Serpins: folding, misfolding and conformational change.
The serpins are an unusual class of serine and cysteine protease inhibitors that inhibit their target proteases through a unique mechanism. Serpins initially fold to a metastable structure and subsequently undergo a massive conformational change to a stable structure when they inhibit their target proteases. When the protease (orange) cleaves this reactive center loop (RCL, shown in green), the reaction proceeds through the formation of an intermediate in which the protease and the serpin are covalently linked. Before the breakdown of the intermediate brings the reaction to completion the RCL inserts into the central β-sheet (β-sheet A) and becomes a sixth strand, in the process translocating the target protease to the opposite end of the serpin molecule. The protease active site is distorted in this process, leaving it irreversibly trapped in a protease-serpin complex.
This "molecular mousetrap" inhibitory mechanism raises a number of questions. How do serpins get trapped in a metastable conformation during folding? How is the energy required for translocation and inhibition of the target protease stored in the metastable structure and how is the energy utilized during inhibition? The strained, metastable nature of serpin's native structure leaves them highly susceptible to disruption by mutations. A class of genetic disorders known as the serpinopathies have as their basis the propensity of mutant serpins to misfold and polymerize, resulting in decreased levels of secreted serpins and, ultimately, cell death when they accumulate in the ER. We are actively studying two specific serpinopathies: 1) alpha-1antitrypsin deficiency, which results from the misfolding of the serpin alpha-1 antitrypsin and leads to both liver disease and emphysema, and 2) Familial encephalopathy with neuroserpin inclusion bodies (FENIB), which results from the misfolding of neuroserpin and leads to early onset dementia.
We are using chemical labeling with mass spectrometry, fluorescence spectroscopy, and electron paramagnetic resonance spectroscopy to probe the folding and misfolding pathways of serpins as well as the structure of pathogenic misfolded serpin polymers. More information on the serpins can be found here.
Simulating protein folding and conformational change using the Dominant Reaction Pathways (DRP) formalism
In collaboration with Professor Pietro Faccioli's group at the University of Trento, we are applying the recently developed Dominant Reaction Pathways (DRP) method to simulate protein folding and conformational change. The extreme computational efficiency of the DRP method allows us to avoid coarse graining and simulate systems in all atom detail using realistic physics based force fields. As a result, we are currently performing all atom simulations of conformational changes, folding and misfolding in systems of unprecedented size and complexity.
Allostery and Inhibition in Viral Polymerases
We are using hydrogen/deuterium exchange in conjunction with mass spectrometry to learn how dynamics mediate the function and inhibition of viral polymerases including HIV-1 reverse transcriptase (left) and the NS5B polymerase from human hepatitis C virus (right). HDX has revealed that conformational dynamics play a role in long rang allosteric communication between remote sites in these proteins. In particular, we have found that small molecule inhibitors binding to regions distant from the active site induce large scale suppression of conformational dynamics. We believe that this suppression of molecular mobility is the mechanism through which these small molecules inhibit polymerase activity. A better understanding of these two systems will enhance our ability to design effective inhibitors and overcome evolving drug resistance. It will also increase our general understanding of the phenomenon of allosteric enzyme inhibition.