Protein Design Assisted Residue Conservation and Functional Stability Analysis for Bacterial Chemotaxis

Chemotaxis in Bacillus subtilis (B. subtilis) is dependent on the rate of phosphorylation and dephosphorylation of CheY protein. B. subtilis contains CheC and CheD playing a significant role in the adaptation mechanism of chemotaxis, mainly involving the excitatory mechanism of phosphorylation. To understand the adaptation mechanism followed in chemotaxis, we need to identify the critical residues for CheC-CheD interaction. This necessitates modeling the structure of the CheC-CheD complex in B. subtilis that is unavailable. Next, we aimed to identify critical residues in the interface of CheC-CheD which may assist in understanding the mechanism of bacterial chemotaxis. Using computational protein design and stability analysis, we are successful in identifying such critical residues in the interface of CheC-CheD. Our analysis demonstrates that CheC is more conserved than CheD for the interaction. Mutation in the interface residues of CheC may lead to loss of stability as well as a change in functionality for CheC-CheD complex thereby affecting chemotaxis. Our fourth design model of CheD also suggests the possible mutations in CheD when in complex with wild-type CheC leading to higher stability and stronger interaction energy. Interestingly, our computational findings includes Asp149 of CheC for which experimental evidence informs mutation at Asp149 leads to poor chemotaxis. Our result would be helpful for the biologists in performing further experimental studies.