Molecular dynamics simulations of the mechanical unfolding of proteins

Abstract

A number of proteins perform load-bearing functions in living organisms and often have unique mechanical properties. In recent years, there has been considerable effort to understand the relationships between the molecular structure of such proteins and their mechanical response. Several of them have been studied in great detail through single molecule mechanical pulling experiments. Interpretation of these experiments requires the use of atomistic simulations. However typical simulation time scales are many orders of magnitude shorter than relevant experimental and/or physiological time scales. In this dissertation, we have developed a simulation methodology that provides a direct link between experiments and simulations and is capable of predicting the outcome of single molecule pulling experiments. By using this methodology, we have been able to understand the relationships between the molecular structure and the mechanical properties of a number of proteins. I report on our studies of the mechanical unfolding of the I27 domain of the muscle protein titin, ubiquitin, and protein G and compare them with the existing experimental data. The distribution of the unfolding force as well as its dependence on the pulling rate predicted by our simulations is found to be in good agreement with AFM experiments. We demonstrate that the mechanical unfolding pathway can be altered by changing the pulling geometry and that the presence of a hydrogen bonded clamp between terminal parallel strands of these domains is the key property that is responsible for their high mechanical stability. We have also extended our studies of single protein domains to protein dimers. Our replica-exchange molecular dynamics simulation study of the mechanical unfolding of a segment-swapped protein G dimer suggests that the mechanical resistance of a protein complex may be controlled not only by the mechanical stability of individual domains but also by the inter-chain interactions between domains.