Trapping Conformational States Along Ligand-Binding Dynamics of Peptide Deformylase: The Impact of Induced Fit on Enzyme Catalysis
PLoS Biol, 9 (5):
1-17 (May 2011)DOI: 10.1371/journal.pbio.1001066
Abstract
<title>Author Summary</title>
<p>The notion of induced fit when a protein binds its ligand?like a glove adapting to the shape of a hand?is a central concept of structural biochemistry introduced over 50 years ago. A detailed molecular demonstration of this phenomenon has eluded biochemists, however, largely due to the difficulty of capturing the steps of this very transient process: the ?conformational change.? In this study, we were able to see this process by using X-ray diffraction to determine more than 10 distinct structures adopted by a single enzyme when it binds a ligand. To do this, we took advantage of the ?slow, tight-binding? of a potent inhibitor to its specific target enzyme to trap intermediates in the binding process, which allowed us to monitor the action of an enzyme in real-time at atomic resolution. We showed the kinetics of the conformational change from an initial open state, including the encounter complex, to the final closed state of the enzyme. From these data and other biochemical and biophysical analyses, we make a coherent causal reconstruction of the sequence of events leading to inhibition of the enzyme's activity. We also generated a movie that reconstructs the sequence of events during the encounter. Our data provide new insights into how enzymes achieve a catalytically competent conformation in which the reactive groups are brought into close proximity, resulting in catalysis.</p>