Agenda

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Agenda

• Agenda lt
• 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

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Post-translational Modifications

• Agenda
• Introduction to PTM lt
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements

Post-translational modification is the chemical
modification of a protein after its translation.
Translation is the process of synthesizing the
peptide chain of amino acids specified by the
nucleotide sequence on the mRNA.
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The central Dogma

• Agenda
• Introduction to PTM lt
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements

• Transcription
• Translation

It is not necessary that the final product of
translation should be the final product of
protein synthesis.
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Changes after Translation

• Agenda
• Introduction to PTM lt
• 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

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Changes after Translation

• Agenda
• Introduction to PTM lt
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements

Post-translational Modifications
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Types of Post-translational modifications

• Agenda
• Introduction to PTM
• PTM Types lt
• Significance
• PTMs and Cancer
• Identification and Prediction
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements

• Several types of PTMs characterized. Some of
  them
• Proteolytic cleavage
• Glycosylation
• Methylation
• Hydroxylation
• Phosphorylation
• Sulfation
• Acylation
• Carboxylation
• Prenylation
• Selenation
• Formylation
• Disulfide bond formation

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Phosphorylation

• Agenda
• Introduction to PTM
• PTM Types lt
• Significance
• PTMs and Cancer
• Identification and Prediction
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements

Phosphorylation is the addition of a phosphate
(PO4) group to a protein or a small molecule

• 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

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Glycosylation

• Agenda
• Introduction to PTM
• PTM Types lt
• Significance
• PTMs and Cancer
• Identification and Prediction
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements

Glycosylation is the addition of saccharide to a
protein or a lipid molecule

• N-Linked Glycosylation
• Amide nitrogen of Asparagine
• O-Linked Glycosylation
• - Hydroxy oxygen of Serine and Threonine

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PTMs have significant biological functions

• Agenda
• Introduction to PTM
• PTM Types
• Significance lt
• PTMs and Cancer
• Identification and Prediction
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements

• 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
• Signal transduction
• Protein degradation
• Blood coagulation
• Immune system

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PTMs and Cancer

• Agenda
• Introduction to PTM
• PTM Types
• Significance
• PTMs and Cancer lt
• Identification and Prediction
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements

• 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

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PTMs can be characterized or predicted

• Agenda
• Introduction to PTM
• PTM Types
• Significance
• PTMs and Cancer
• Identification and Prediction lt
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements

• Experimental methods
• Crystallography
• Mass Spectrometry
• PTM Prediction tools
• Auto-motif server
• Sulfinator
• NetPhos server
• Predphospho server
• eMOTIF
• PROSITE

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PTM Databases

• Agenda
• Introduction to PTM
• Existing Databases lt
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements

• General PTM Databases
• RESID
• Unimod
• Delta Mass
• 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

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Limitations of current PTM databases

• Agenda
• Introduction to PTM
• Existing Databases lt
• 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.

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The Information System

• Agenda
• Introduction to PTM
• Existing Databases
• Why ISPTM? lt
• 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

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ER Model

• Agenda
• Introduction to PTM
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM lt
• Targets for Future
• References
• Acknowledgements

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Database

• Agenda
• Introduction to PTM
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM lt
• Targets for Future
• References
• Acknowledgements

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The Information System

• Agenda
• Introduction to PTM
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM lt
• Targets for Future
• References
• Acknowledgements

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The Information System

• Agenda
• Introduction to PTM
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM lt
• Targets for Future
• References
• Acknowledgements

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The Information System

• Agenda
• Introduction to PTM
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM lt
• Targets for Future
• References
• Acknowledgements

• URL http//discover.uits.indiana.edu8410

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Implementations for future

• Agenda
• Introduction to PTM
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future lt
• 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

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References

• Agenda
• Introduction to PTM
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References lt
• Acknowledgements

• Caraglia, M., Tagliaferri, P., Budillon, A., and
  Abbruzzese, A. (1999). Post-translational
  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 post-translational 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, 813-838.
• 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
  post-translational 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

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References

• Agenda
• Introduction to PTM
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References lt
• 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, 3635-3641.
• 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.

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Acknowledgements

• Agenda
• Introduction to PTM
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements lt

• Thanks to
• Dr. Haixu Tang (Primary Advisor)
• Assistant Professor of Informatics
• 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

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Acknowledgements

• Agenda
• Introduction to PTM
• Existing Databases
• Why ISPTM?
• Feautures of ISPTM
• Targets for Future
• References
• Acknowledgements lt

• Special thanks to my wife Roopa Kiran.

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Discussion
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