dhfr pymol assignment

Please use the two attachments as your ref and answer the following: (PDB codes are in the manuscripts)

I have posted Journal articles that describe structural properties of various dihydrofolate reductase (DHFR) structural complexes. Please compare the terahydrofolate (FH4) structure, PDB:6CW7, with the apo-DHFR, dihdrofolate (FH2:DHFR), methotrexate (MTX) and ternary complexes. PDB codes are as found in the Data Availability and/or Table 1 in the posted journal articles.

  1. What regions of the protein occupy different conformations upon ligand binding? Please show a figure from pymol that illustrates the significant changes in structure.
  2. Do all the ligands occupy the same space with similar conformations? Please show the various ligands and indicate where they may deviate from one another in stick figures of the ligands only. Please show a structural comparison of the active site ligands and nearby protein regions from pymol to illustrate the effects of ligand binding on structure. Do areas outside the ligand binding pocket change with ligand binding?
  3. What is the significance of the Met20 loop? Explain in 4 or less sentences.
  4. What is the effect of cofactor binding on the FH2 bound structure? Please show a pymol figure.

Please upload your answers in DOC or PDF format.

 

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