Figure 6. eEF1A interacts with accommodating aa-tRNA through R69 and conserved basic amino acids in Domain III.

(A) R69 of switch I of eEF1A interacts with the minor groove of the aa-tRNA adjacent to the 3’CCA end. R69 is highlighted interacting with the phosphodiester backbone of the tRNA. (B) Approximate free energy landscape of ${\mathsf{R}}_{\mathsf{elbow}}$ in comparison to the distance between eEF1A R69 and A425 of domain III $({\mathsf{R}}_{\mathsf{swi}\text{-}\mathsf{DIII}})$, generated from potential 2 simulations. This landscape indicates that for aa-tRNA to accommodate, R69 of switch I needs to pass through the 3’CCA-minor groove of the aa-tRNA and dock on domain III. (C) Approximate free energy landscape of ${\mathsf{R}}_{\mathsf{swi}\text{-}\mathsf{DIII}}$ with respect to the distance of R69 and A76 of aa-tRNA, generated from potential 2 simulations. This landscape highlights that only the path where R69 passes by the 3’CCA-minor groove is available. (D) Interactions of eEF1A domain III with in proximity to the accommodating aa-tRNA. (E) Zoomed in image of domain III of eEF1A interacting with the accommodating aa-tRNA. Basic amino acids are highlighted that could interact with the aa-tRNA. (F) Approximate free energy landscape of ${\mathsf{R}}_{\mathsf{elbow}}$ distance with respect to K378 to U55 O3’ distance, generated from potential 2 simulations. This demonstrates that domain III approaches the accommodating aa-tRNA in all simulations at an ${\mathsf{R}}_{\mathsf{elbow}}$ of ~52 Å.