Abstract:
Mammalian target of rapamycin (mTOR) is a large (-250 kDa) naturally occurring
biological molecule that plays a critical role in controlling cell growth. Using adenosine
triphosphate (ATP) as a substrate, mTOR tags target proteins with phosphate groups
(phosphorylation) to turn on their activity. Deregulation of mTOR has been linked to
diseases such as cancer and diabetes, therefore in recent times a lot of attention has been
paid to developing mTOR inhibitors having high efficacy and specificity. While ATPcompetitive
inhibitors have shown promising results in experimental studies, a high
resolution picture of ligand binding to mTOR that can guide design of better drugs has been
missing. Recently, a low resolution (3.5 A) crystal structure of the mTOR protein complex
was captured 1, which might provide a starting point to study ligand binding in mTOR.
However, major challenges remain in providing a structural basis for the binding and action
of various ligands to mTOR. These include the lack of suitable techniques for quantitatively
studying structural changes in such a large protein complex (- 1500 amino acids), and the
lack of information on protein conformation changes and flexibility in the presence and
absence of ligands. Further, the recently solved low resolution crystal structure has many
unresolved (missing atoms) protein segments. In this study, we complete the missing
structural information in the low resolution crystal structure and set up a high resolution
fully solvated atomistic model of the mTOR protein. Further, as a step towards
incorporating thermally induced conformational changes, we have created a molecular
dynamics model for the solvated mTOR complex in the absence and presence of its natural
ATP substrate. Finally, we report a novel analysis technique which we have developed to
quantify the conformational and dynamic changes taking place in mTOR during ATP
binding. We have successfully validated this technique by testing on amyloid beta for which
deformation path is well-known.
