its about the techniques to determine the structure of proteins

2. Structural proteomics
• Structural proteomics is the application of protein chemistry and
modern mass spectrometric techniques to problems such as the
characterization of protein structures and to determine the 3D
configuration.
• Term
Protein structure

3. Protein structure

5. Techniques for protein structure
determination
Primary structure
• Edman degaradation
• Mass spectroscopy
• MALDI
• ESI
SECONDARY STRUCTURE
• Circular dichroism
Tertiary and Quaternary structure
• NMR
• X-ray crystallography

6. Primary structure determination
Edman degradation
• Edman degradation is the process of purifying protein by sequentially removing
one residue at a time from the amino end of a peptide.
• It was developed by Pher Edmanin 1950
• Process
• PITC react to the
amino acid
• Converted to PTC .
Coupling
(alkaline)
• Thiocarbonyl sulfur
attacks the carbonyl
carbon of aminoacid
• ATZ-aminoacid is
cleaved
Cleavage
(acidic) • ATZ-aminoacid is
converted to PTH-
aminoacid
• Extraction occurs
with ethyl acetate.
Conversion
(acidic)

8. Mass spectroscopy
• Mass spectrometry (MS) is an analytical technique that separates ionized particles such as
atoms, molecules, and clusters by using differences in the ratios of their charges to their
respective masses (mass/charge; m/z), and can be used to determine the molecular weight
of the particles.
• It includes
1. An ion source
2. A mass analyzer
3. A detector
4. A computer
Limitations
• Morphological abnormalities in tissue samples observed by traditional microscopes do not
provide us with any biochemical information.
• On the other hand, conventional biochemical techniques generally lose the positional
information of the tissues.
• Due to such limitations today we are using imaging mass spectroscopy (IMS) with several
mass analyzer and ionization methods variations.

9. MALDI
• The mostly used ionization method is MALDI matrix which is used for ionizing materials.
• Matrix-Assisted Laser Deposition/Ionization (MALDI) is a sample preparation technique
used to prepare an analyte for mass spectrometry. MALDI is a relatively gentle technique,
which usually allows molecules to be analyzed without significant fragmentation.
• Sample preparation
• TOF mass analyzer

10. ESI
• Electrospray ionization is another method to ionize peptides and
was developed by Fenn and coworkers in 1989.
• Mechanism

11. Circular dichroism
• Circular Dichroism, an absorption spectroscopy, uses
circularly polarized light to investigate structural aspects
of optically active chiral media.
• Circular Dichroism (CD) is an absorption spectroscopy
method based on the differential absorption of left and
right circularly polarized light.
• Terms include:
1. Chiral molecule
2. Electromagnetic waves
3. Linear polarization
4. Circular polarization
5. Ellipse polarization
https://www.youtube.com/watch?v=Fu-aYnRkUgg

14. X-ray crystallography
• X-ray Crystallography is a scientific method used to determine the
arrangement of atoms of a crystalline solid in three dimensional space.
• Process
1. Crystallization through drop diffusion method
2. Sample preparation
3. X-ray scattering
4. Electron density maps
5. A three dimensional structure of protein

15. NMR Spectroscopy
• Nuclear magnetic resonance (NMR) spectroscopy is the study of molecules by recording
the interaction of radiofrequency (Rf) electromagnetic radiations with the nuclei of
molecules placed in a strong magnetic field.
• Nuclei of atoms
• Sample preparation
• Principle of NMR
• Chemical shift

16. THANK YOU

17. ANY QUESTIONS