Investigating the disorder-order transition of calmodulin binding domain upon binding calmodulin using molecular dynamics simulation.
We have studied the conformational transition of the calmodulin binding domains (CBD) in several calmodulin-binding kinases, in which CBD changes from the disordered state to the ordered state when binding with calmodulin (CaM). Targeted molecular dynamics simulation was used to investigate the binding process of CaM and CBD of CaM-dependent kinase I (CaMKI-CBD). The results show that CaMKI-CBD began to form an alpha-helix and the interaction free energy between CaM and CaMKI-CBD increased once CaM fully encompassed CaMKI-CBD. Two series of CaM/CBD complex systems, including the complexes of CaM with the initially disordered and the final ordered CBD, were constructed to study the interaction using molecular dynamics simulations. Our analyses suggest that the VDW interaction plays a dominant role in CaM/CBD binding and is a key factor in the disorder-order transition of CBD. Additionally, the entropy effect is not in favor of the formation of the CaM/CBD complex, which is consistent with the experimental evidence. Based on the results, it appears that the CBD conformational change from a non-compact extended structure to compact alpha-helix is critical in gaining a favorable VDW interaction and interaction free energy.
Zhang
Yong
Y
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China.
Tan
Hongwei
H
Chen
Guangju
G
Jia
Zongchao
Z
D001665:Binding Sites; D017871:Calcium-Calmodulin-Dependent Protein Kinases / Q000737:chemistry* / Q000378:metabolism*; D002147:Calmodulin / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017433:Protein Structure, Secondary
D002147:Calmodulin; D017871:Calcium-Calmodulin-Dependent Protein Kinases