Paper Citing NAMD - Abstract
Eargle, John; Black, Alexis A.; Sethi, Anurag; Trabuco, Leonardo G.; Luthey-Schulten, Zaida
Dynamics of recognition between tRNA and elongation factor Tu
JOURNAL OF MOLECULAR BIOLOGY, 377:1382-1405, APR 11 2008
Elongation factor Tu (EF-Tu) binds to all standard aminoacyl transfer RNAs (aa-tRNAs) and transports them to the ribosome while protecting the ester linkage between the tRNA and its cognate amino acid. We use molecular dynamics simulations to investigate the dynamics of the EF-Tu-guanosine 5'-triphosphate-aa-tRNA(Cys) complex and the roles played by Mg2+ ions and modified nucleosides on the free energy of protein RNA binding. Individual modified nucleosides have pronounced effects on the structural dynamics of tRNA and the EF-Tu-Cys-tRNA(Cys) interface. Combined energetic and evolutionary analyses identify the coevolution of residues in EF-Tu and aa-tRNAs at the binding interface. Highly conserved EF-Tu residues are responsible for both attracting aa-tRNAs as well as providing nearby nonbonded repulsive energies that help fine-tune molecular attraction at the binding interface. In addition to the 3' CCA end, highly conserved tRNA nucleotides G1, G52, G53, and U54 contribute significantly to EF-Tu binding energies. Modification of U54 to thymine affects the structure of the tRNA common loop resulting in a change in binding interface contacts. In addition, other nucleotides, conserved within certain tRNA specificities, may be responsible for tuning aa-tRNA binding to EF-Tu. The trend in EF-Tu-CystRNA(Cys) binding energies observed as the result of mutating the tRNA agrees with experimental observation. We also predict variations in binding free energies upon misacylation of tRNA(Cys) with D-cysteine or O-phosphoserine and upon changing the protonation state of L-cysteine. Principal components analysis in each case reveals changes in the communication network across the protein-tRNA interface and is the basis for the entropy calculations. (C) 2008 Published by Elsevier Ltd.
