Disrupting enzyme fluidity

Abstract

A combination of X-ray crystallography, NMR, and mass spectrometry has revealed how diverse small-molecule inhibitors bind Bruton's tyrosine kinase and alter the conformation of this enzyme.

Keywords: allostery; bruton tyrosine kinase; drug resistance; hydrogen/deuterium exchange mass spectrometry; kinase inhibitor; molecular biophysics; none; nuclear magnetic resonance; structural biology.

Figure 1.. Active and inactive forms of the enzyme BTK.

(A) Top: In solution BTK populates an ensemble of inactive (left), intermediate (middle) and active (right) conformations. These schematics show the regulatory domain (red), the catalytic domain (blue or green) and activation loop (red or yellow). Activation involves the regulatory domain moving away from the catalytic domain, and the activation loop moving away from the Glu-Lys switch (not shown) in the catalytic domain. Bottom: Structure of the catalytic domain in the inactive (blue, left) and active (green, right) conformations showing the Glu-Lys switch turned away in the inactive state and positionally close together in the active states (Marcotte et al., 2010). These structures of inactive (PDB ID: 3GEN) and active (PDB ID: 3K54) BTK were rendered using the PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC. (B) The effect of a small-molecule inhibitor on an enzyme can be visualized in terms of the way it changes the free energy of an ensemble of interchangeable conformational states of the enzyme. In the absence of the small-molecule inhibitors, the free energy (vertical axis) is different for each of the individual conformations (horizontal axis); the lower the free energy, the more likely the enzyme is likely to exist in that conformation. In this example, small-molecule inhibitor 1 (blue) lowers the free energy to the right of the graph, favoring these specific conformations, whereas small-molecule inhibitor 2 (green) lowers the free energy to the left of the graph, favoring those specific conformations. Mutations in the enzyme can also change the free energy to favor certain conformations. Knowing how different small molecules influence the free energy of the enzyme could help develop new small-molecule inhibitors.