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Structural biology - Coggle Diagram
Structural biology
Crystallization of proteins (P8)
Microseeding
Protein solution and crystal seeds are added together which under proper conditions would cause the crystal seeds to grow
Vapour diffusion
Hanging drop
A drop with protein with water over reservoir with precipitant,where the protein would be crystalize when the water is evaporated out of the drop
Sitting drop
Similar concept to hanging drop,but instead of hanging above the precipant,the protein solution is sitting on top of the precipant
Dialysis
diffusion and equilibration of precipitant molecules through a semi-permeable membrane, which causes the protein to slowly crystalize
Crystals of proteins have their molecules organizesd into periodic arrangment
Zones in crystallization
Metastable zone
Growth of the crystals
Unsaturated region
Labile zone
Crystal nucleation occurs producing many small crystals
Precipitaion zone
No crystal growth or formation, only precipitation is present
Validation of protein structure (P10)
Dihedral angles
Psi angle(ψ)
Angle between C(alpha) and N in amino group
Phi Angle(φ)
Angle between C(alpha) and C in carboxyl group
Ramachandran plot
Allowed regions
amino acids are of low steric hindrance and maintains low energy
Upper left qudrants (beta sheets)
Lower left qudrant (right handed alpha helixes)
upper right qudrant (left handed alpha helixes)
Must normally exclude proline and glycin as they are normally found in disallowed regions due to their property
Disallowed region
Glycine commonly found in this region due to small size of amino acid
95 % of residue must be in the allowed regions in order for protein structure to be acceptable
Identifying the crystal structure (P9)
XRD (X-ray diffraction)
shines X-ray through crystalize protein
crystal structure cause the diffraction of the X ray which then hits a photographic film
The angles and intensities are then measured to determine the proteins 3D structure
Electron density map can then be plotted
The position of atoms,chemical bonds can be identified via the electron density
NMR (Nuclear magnetic resonance)
Places liquid samples of protein in a strong magnetic field
Nuclei field align against or with the magnetic field
Radiofrequency is then introduced to the samples to get them 'excited'
the resonance associated with the excitation is detected with sensitive receivers giving the details of the structure