Solution 3D structure and conformational flexibility of the endothelial monocyte activating polypeptide II (EMAP II)...

Endothelial monocyte activating polypeptide II (EMAP II) is the C-terminal domain of its precursor, AIMP1/p43 polypeptide, a multifunctional protein with diverse functional cytokine activities and tRNA-binding abilities. Several X-ray crystallographic structures of EMAP II are available in the PDB database. However, its NMR-based structure, presented in this work indicates partition of its structure into two domains characterized by substantial differences in structural dynamics. Based on ¹⁵N relaxation experiments, hydrogen-deuterium exchange (HDX) data and molecular dynamics simulations we conclude that observed differences in dynamics may enable dual mechanisms of tRNA binding and cytokine function of EMAP II. Although in general in-solution EMAP II structure studied here is highly similar to its in-crystal X-ray structure, the N-terminal segment responsible for cytokine activity exhibited reduced deuterium exchange rate and demonstrated higher accessibility to the solvent compared to X-ray structures and the AlphaFold2 model. Such differences may be important for understanding cytokine function of EMAP II. The tRNA-binding motif characterized by different orientation of the side chain of tryptophan 128, which can play a significant role in the regulation of tRNA binding.