Affects On The Mechanical Stability Of GB1 By Ligand Binding

Protein mechanical stability plays important roles in many biological processes, such as cell adhesion, muscle contraction and so on. How to effectively regulate protein mechanical properties is an unresolved problem in the area of structural biology. At present, the strategies to regulate protein mechanical stability mainly focus on direct modulation of the force-bearing region of proteins. Interestingly, using atomic force microscopy, a research group found that the mechanical stability of GB1 can be significantly enhanced by the binding of Fc fragments of human Ig G antibody(h Fc), where the binding site is distant from the force-bearing region of protein. In this case, h Fc does not directly interact with the force-bearing region of GB1, and the mechanical stability of the protein is regulated through a long-range allosteric effect. While, the mechanism for this long-range allosteric control of protein mechanics is still elusive.In this thesis, the mechanical stability of GB1 with and without the binding of h Fc was respectively investigated by using steered molecular dynamics simulation method, and based on the simulation trajectories, a mechanism for the regulation of mechanical stability of GB1 was proposed.Firstly, the force-induced unfolding process was investigated and the value of unfolding force was calculated for GB1 and GB1-h Fc complex, respectively, by using the constant-velocity SMD(cv-SMD) and constant-force SMD(cf-SMD) simulations. Then, the impacts of h Fc binding on the mechanical properties of GB1 were discussed.Secondly, based on the SMD simulation trajectories, the disruption process of the hydrogen bonds in β1-β4, β1-β2 and β3-β4 was monitored for GB1 and GB1-h Fc complex, respectively. Then, the force-resistant region in the structure of GB1 was identified. It is found that the binding of h Fc does not change the location of the force-resistant region of GB1.Finally, the deformations of the force-bearing region and the ligand-binding sites induced by the external forces were analyzed. Based on these analyses, a mechanism for the modulation of GB1 mechanics by the binding of h Fc was proposed. It is found that the external force induces the deformation of both force-bearing region and ligand binding sites. There is a long-range coupling between these two regions. The h Fc binding restricts the distortion of the binding sites and then reduces the deformation of the force-bearing region through a long-range allostery, which thus improves the mechanical stability of the protein. Our studies not only provide atomic-level insights into the mechanical unfolding process of GB1, but also explain the impacts of ligand binding on the mechanical properties of the protein.