Abstract
The zinc sensing transcriptional repressor Staphylococcus aureus CzrA represents an excellent model system to understand how metal sensor proteins maintain cellular metal homeostasis. Zn(II) binding induces a quaternary structural switch from a "closed" conformation to a more "open" conformation, reducing the DNA binding affinity by 4 orders of magnitude. In this study, we use classical molecular dynamics and quantum mechanical/molecular mechanical molecular dynamics simulations to investigate the molecular basis for the large conformational motions and allosteric coupling free energy (~6 kcal/mol) associated with Zn(II) binding. Our simulations successfully capture the closed to open allosteric switching in DNA bound CzrA on Zn(II) binding. They reveal that zinc binding quenches global conformational sampling by CzrA, whereas DNA binding enhances the mobility of residues in the allosteric metal binding sites. These findings are in close agreement with experiments. We also identify networks of residues involved in correlated and anticorrelated motions that connect the metal binding and DNA binding sites. Our analysis of the essential dynamics shows metal ion binding to be the primary driving force for the quaternary structural change in CzrA. We also show that Zn(II) binding limits the conformational space sampled by CzrA and causes the electrostatic surface potential at the DNA binding interface to become less favorable toward DNA binding. Finally, our simulations provide strong support for a proposed hydrogen-bonding pathway that physically connects the metal binding residue, His97, to the DNA binding interface through the αR helix that is present only in the Zn(II)-bound state. Overall, our simulations provide molecular-level insights into the mechanism of allosteric regulation by CzrA and demonstrate the importance of protein motion in its biological activity.
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.