Molecular determinants of TNFR1:TNFα binding and dynamics in a physiological membrane environment

TL;DR

This study explores how the membrane environment affects the binding and stability of TNFα and its receptor TNFR1 using molecular dynamics simulations.

Contribution

The study reveals new residues involved in TNFR1-TNFα binding and shows how lipid interactions influence the complex in a membrane environment.

Findings

Key residues on TNFα and TNFR1 were identified that are important for complex assembly and stability.

Membrane anchoring affects the global motions of the TNFα–TNFR1 complex.

Some identified amino acids are linked to pathogenic mutations, suggesting their clinical relevance.

Abstract

Tumor Necrosis Factor alpha (TNFα) is a pro-inflammatory cytokine critical for regulating cell survival and death. Under pathological conditions, excessive TNFα activity can lead to chronic inflammation, contributing to diseases such as inflammatory bowel disease and other autoimmune disorders. While structural studies have elucidated the atomistic details of TNFα binding to its receptor, TNF Receptor 1 (TNFR1), the influence of the membrane environment on this interaction remains poorly characterized experimentally. In this study, we employed advanced all-atom Gaussian accelerated molecular dynamics simulations to investigate how lipid-mediated interactions modulate the TNFα–TNFR1 complex. We identified key residues on both the cytokine and its receptor that govern trimer assembly, receptor binding, and potential pathological alterations. Our analysis confirmed previously identified functional sites and revealed new residues likely to contribute to the structural stability and dynamics of the complex. These findings provide a more comprehensive understanding of the molecular determinants of TNF signaling and offer a foundation for future experimental investigations into the receptor-ligand interface and membrane-mediated regulation.

Image 1

•Molecular dynamics simulation of TNF-ɑ bound to a membrane-anchored TNFR1.•Detailed MM/PBSA analysis allowed the identification of most contributing amino acids.•Membrane anchoring impacts global motions of the system.•Protein:lipids interactions extend beyond transmembrane region.•Some of the most contributing amino acids are already linked to pathogenic mutations.

Molecular dynamics simulation of TNF-ɑ bound to a membrane-anchored TNFR1.

Detailed MM/PBSA analysis allowed the identification of most contributing amino acids.

Membrane anchoring impacts global motions of the system.

Protein:lipids interactions extend beyond transmembrane region.

Some of the most contributing amino acids are already linked to pathogenic mutations.

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