Increasing evidence suggests that mechanical load on the T cell receptor (TCR) is crucial for recognizing the antigenic peptide-loaded major histocompatibility complex (pMHC) molecule. Our recent all-atom molecular dynamics (MD) simulations revealed that the inter-domain motion of the TCR is responsible for the load-induced catch bond behavior of the TCR-pMHC complex and peptide discrimination. To further examine the generality of the mechanism, we perform all-atom MD simulations of the B7 TCR under different conditions for comparison with our previous simulations of the A6 TCR. The two TCRs recognize the same pMHC and have similar interfaces with pMHC in crystal structures. We find that the B7 TCR-pMHC interface stabilizes under ~15-pN load using a conserved dynamic allostery mechanism that involves the asymmetric motion of the TCR chassis. However, despite forming comparable contacts with pMHC as A6 in the crystal structure, B7 has fewer high-occupancy contacts with pMHC during the simulation. These results suggest that the dynamic allostery common to the TCR chassis can amplify slight differences in interfacial contacts into distinctive mechanical responses and potentially nuanced biological outcomes.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11507873PMC
http://dx.doi.org/10.1101/2024.10.16.618634DOI Listing

Publication Analysis

Top Keywords

dynamic allostery
12
motion tcr
8
simulations tcr
8
pmhc crystal
8
tcr chassis
8
contacts pmhc
8
pmhc
6
tcr
6
load-based divergence
4
divergence dynamic
4

Similar Publications

Allosteric regulation is a powerful mechanism for controlling the efficiency of enzymes. Deciphering the evolutionary mechanisms by which allosteric properties have been acquired in enzymes is of fundamental importance. We used the malate (MalDH) and lactate deydrogenases (LDHs) superfamily as model to elucidate this phenomenon.

View Article and Find Full Text PDF

The inherent antigen cross-reactivity of the T cell receptor (TCR) is balanced by high specificity. Surprisingly, TCR specificity often manifests in ways not easily interpreted from static structures. Here we show that TCR discrimination between an HLA-A*03:01 (HLA-A3)-restricted public neoantigen and its wild-type (WT) counterpart emerges from distinct motions within the HLA-A3 peptide binding groove that vary with the identity of the peptide's first primary anchor.

View Article and Find Full Text PDF

Aminoglycoside-phosphotransferases (APHs) are a class of bacterial enzymes that mediate acquired resistance to aminoglycoside antibiotics. Here we report the identification of small molecules counteracting aminoglycoside resistance in Enterococcus casseliflavus. Molecular dynamics simulations were performed to identify an allosteric pocket in three APH enzymes belonging to 3' and 2'' subfamilies in which we then screened, in silico, 12,000 small molecules.

View Article and Find Full Text PDF

The role of ribosomal protein networks in ribosome dynamics.

Nucleic Acids Res

January 2025

Institut de Mathématiques de Jussieu - Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS, Université Paris Diderot, 8, Pace Aurélie Nemours, 75013 Paris, France.

Accurate protein synthesis requires ribosomes to integrate signals from distant functional sites and execute complex dynamics. Despite advances in understanding ribosome structure and function, two key questions remain: how information is transmitted between these distant sites, and how ribosomal movements are synchronized? We recently highlighted the existence of ribosomal protein networks, likely evolved to participate in ribosome signaling. Here, we investigate the relationship between ribosomal protein networks and ribosome dynamics.

View Article and Find Full Text PDF

Computational advances in discovering cryptic pockets for drug discovery.

Curr Opin Struct Biol

January 2025

Computer-Aided Drug Design, In Silico Discovery, Therapeutics Discovery, Johnson & Johnson Innovative Medicine, Turnhoutseweg 30, 2340 Beerse, Belgium. Electronic address:

A number of promising therapeutic target proteins have been considered "undruggable" due to the lack of well-defined ligandable pockets. Substantial research in protein dynamics has elucidated the existence of "cryptic" pockets that only exist transiently and become favorable for binding in the presence of a ligand. These pockets provide an avenue to target challenging proteins, inspiring the development of multiple computational methods.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!