Kinetic and Thermodynamic Allostery in the Ras Protein Family

Abstract

The general metadata -- e.g., title, author, abstract, subject headings, etc. -- is publicly available, but access to the submitted files is restricted to UT Southwestern campus access and/or authorized UT Southwestern users.An understanding of allosteric communication is necessary for interpreting protein function and regulation. For proteins involved in disease, such knowledge can lead to discovery of new sites for therapeutic targeting. However allosteric mechanisms have proven to be diverse, and allosteric communication in many proteins cannot currently be explained by their structure or dynamics. Progress has been made in elucidating the ensemble nature of allosteric communication, especially using MD simulations to provide structural specificity of previously averaged conformations. Here I show how kinetic (i.e. temporal) correlations encode information that is orthogonal to existing work on thermodynamic correlations. I performed atomistic simulations on H, K, and NRas isoforms in various states in the Ras cycle, for a total of 0.5 milliseconds. I show that Ras' most important structural motifs, switch I and switch II, are the primary members of my calculated thermodynamic and kinetic allosteric networks, consistent with the known roles of these two motifs in Ras function. I also reveal how these communication networks are altered by the presence of the -phosphate, as well as binding of the downstream effector Raf kinase. Strikingly, these communication networks correspond to structural motifs that are functionally engaged in the Ras cycle step being simulated. I find that kinetics-based allosteric communication is not restricted to the boundaries of secondary structure elements and can occur across long distances. I show that known features of Ras regulation, such as activation of allostery upon Raf binding, necessitate kinetic allostery. These data explain experimentally observed allosteric relationships by revealing the kinetic and thermodynamic communication pathways, and show how both modes of communication are needed to relay information within proteins. This work suggests that kinetics-based communication is a key mechanism of protein function and regulation