The Odd Faces of Oligomers: The Case of TRAF2-C, A Trimeric C-Terminal Domain of TNF Receptor-Associated Factor.

Almerinda Di Venere,Giampiero Mei,Eleonora Nicolai,Velia Minicozzi,Luisa Di Paola,Anna Maria Caccuri

doi:10.3390/ijms22115871

Abstract

TNF Receptor Associated Factor 2 (TRAF2) is a trimeric protein that belongs to the TNF receptor associated factor family (TRAFs). The TRAF2 oligomeric state is crucial for receptor binding and for its interaction with other proteins involved in the TNFR signaling. The monomer-trimer equilibrium of a C- terminal domain truncated form of TRAF2 (TRAF2-C), plays also a relevant role in binding the membrane, causing inward vesiculation. In this study, we have investigated the conformational dynamics of TRAF2-C through circular dichroism, fluorescence, and dynamic light scattering, performing temperature-dependent measurements. The data indicate that the protein retains its oligomeric state and most of its secondary structure, while displaying a significative increase in the heterogeneity of the tyrosines signal, increasing the temperature from ≈15 to ≈35 °C. The peculiar crowding of tyrosine residues (12 out of 18) at the three subunit interfaces and the strong dependence on the trimer concentration indicate that such conformational changes mainly involve the contact areas between each pair of monomers, affecting the oligomeric state. Molecular dynamic simulations in this temperature range suggest that the interfaces heterogeneity is an intrinsic property of the trimer that arises from the continuous, asymmetric approaching and distancing of its subunits. Such dynamics affect the results of molecular docking on the external protein surface using receptor peptides, indicating that the TRAF2-receptor interaction in the solution might not involve three subunits at the same time, as suggested by the static analysis obtainable from the crystal structure. These findings shed new light on the role that the TRAF2 oligomeric state might have in regulating the protein binding activity in vivo.

Highlights

IntroductionProtein complexes play fundamental roles in cells life
Thanks to the analysis of pressure-induced dissociation measurements and to molecular dynamics (MD) simulation we have found that TNF Receptor Associated Factor 2 (TRAF2)-C probably exists in the solution as an “asymmetric” trimer, in which two subunits cluster together while the third becomes more independent from the others [29]
The study of protein interfaces in oligomers has has led led to important discoveries on the manifold functional roles and evolutionary advantages that the assodiscoveries on the manifold functional roles and evolutionary advantages that the associciation of several monomeric subunits provides in several aspects of cell life

Summary

Introduction

Protein complexes play fundamental roles in cells life. The vast majority of protein oligomeric structures examined so far is represented by homomers, which are oligomers composed by identical subunits [6,7,8]. The reason for the prevalence of homomers (and, in particular, homodimers) arises from the enhanced interaction propensity displayed by monomers with similar surfaces [9]. This feature is due to statistical reasons and has been used by evolution to select a number of possible architectures that provides functional and structural advantages to complexes made by identical subunits [9,10].

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