2.0 Application of Biophysical Chemistry Related Technique in Proteomic Research 2.

1 X-ray crystallography X-Ray Crystallography is an analytical method in which x-ray diffraction patterns are used to determine the three-dimensional arrangement of atoms in a crystal. The crystal used for xray crystallography are less than 1 millimetre in diameter. Crystals can diffract X-rays and Xrays have a proper wavelength (in the ngstrm range, ~10-8cm) to be scattered by the electron cloud of an atom that have a comparable size. The electron density is constructed based on the diffraction pattern obtain from X-ray scattering off the periodic assembly of molecules or atoms in the crystals. A model will then build into the experimental electron density. This will result a quite accurate molecular structure. Beside structure, X-ray crystallography provide the information about the position of atoms in the crystal and also their chemical bonds. X-ray crystallography start by protein crystallization. There are application of biophysical chemistry technique here. Protein crystallization have four important steps; a) The determination of protein purity. If it is not extremely pure, further purification is required to achieve crystallization. b) The protein is dissolved in a suitable solvent from which it must be precipitated in crystalline form. The solvent like a water-buffer solution or organic solvent such as 2methyl-2,4-pentanediol (MPD) is add. Precipitant solution is also add at a low concentration so that no precipitation occur. As protein has a membrane that insoluble in water-buffer or organic solvent, detergent is add. c) The solution undergo supersaturation where small aggregates are form. This small aggregates is the nuclei for crystal growth. The spontaneous formation of nuclei requires a supply of surface tension energy. Crystal growth begin when energy barrier is overcome. At higher level of supersaturation, the energy barrier become more easier to overcome. d) When nuclei is form, the actual crystal growth begin. Crystal growth must occur slowly in order to achieve high degree of order on their structure.

In protein crystals, the spherical and egg-shaped molecules are loosely with large solvent-filled holes and channels. After the protein crystal was obtained, the crystal will

be placed in an intense beam of X-rays, usually a single wavelength to produce a regular pattern of reflections. The data was collected and combine computationally. In proteomics research, X-ray crystallography is important to determine the protein structure with post-translational modifications that usually found in living organisms. 2.2 Nuclear Magnetic Resonance (NMR)

REFERENCES http://www.ruppweb.org/Xray/101index.html http://chemistry.about.com/od/chemistryglossary/a/xraycrystaldef.htm Jung, J., W., Lee, W., (2004) Journal of Biochemistry and Molecular Biology; Structure-based Functional Discovery of Proteins: Structural Proteomics, Yonsei University, Korea Messerschmidt, A., (2007) X-ray crystallography of biomacromolecules: A Practical Guide, WileyWCH GmbH& Co., German