Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online


D:  mTOR and Nutrient Signaling  


Last Update:  6/22/16

Learning Goals/Objectives for Chapter 9D:
After this reading, students will be able to

  • Describe the structure of mTOR Complex I and II;
  • Describe how rapamycin inhibits mTORC1;
  • Draw a cartoon of a generic protein kinase showing how its activity and specificity is regulated by activation and catalytic loops along with other protein binding partners;
  • Describe the structural differences between mTORC1 kinase and other kinases.
  • List typical substrates of mTORC1 and mTORC2;
  • Draw cartoons to show how Leu interacts with sestrin 2 and how this interaction activates mTORC1;
  • Describe how mTORC1 is recruited to lysosomal membranes and regulated by leucine through sestrin2, GATOR (GAP) proteins, Rag (small G) proteins, and Ragulator (GEF) proteins;
  • Explain how interactions of mTORC1 with Tsc 2/1 (GAP) proteins and Rheb (small G) proteins regulate mTORC1;
  • Describe how mTORC1 kinase activity is regulated by insulin through Akt and growth factors through MAP kinases;
  • Describe the different effects in metabolism mediated by AMPK and mTORC1;

D2.  mTOR Inhibition by Rapamycin

The structure of the mTORC1 complex is complex itself, in part, since some of its components were studied and named before their roles in the mTORC1 complex were elucidated.  Investigators were obviously interested in the molecular target(s) of rapamycin.  Yeast (a fungus) was an easy organism to study using genetic techniques.  Three genes were found that when mutated inhibited the effect of the inhibitor rapamycin (i.e. so that rapamycin did not inhibit mTOR).  Two of these were the Ser/Thr kinases mTOR1 and mTOR2.  The other was an analog of a protein found in humans (FK Binding Protein 12  - FKBP12).  The family of FK binding proteins act as protein chaperones and have Pro-X peptidyl prolyl isomerase activity (PPI).  FKBP12 specifically binds a drug (FK506 also called Tacrolimus) that is an immunosuppressant (do you see the general link with immune cell division and growth?).  The binary complex of FK506 and FKBP12 bind a third protein, a phosphatase called calcineurin, and block its phosphatase activity and signal transduction required for T cell activation and proliferation.  This activity of FKBP12 strangely does not require its PPI activity.

Now back to mTORC1.  Here are the known components of the core complex:

In addition, other proteins  associate with the core complex

mTORC2 is not sensitive to rapamycin. Instead of RAPTOR, it has a protein called RICTOR (rapamycin insensitive companion of TOR).

A structure (5flc) of the human mTORC1 containing mTOR, Raptor and mLST8 bound to FK506 binding protein (FKBP)-rapamycin complex has been solved with cryomicroscopy.  An image created by Pymol and a 3D Jsmol structure are shown below.,


Jmol:   human mTORC1 (5flc) Jmol14 (Java) |  JSMol  (HTML5)


The complex acts physiologically as a dimer with rotational C2 symmetry. 

  • Raptor has been liken to tape as it interacts with the two mTOR subunits, holding them together into a larger, donut-like structure, stabilizing the dimer.

  • How does rapamycin inhibit mTOR?  You have studied many kinds of inhibitors (competitive, uncompetitive, mixed or noncompetitive inhibition) in which the inhibitor binds to either free E or the ES complex.   The figure above suggests that rampamycin binds at the interface of the mTOR kinase (red) and FKBP.  Presumably the RAP:FKBP complex binds to mTOR. 

  • The figure below shows how rapamycin (shown in sticks) is sandwiched between mTOR (red) and FKBP (light blue).  This offers clues as to how it inhibits mTOR.   The rapamycin:FKBP complex is an allosteric inhibitor with its effect dependent on both substrate and post-translational phosphorylation. 



    Right across from the light blue FKBP protein is the green LST8 protein (see above).  In between these is a cleft which is the active site.  One could imagine that RAP:FKBP binding to mTOR might interfere with substrate binding in mTORC1 but not in mTORC2.    RAPTOR in mTORC1 probably helps recruit substrates and hence is involved in determination of substrate specificity.  RAPTOR interacts with short section called the TOR signaling (TOS) motif in mTORC1 substrates.  The part of RAPTOR that binds TOS in substrates is at the base of the mTORC1 active site, probably narrowing it further as it provides exquisite substrate selectivity.  



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