Protein dynamics help explain protein behavior


The traditional approach for structural biology is to focus on static images. While these images capture the essence of their subject, they’re lacking in relevant insight into the behavior of the subject in different environments. Our approach builds upon the static images by adding an additional dimension of protein dynamics, thereby giving insight into the process of an event rather than looking only at the outcome of an event. We can monitor dynamics by measuring how quickly proteins exchange protons with their environment. Stable, well-folded proteins take up fewer protons. Dynamic or unfolded proteins take up more protons To illustrate a simple use for this technique, We’ll look at two model proteins which form a complex. The binding site is more flexible than the rest of the protein and these two segments must come together to create the binding site for protein 2, thus allowing the protein complex to form. Now let’s expand our example to include a small-molecule X, which enhances the binding affinity between these proteins. The binding site for X was mapped and it’s surprisingly distant from the binding site for protein 2. How does this work? When we look at the dynamics of this protein in the presence of X, we see that upon binding, X stabilizes the protein 2 binding site, thus shifting equilibrium toward complex formation. It’s now clear why X enhances the binding affinity between these proteins. This is just one simple illustration of how studying protein dynamics can give us insight into protein behavior. Thanks for watching!

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