Prediction of the binding mode between GSK3β and a peptide derived from GSKIP using molecular dynamics simulation

Abstract GSK3β plays an important role in many physiological functions; dysregulated GSK3β is involved in human diseases such as diabetes, cancer, and Alzheimer's disease. This study uses MD simulations to determine the interaction between GSK3β and a peptide derived from GSKIP, a novel GSK3β interacting protein. Results show that GSKIPtide is inlaid in a binding pocket consisting of an α‐helix and an extended loop near the carboxy‐terminal end. This binding pocket is hydrophobic, and is responsible for the protein–protein interaction of two other GSK3β interacting proteins: FRAT and Axin. The GSKIPtide binding mode is closer to that of AxinGID (in the Axin‐GSK3‐interacting domain). The single‐point mutations of V267G and Y288F in GSK3β differentiate the binding modes between GSK3 and GSKIPtide, AxinGID, and FRATide. The V2677G mutation of GSK3β reduces the GSKIPtide binding affinity by 70% and abolishes the binding affinity with AxinGID, but has no effect on FRATide. However, GSK3β Y288F completely abolishes the FRATide binding without affecting GSKIPtide or AxinGID binding. An analysis of the GSK3β–GSKIPtide complex structure and the X‐ray crystal structures of GSK3β‐FRATide and GSK3β‐AxinGID complexes suggests that the hydroxyl group of Y288 is crucial to maintaining a hydrogen bond network in GSK3β‐FRATide. The hydrophobic side chain of V267 maintains the integrity of helix–helix ridge‐groove hydrophobic interaction for GSK3β‐GSKIPtide and GSK3β‐AxinGID. This study simulates these two mutant systems to provide atomic‐level evidence of the aforementioned experimental results and validate the wild‐type complex structure prediction. © 2011 Wiley Periodicals, Inc. Biopolymers 95: 461–471, 2011.