Paper Citing NAMD - Abstract
Wieden, Hans Joachim; Mercier, Evan; Gray, John; Steed, Brett; Yawney, Davis
A Combined Molecular Dynamics and Rapid Kinetics Approach to Identify Conserved Three-Dimensional Communication Networks in Elongation Factor Tu
BIOPHYSICAL JOURNAL, 99:3735-3743, DEC 1 2010
Elongation factor (EF) Tu delivers aminoacyl tRNAs to the actively translating bacterial ribosome in a GTP hydro lysis dependent process Rapid recycling of EF Tu catalyzed by EF Ts is required for efficient protein synthesis in vivo Here we report a combined theoretical and experimental approach aimed at identifying three dimensional communication networks in EF Tu As an example we focus on the mechanistic role of second shell residue Asp(109) We constructed full length structural models of EF Tu from Escherichia coli in the GDP /GTP bound state and performed several 10 ns long molecular dynamics simulations During these simulations the side chain of Asp(109) formed a previously undetected transient hydrogen bond to His(22) an invariant residue in the phosphate binding loop (P loop) To experimentally validate our molecular dynamics results and further analyze the role of this hydrogen bond we determined all rate constants for the multistep reaction between EF Tu (wild type and two mutants) EF Ts GDP and GTP using the stopped flow technique This mutational analysis revealed that the side chain of Asp(109) is important for acceleration of GDP but not for GTP dissociation by EF Ts The possibility that the Asp(109) side chain has a role in transition state stabilization and coupling of P loop movements with rearrangements at the base side of the nucleotide is discussed
