Abstract/Summary

Most cells or proteins exist in a high force environment, meaning that they must be able to generate, withstand or transmit high levels of forces. The signalling response of talin (a core structural and signalling protein in platelet focal adhesions), for example, is the product of its rod domains unfolding and either ejecting bound ligands or allowing new ligands to bind. Modelling force effects at a molecular level is therefore helpful in understanding when talin signals other platelet processes, such as focal adhesion maturation and platelet contraction. This, in turn, may impact the understanding of diseases related to platelet binding and aggregation, as well as thrombus formation, contraction, and lysis. Therefore, the aim of this thesis was to improve the calculated magnitude and range of force values for the unfolding thresholds of talin’s rod domain. This was done by creating a novel model of talin’s rod domain alpha-helices. This model was subsequently used in a newly developed force-based simulation framework to calculate intermolecular electrostatic interactions. The unique features of this method were: the new coarse-grain-like alpha-helix models derived from protein structural data, the use of a coordinate frame system to manage and manipulate the objects within the simulation, and the direct calculation of interaction forces. This approach was chosen as other computational methods such as molecular dynamics simulations produce erroneously large unfolding force ranges that are up to ∼ 7500% larger than the physiologically relevant range of forces for the unfolding of talin’s rod domain. Through the method developed for this thesis, a range of unfolding forces were calculated for talin’s rod subdomains of ∼1 pN to ∼49 pN. This is an improvement compared to previous computational methods. Thus, the improvements in results are significant enough to warrant the effort in developing these new simulation approaches targeted at force interactions at the molecular level.