Substantial Conformational Change Mediated by Charge-Triad Residues of the Death Effector Domain in Protein-Protein Interactions

Abstract

Protein conformational changes are commonly associated with the formation of protein complexes. The non-catalytic death effector domains (DEDs) mediate protein-protein interactions in a variety of cellular processes, including apoptosis, proliferation and migration, and glucose metabolism. Here, using NMR residual dipolar coupling (RDC) data, we report a conformational change in the DED of the phosphoprotein enriched in astrocytes, 15 kDa (PEA-15) protein in the complex with a mitogen-activated protein (MAP) kinase, extracellular regulated kinase 2 (ERK2), which is essential in regulating ERK2 cellular distribution and function in cell proliferation and migration. The most significant conformational change in PEA-15 happens at helices α2, α3, and α4, which also possess the highest flexibility among the six-helix bundle of the DED. This crucial conformational change is modulated by the D/E-RxDL charge-triad motif, one of the prominent structural features of DEDs, together with a number of other electrostatic and hydrogen bonding interactions on the protein surface. Charge-triad motif promotes the optimal orientation of key residues and expands the binding interface to accommodate protein-protein interactions. However, the charge-triad residues are not directly involved in the binding interface between PEA-15 and ERK2.

PEA-15 C-Terminal Tail Allosterically Modulates Death-Effector Domain Conformation and Facilitates Protein–Protein Interactions

“…Structurally, PEA-15 possesses a canonical six-helix bundled DED and an irregularly structured C-terminal tail [19,20]. Recent nuclear magnetic resonance (NMR) studies suggested that PEA-15 utilizes its DED residues from helices α1, α5, and α6 to bind to ERK2 [21], while the other three helices α2, α3, and α4 undergo substantial conformational change, but are not directly involved in binding [22]. Recent crystal structures of PEA-15/ERK2 complex confirmed most findings of our NMR studies, including the binding interface between PEA-15 and ERK2, and identified a few key residues on helix α5 that are directly involved in binding [23].…”

Investigation and Prediction of Human Interactome Based on Quantitative Features

“…Therefore, molecular weight induced by different amino acid substitution may affect PPIs. The associations among different proteins were reported to be possibly strongly affected by long-range electrostatic interactions, and similar proteins with different surface charges may have different interaction patterns (Twomey et al, 2013 ; Raut and Kalonia, 2015 ). Therefore, the charge distribution of PPI participants affected the interactions between proteins.…”

On the Quest of Cellular Functions of PEA-15 and the Therapeutic Opportunities

“…This finding was later confirmed by a crystallographic study of the complex, which illustrated that the binding interface involves residues D 19 , E 68 , R 71 , P 73 , L 76 , and V 80 from PEA-15, while the charge-triad residues R 72 -D 74 L 75 are not at involved in direct interaction with ERK2 [ 25 ]. Upon ERK2 binding, PEA-15 DED undergoes substantial conformational change, particularly at the helices α2, α3, and α4 [ 26 , 27 ]. Both NMR relaxation experiments [ 26 ] and PEA-15/ERK2 crystal structures [ 25 ] suggested a disordered region around helix α3 in the complex.…”

“…Both NMR relaxation experiments [ 26 ] and PEA-15/ERK2 crystal structures [ 25 ] suggested a disordered region around helix α3 in the complex. A plausible allosteric binding model suggested that upon recognition of ERK2 DRS by its C-terminal tail, PEA-15 induces significant conformational changes at DED to reveal binding interface to ERK2, and the conformational changes are mediated by the polar interactions on the DED surface, including the charge-triad hydrogen bonding network [ 26 , 27 ]. D74A mutation disrupts this crucial hydrogen bonding network, disabling the conformational flexibility necessary for ERK2 binding [ 27 ].…”

“…PEA-15 appears to adopt different surfaces to interact with its binding partners. PEA-15 interacts with FADD DED using a surface patch adjacent to helix α2 [ 24 ]; it utilizes both DED residues on helices α1, α5 and α6 and C-terminal tail residues to bind to ERK2 [ 25 ], while its conformation at helices α2, α3, and α4 undergoes significant changes [ 26 , 27 ]; it binds to RSK2 with its C-terminus but not the N-terminal DED [ 16 ]; and it likely utilizes its first 24 residues to interact with PLD1 C-terminal D4 domain [ 28 , 29 ]. PEA-15 has been recognized as a key multi-protein binding molecule modulating a number of cellular processes, including proliferation, apoptosis, and glucose metabolism [ 23 ].…”