Hello,
I have taken three different stretches of DNA to see their binding
with my protein. When experimentally done, it shows that stretch 1 binds to
the protein whereas stretch 2 binds with higher affinity while 3 does not
bind at all as seen by their Kd values. However, when the binding energy
for the same 3 DNA stretches was calculated for the protein using MMPBSA it
showed that stretch 2 which exhibited maximum affinity in wet lab
experiment showed significantly lesser value than stretch 1 in MMPBSA.
Also, stretch 3 which did not show any binding in wet lab experiment,
showed significant binding in MMPBSA. So, how reliable are the binding
energy values calculated by MMPBSA? Also, why is there such a negative
trend between the binding energy calculated from wet lab and MMPBSA?
Sincerely,
*Manish*
*Ph.D. Scholar*
Multidisciplinary Centre For Advanced Research and Studies
Jamia Millia Islamia
Delhi-110025
Ph.no: 9518014737
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Received on Tue Apr 06 2021 - 08:00:03 PDT
