PMID- 34070875 OWN - NLM STAT- MEDLINE DCOM- 20210623 LR - 20210623 IS - 1422-0067 (Electronic) IS - 1422-0067 (Linking) VI - 22 IP - 11 DP - 2021 May 30 TI - The Odd Faces of Oligomers: The Case of TRAF2-C, A Trimeric C-Terminal Domain of TNF Receptor-Associated Factor. LID - 10.3390/ijms22115871 [doi] LID - 5871 AB - 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 approximately 15 to approximately 35 degrees 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. FAU - Di Venere, Almerinda AU - Di Venere A AD - Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy. FAU - Nicolai, Eleonora AU - Nicolai E AUID- ORCID: 0000-0003-1415-9808 AD - Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy. FAU - Minicozzi, Velia AU - Minicozzi V AUID- ORCID: 0000-0001-9851-9932 AD - Department of Physics, Tor Vergata University of Rome, Via Della Ricerca Scientifica 1, 00133 Rome, Italy. FAU - Caccuri, Anna Maria AU - Caccuri AM AD - Department of Chemistry, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy. FAU - Di Paola, Luisa AU - Di Paola L AD - Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Engineering, University Campus Bio-Medico of Rome, Via Alvaro del Portillo 21, 00128 Rome, Italy. FAU - Mei, Giampiero AU - Mei G AD - Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy. LA - eng GR - E84I20000560005/Universita degli Studi di Roma Tor Vergata/ PT - Journal Article DEP - 20210530 PL - Switzerland TA - Int J Mol Sci JT - International journal of molecular sciences JID - 101092791 RN - 0 (AGFG1 protein, human) RN - 0 (Inhibitor of Apoptosis Proteins) RN - 0 (Nuclear Pore Complex Proteins) RN - 0 (Protein Isoforms) RN - 0 (Protein Subunits) RN - 0 (RNA-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 0 (TNF Receptor-Associated Death Domain Protein) RN - 0 (TNF Receptor-Associated Factor 2) RN - 42HK56048U (Tyrosine) RN - EC 2.3.2.27 (TRAIP protein, human) RN - EC 2.3.2.27 (Ubiquitin-Protein Ligases) RN - EC 3.4.21.- (Proprotein Convertases) RN - EC 3.4.21.- (Serine Endopeptidases) RN - EC 3.4.21.112 (membrane-bound transcription factor peptidase, site 1) SB - IM MH - Binding Sites MH - Cloning, Molecular MH - Escherichia coli/genetics/metabolism MH - Gene Expression MH - Genetic Vectors/chemistry/metabolism MH - Humans MH - Inhibitor of Apoptosis Proteins/chemistry/genetics/metabolism MH - Molecular Docking Simulation MH - Molecular Dynamics Simulation MH - Nuclear Pore Complex Proteins/chemistry/genetics/metabolism MH - Proprotein Convertases/chemistry/genetics/metabolism MH - Protein Binding MH - Protein Conformation, alpha-Helical MH - Protein Conformation, beta-Strand MH - Protein Interaction Domains and Motifs MH - Protein Isoforms/chemistry/genetics/metabolism MH - Protein Multimerization MH - Protein Structure, Tertiary MH - Protein Subunits/*chemistry/genetics/metabolism MH - RNA-Binding Proteins/chemistry/genetics/metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Serine Endopeptidases/chemistry/genetics/metabolism MH - TNF Receptor-Associated Death Domain Protein/chemistry/genetics/metabolism MH - TNF Receptor-Associated Factor 2/*chemistry/genetics/metabolism MH - Thermodynamics MH - Tyrosine/*chemistry/metabolism MH - Ubiquitin-Protein Ligases/chemistry/genetics/metabolism PMC - PMC8198530 OTO - NOTNLM OT - protein clusters analysis OT - protein-protein interface OT - trimeric protein COIS- The authors declare no conflict of interest. EDAT- 2021/06/03 06:00 MHDA- 2021/06/24 06:00 PMCR- 2021/05/30 CRDT- 2021/06/02 01:30 PHST- 2021/04/26 00:00 [received] PHST- 2021/05/20 00:00 [revised] PHST- 2021/05/26 00:00 [accepted] PHST- 2021/06/02 01:30 [entrez] PHST- 2021/06/03 06:00 [pubmed] PHST- 2021/06/24 06:00 [medline] PHST- 2021/05/30 00:00 [pmc-release] AID - ijms22115871 [pii] AID - ijms-22-05871 [pii] AID - 10.3390/ijms22115871 [doi] PST - epublish SO - Int J Mol Sci. 2021 May 30;22(11):5871. doi: 10.3390/ijms22115871.