Proteomics in the Context of Thailand

1
Proteomics in the Context of Thailand

• Professor M.R. Jisnuson Svasti
• Center for Excellence in
• Protein Structure and Function
• and Dept of Biochemistry,
• Faculty of Science, Mahidol University
• Laboratory of Biochemistry,
• Chulabhorn Research Institute, Bangkok
• e-mail scjsv_at_mahidol.ac.th

2
Roles of Proteins

• Proteins are the instruments through which the
  genetic potential of an organism are expressed
• Proteins are involved in almost all processes of
  body and fulfil many functions
• Functions of Proteins
• enzyme catalysis, transport, mechanical
  support, organelle constituents, coordinated
  motion, storage reserves, metabolic control,
  sensory perception, protection mechanisms,
  toxins, and osmotic pressure

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Importance of Studying Proteins

• Human Genome Data - complete, but does not show
  how proteins function - or how biological
  processes occur
• Proteins sometimes chemically modified after
  synthesis - Proteolytic cleavage, hydroxylation,
  oxidation, carboxylation, methylation,
  acetylation, phosphorylation, glycosylation,
  transamidation, crosslinkage
• Proteins also fold into specific
  three-dimensional structure which determines
  function

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Some covalent post-translational modifications
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Approaches for Study of Proteins

• Purification, characterisation of properties
  primary structure
• Study of molecular mechanism of action -
  correlation of structure activity drug design
  - need 3-D structure - X-ray crystallography
  (n.m.r. for small mols)
• Changes in expression and/or properties of
  proteins - proteomics approach - study all
  proteins at all states at all times

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2-DE Comparison of Proteins from two different
conditions
From Pandey Mann, 2000
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Sample preparation First dimension IEF
Second dimension SDS-PAGE Protein detection
Image analysis Identification - Edman
Degradation - MALDI-TOF -
Nanospray/MS/MS Bioinformatics - Protein
Informatics
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Defining proteomics

• 1. Proteomics-the classical definition
• Two-dimensional gels of cell lysates and
  annotation
• Two-dimensional gels to visualize differential
  protein expression

• 2. Proteomics-in the post-genomic era
• Protein identification
• Post-translational modifications
• Protein-protein interaction

Pandey and Mann. Nature, 405, 2000
(www.nature.com)

• 2-D HPLC
• Affinity purification

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Protein Enzyme Research in Biochemistry Section
of 27th STT Conference

• Enzymes (34)
• Purification and catalytic properties of enzymes
• Screening enzyme activities in microorganisms
• Applications-orientated studies
• Less on basic studies of mechanism and tertiary
  structure, and site directed mutagenesis
• Protein/Enzyme and DNA/RNA (24)
• cloning, sequencing and expression.
• Proteins (6)
• some characterisation of mutations
• 1-2 proteomic studies

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Equipment Available for Research on Protein
Structure in Thailand

• E-mail survey of some 30 departments at different
  universities
• Amino Acid Analysis
• Protein Sequencer
• 2-D Electrophoresis
• MALDI/TOF ESI/MS/MS or MS/MS
• Circular dichroism, protein NMR
• Macromolecular X-ray crystallography
• Computer modelling of protein structure
• Currently available/ in routine operation or not
• Planned to obtain in 2 years

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Amino acid analysis Protein sequencer

• Amino Acid Analysis
• CRI HPLC method, in routine operation
• FS-MU amino acid analyser not operating

• Protein Sequencer
• CRI in routine operation obsolete
• FS-MU - not operating
• IMBG-MU operating?
• BIOTEC/NSTDA operating?
• Rice Research unit, Pathumthani - new

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Proteomic Equipment

• 2-D Electrophoresis
• CRI routine
• BIOTEC/NSTDA routine
• FS-MU routine
• IMBG- MU planned
• Others planned

• MALDI/TOF, ESI/MS/MS,
• MS/MS
• FS- Chula MALDI/TOF (Bruker)
• FS-ChiangmaiQTOF II-new
• Rice Research unit, MALDI/TOFABI-new
• IMBG-MU MS/MS ?
• BIOTEC MALDI/TOF -PSD Bruker - new
• Thaksin U- Ion trap MS -new
• CRI planned?

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3-D Structure and Conformation

• CD/ Protein NMR
• IMBG-MU Circular Dichroism
• Macromolecular X-Ray facilities
• FS-MU planned
• BIOTEC/NSTDA - planned

• Computer Modelling of Protein 3-D Structure
• FS-MU
• IMBG-MU
• BIOTEC/NSTDA
• FS-Kasetsart
• Others

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Conclusions

• New equipment available or soon to be available
  for protein research
• But much existing equipment not in routine
  operation
• Not broken down because of intensive use
• Not operational because not used for a long time,
  so condition deteriorates
• Lack of qualified manpower to operate properly

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Institutions Equipped and Active for Protein
Research

• Faculty of Science, Mahidol University
• Institute of Molecular Biology and Genetics,
  Mahidol University
• BIOTEC/ NSTDA
• Chulabhorn Research Institute

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Proteomics Research in Thailand

• Chulabhorn Research Institute
• Protein changes in cancer thyroid,
  cholangiocarcinoma
• Proteomics of cancer cells anti-cancer agents
• TARUN program, NSTDA/BIOTEC
• Proteomics of malaria
• Faculty of Science, Chiangmai University with
  Academica Sinica, Taipei
• Proteomics of snake venom
• KMUTT with Academica Sinica, Taipei
• Proteomics of rice hull

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Other Areas for Proteomic Research in Thailand

• Proteomics of Parasite Vectors
• Mosquito
• Faculty of Science, Mahidol University
• Shrimp Proteomics
• Disease resistant and disease tolerance
• Faculty of Science, Mahidol University
• Rice Proteomics
• Insect resistance
• Salt tolerance or drought tolerance
• Rice Research Institute ? Collaboration ?

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Networking and Resource Sharing

• Since protein research requires expensive
  hardware, we should consider to
• form links and networks to share expertise
• set up core laboratories for routine services
• Make sure that all equipment functions
• Quality personnel, supervised by leader actively
  engaged in research
• encourage collaboration to provide access to
  equipment and maximise utilisation
• Most equipment does not breakdown through
  overuse, but degenerates through lack of use
• Equipment becomes outdated quickly
• Both collaboration or charging are possible

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International Linkages

• Assistance for analyses needed for some
  specialist equipment not available here
• Sending samples for analysis
• Thai staff travel abroad with sample
• Charge or collaboration ?
• Student Research Abroad (e.g. RGJ)
• Should be collaboration between Thai and overseas
  in formulation of project
• Students should do research both locally and
  overseas
• Should strenghten local graduate program