Question

BINF4000 chapter 7, question 6

You have a protein sequence and you want to know iis structure in a short time. you perform BLAST and PSI-BLAST searches of the PDB and you find a sequence with 15% amino acid identity to your protein. The e-value is .5. Which of the following options would you choose to achieve your goal.

A. Use X-ray crystallography

B. Use NMR spectroscopy

C. Submit your sequence to a protein structure prediction server that performs homology modeling

D. Submit your sequence to a protein structure prediction server that performs molecular mechanics modeling.

Answer 1

both NMR and X-Ray crystallography takes less time as long as the machine readings are concern but both of them require purified pure protein for analysis. This step takes a lot of time at least if not known protein.

Also, mechanistic modelling servers the purpose if your protein of interest has catalytic activity and then on the basis of substrate binding it

Easy and fast way to know the structure is C. Submit your sequence to a protein structure prediction server that performs homology modeling, this uses the propensity of a particular amino acid stretch to attain a particular motif and structural domain. This way at least you would know the outline or most probable structure in shortest time.