onetwo wrote:
Hello All,
I want to know one thing that if MD could be used in my case, i have a
protein for which crystal structure is known with a conenzyme bound to
it. It is given in literature that related proteins of this family shows
large conformational change near the substrate binding region when the
substrate binds to the protein.
In absence of the crystal structure, if doing simulation with the
protein complexed with the coenzyme and the docked substrate will be
useful? , i.e, if this complex with the help of the simulation could be
capable of displaying such conformational change ? or what could be the
probable limitaions ?
Possibly. The limitation is time. Conformational changes are generally slow,
so your simulations would likely have to be fairly long.
-Justin
Regards and thanks for your time.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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