Structural insights into the role of deleterious mutations at the dimeric interface of Toll‐like receptor interferon‐β related adaptor protein

Abstract

Toll‐like receptors (TLRs) are major players in the innate immune system—recognizing pathogens and differentiating self/non‐self components of immunity. These proteins are present either on the plasma membrane or endosome and recognize pathogens at their extracellular domains. They are characterized by a single transmembrane helix and an intracellular toll‐interleukin‐1 receptor (TIR) domain. Few TIRs directly invoke downstream signaling, while others require other TIR domains of adaptors like TIR domain‐containing adaptor‐inducing interferon‐β (TRIF) and TRIF‐related adaptor molecule (TRAM). On recognizing pathogenic lipopolysaccharides, TLR4 dimerises and interacts with the intracellular TRAM dimer through the TIR domain to recruit a downstream signaling adaptor (TRIF). We have performed an in‐depth study of the structural effect of two mutations (P116H and C117H) at the dimeric interface of the adaptor TRAM, which are known to abrogate downstream signaling. We modeled the structure and performed molecular dynamics studies in order to decipher the structural basis of this effect. We observed that these mutations led to an increased radius of gyration of the complex and resulted in several changes to the interaction energy values when compared against the wild type (WT) and positive control mutants. We identified highly interacting residues as hubs in the WT dimer, and a few such hubs that were lost in the mutant dimers. Changes in the protein residue path, hampering the information flow between the crucial A86/E87/D88/D89 and T155/S156 sites, were observed for the mutants. Overall, we show that such residue changes can have subtle but long‐distance effects, impacting the signaling path allosterically.

Sequence and structural analysis of adaptors of Toll-like receptor 4 sheds light on the evolutionary trajectory and functional emergence

“…We used multiple approaches for modelling proteins dimer, trimer, and tetramer complex. In a previous study from our lab, we had established the dimer model of TRAM protein using various parameters [39]. In one of the approaches, we used the TRAM MD stabilized structure as our starting dimer model and use protein docking algorithm to model the TRAM dimer and TRIF complex.…”

The identification of toll-like receptor genes in large yellow croaker (Larimichthys crocea): provides insights into its environmental adaptation to biological and abiotic stresses

“…To date, studies have shown that TLRs bear the responsibility of playing important roles in innate immunity in organisms (Verma et al, 2024). Innate immune cells, such as dendritic cells (DCs), are activated when the immune system detects microorganisms through a variety of receptors known as pattern recognition receptors (PRRs), which are encoded by germ-line genes and recognize a wide range of microbial structures (Wang et al, 2024).…”