title: Structural Dynamics in Ras and Related Proteins upon Nucleotide Switching.
abstract: Structural dynamics of Ras proteins contributes to their activity in signal transduction cascades. Directly targeting Ras proteins with small molecules may rely on the movement of a conserved structural motif, switch II. To understand Ras signaling and advance Ras-targeting strategies, experimental methods to measure Ras dynamics are required. Here, we demonstrate the utility of hydrogen-deuterium exchange (HDX) mass spectrometry (MS) to measure Ras dynamics by studying representatives from two branches of the Ras superfamily, Ras and Rho. A comparison of differential deuterium exchange between active (GMPPNP-bound) and inactive (GDP-bound) proteins revealed differences between the families, with the most notable differences occurring in the phosphate-binding loop and switch II. The P-loop exchange signature correlated with switch II dynamics observed in molecular dynamics simulations focused on measuring main-chain movement. HDX provides a means of evaluating Ras protein dynamics, which may be useful for understanding the mechanisms of Ras signaling, including activated signaling of pathologic mutants, and for targeting strategies that rely on protein dynamics.
authors.affiliation: Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
authors.forename: Rane A
authors.initials: RA
authors.lastname: Harrison
authors.affiliation: Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Jia
authors.initials: J
authors.lastname: Lu
authors.affiliation: Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Carrasco
authors.affiliation: Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: John
authors.initials: J
authors.lastname: Hunter
authors.affiliation: Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Anuj
authors.initials: A
authors.lastname: Manandhar
authors.affiliation: Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Sudershan
authors.initials: S
authors.lastname: Gondi
authors.affiliation: Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address: kenneth.westover@utsouthwestern.edu.
authors.forename: Kenneth D
authors.initials: KD
authors.lastname: Westover
authors.affiliation: Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA. Electronic address: j.engen@northeastern.edu.
authors.forename: John R
authors.initials: JR
authors.lastname: Engen
mesh_terms: D000818:Animals; D006801:Humans; D013058:Mass Spectrometry; D056004:Molecular Dynamics Simulation; D009711:Nucleotides / Q000378:metabolism*; D018631:ras Proteins / Q000737:chemistry* / Q000378:metabolism*; D020741:rho GTP-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D009711:Nucleotides; D018631:ras Proteins; D020741:rho GTP-Binding Proteins
keywords: Rho; guanosine diphosphate (GDP); hydrogen–deuterium exchange mass spectrometry; protein dynamics; signal transduction