT database. Proteomics 1, 262-268. Kim, J.H., Lee, J., Oh, B., Kimm, K., and Koh, I. (2004). Prediction of phosphorylation sites using SVMs. Bioinformatics 20, 3179-3184. Kreegipuu, A., Blom, N., and Brunak, S. (1999). PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Res 27, 237-239. Kwikkers, K.L., Ruijter, J.M., Labruyere, W.T., McMahon, K.K., and Lamers, W.H. (2005). Effect of arginine deficiency on arginine-dependent posttranslational protein modifications in mice. Br J Nutr 93, 183-189. Mann, M., and Jensen, O.N. (2003). Proteomic analysis of post-translational modifications. Nat Biotechnol 21, 255-261. Monigatti, F., Gasteiger, E., Bairoch, A., and Jung, E. (2002). The Sulfinator: predicting tyrosine sulfation sites in protein sequences. Bioinformatics 18, 769-770. Continued… December 16, 2005 Information System for Post-translational Modifications 22 References •Agenda •Introduction to PTM •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future •References < •Acknowledgements Nevalainen, L.T., Louhelainen, J., and Makarow, M. (1989). Post-translational modifications in mitotic yeast cells. Eur J Biochem 184, 165-172. Obenauer, J.C., Cantley, L.C., and Yaffe, M.B. (2003). Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31, 36353641. O'Donovan, C., Apweiler, R., and Bairoch, A. (2001). The human proteomics initiative (HPI). Trends Biotechnol 19, 178-181. Plewczynski, D., Tkacz, A., Wyrwicz, L.S., and Rychlewski, L. (2005). AutoMotif server: prediction of single residue post-translational modifications in proteins. Bioinformatics 21, 2525-2527. Saito, M., Fujii, K., Tanaka, T., and Soshi, S. (2004). Effect of low- and high-intensity pulsed ultrasound on collagen post-translational modifications in MC3T3-E1 osteoblasts. Calcif Tissue Int 75, 384-395. Wang, W., Vignani, R., Scali, M., Sensi, E., and Cresti, M. (2004). Post-translational modifications of alpha-tubulin in Zea mays L are highly tissue specific. Planta 218, 460-465. Approximate time left: 1 minutes December 16, 2005 Information System for Post-translational Modifications 23 Acknowledgements •Agenda •Introduction to PTM Thanks to •Existing Databases •Why ISPTM? • Dr. Haixu Tang (Primary Advisor) Assistant Professor of Informatics •Feautures of ISPTM •Targets for Future •References •Acknowledgements < • Dr. Mehmet Dalkilic (Secondary Advisor) Assistant Professor of Informatics • Dr. Predrag Radivojac Assistant Professor of Informatics • Dr. Roger Innes Professor, Dept. of Biology • . Dr. Tom Ashfield Postdoctoral Associate, Innes Lab • Stephanie Burks Staff, Vice Pres Information Technology • Gayathri Athreya Graduate Student, School of Informatics • All my Professors who helped me improve my knowledge and skills Approximate time left: 1 minutes December 16, 2005 Information System for Post-translational Modifications 24 Acknowledgements •Agenda •Introduction to PTM •Existing Databases •Why ISPTM? •Feautures of ISPTM •Targets for Future Special thanks to my wife Roopa Kiran. •References •Acknowledgements < Approximate time left: 20 minutes December 16, 2005 Information System for Post-translational Modifications 25 Discussion Approximate time left: 0 minute December 16, 2005 Information System for Post-translational Modifications 26