Modeling Temperature-Dependent Ion Channel Protein Structural Changes with Rosetta

Abstract

Temperature-sensing ion channels are thought to adopt different conformations at varying temperatures, driven by a significant difference in free energy between the closed and open states. In support of this notion, we previously observed with site-directed fluorescence recordings that pore region undergoes substantial structural rearrangements during the heat activation of TRPV1 channels. Temperature-driven structural changes have also been suggested in other protein regions and channel types. To reveal such structural changes, we are exploring the Rosetta modeling method to predict channel protein structural differences at two different temperatures.Rosetta is a de novo/comparative protein structure modeling algorithm. As one of the top-performing programs for protein structure prediction, it has predicted protein structures with high backbone accuracies. As a test case, we modeled the N-domain of Troponin C (NTnC) at both 4®ƒ and 30®ƒ, for which NMR structures are known. Rosetta-predicted structures of NTnC align with the NMR-determined structures at these two temperatures with ∼ 3 A backbone root mean square deviation. Our approach should be generally applicable to modeling temperature-dependent protein conformational rearrangements.