Mechanisms of protein inhibitor recognition elucidated by computer simulations and Markov state modelling
Ilona Christy Unarta · 2020
Molecular dynamics (MD) simulation is a powerful tool that can provide atomistic resolution and ensemble of structures for detailed analysis of the thermodynamics of the protein-inhibitor binding and its binding mechanism. Stapled peptide has been shown to be a novel class of potent protein inhibitors. Using MD simulations and free energy calculation, we have elucidated how the molecular features, such as secondary structures and non-covalent interactions upon binding, affect the entropic and enthalpic contributions in the binding affinity of stapled peptides on protein targets. In particular, a balance between the opposing entropy and enthalpy terms is critical to optimizing their binding affinity to their targets. For large and complex proteins with multiple binding sites, such as RNA polymerase (RNAP), studying the regions or sites that are important to the functionalities of the protein is crucial to elucidate proteins’ functional mechanisms and can facilitate the discovery of more binding sites. RNAP is the enzyme that performs catalysis in transcription, the first step of gene expression. In the second part, we studied the clamp domain motion of RNAP, which is essential in the initiation of transcription. Using MD simulations and Markov State Models, we determined that switch 2 region is the hinge that regulates the clamp domain. Based on our analysis, the inhibitor that targets switch 2 region may go through a sequential conformational selection and induced fit binding mechanism. Specifically, switch 2 region first partially unfolds to provide partial binding pocket to the inhibitor. This is followed by the formation of the full binding pocket upon binding of inhibitor. Lastly, based on our observation, β-lobe may also play an important role in initiation, suggesting its potential as a target for inhibitors.