OC2 - structural methods for locating the amino acid residues in binding sites

Question 1

requirements for X-ray crystallography

Answer 1

a protein in a crystal form
a source of X-rays
proteins primary structure
a detector
an electron density map

Question 2

process of X-ray crystallography

Answer 2

involved bombarding a crystal of the protein with X-rays and then analysing the resultant diffraction pattern caused by the atoms in the protein scattering the X-rays
the diffraction pattern produces an electron density map which with knowledge of the proteins primary structure is used to determine the 3D structure

Question 3

structural analogues

Answer 3

play a crucial role in the understanding of the interactions within the binding sites.
are structurally similar to the ligand so can bind to the binding site, but they do not react with the protein in the normal way
structural analogues are usually non-hydrolysable, so the protein is unable to change the ligand as it normally would
e.g. methotrexate

Question 4

methotrexate

Answer 4

a structural analogue of dihydrofolate which is the substrate for the enzyme dihydrofolate reductase
enzyme-substrate complex allows for biosynthesis of purines and pyrimidines, and the cell cycle advances
enzyme-structural analogue causes inhibition of purine and pyrimidine biosynthesis, and the cell cycle arrests.