Phosphatidylserine-Induced Conformational Modulation of Immune Cell Exhaustion-Associated Receptor TIM3

Jeffrey K Weber,Ruhong Zhou

doi:10.1038/s41598-017-14064-x

Abstract

In the face of chronic cancers and protracted viral infections, human immune cells are known to adopt an exhausted state in which their effector functions are lost. In recent years, a number of inhibitory receptors have been connected to the immune cell exhaustion phenotype; furthermore, ligands capable of activating these receptors have been discovered. The molecular mechanisms by which these ligands affect the exhausted states of immune cells, however, are largely unknown. Here, we present the results of molecular dynamics simulations of one potential exhaustion-associated system: the complex of human inhibitory receptor TIM3 (hTIM3) and its ligand phosphatidylserine (PSF). We find that PSF fundamentally alters the electrostatic environment within hTIM3’s Ca2+ binding site, facilitating the formation of a salt bridge and freeing a tyrosine-containing strand. This liberated tyrosine then collapses into a nearby hydrophobic pocket, anchoring a modified conformational ensemble typified by a β-strand rearrangement. The “electrostatic switching/hydrophobic anchoring” mechanism of conformational modulation reported here suggests a new type of process by which TIM3 activation might be achieved. This work also highlights strategies by which PSF-mediated conformational change could be controlled, either through administration of small molecules, execution of mutations, or modification of receptor phosphorylation states.

Highlights

In recent years, varied roles for the TIM (T cell immunoglobulin and mucin) family of receptors have been elucidated in immune cell regulatory pathways[3,4,5,6,7,8,9,10,11,12,13,14,15]
Leveraging approximately 6 μs of aggregate simulation data initiated from an human inhibitory receptor TIM3 (hTIM3) homology model, we found that PSF induces a dramatic conformational change in hTIM3 marked by (a) an expansion of the FG-CC’ cleft, (b) the formation of a strand-liberating salt bridge, and (c) the burial of a solvent-exposed tyrosine residue
The hTIM3 homology model (Fig. 1a–c) features the FG-CC’ cleft characteristic of the TIM receptor family; the FG and CC’ loops are constrained by two disulfide linkages that are noncanonical within the immunoglobulin superfamily[3]

Summary

Introduction

In recent years, varied roles for the TIM (T cell immunoglobulin and mucin) family of receptors have been elucidated in immune cell regulatory pathways[3,4,5,6,7,8,9,10,11,12,13,14,15]. Leveraging approximately 6 μs of aggregate simulation data initiated from an hTIM3 homology model, we found that PSF induces a dramatic conformational change in hTIM3 marked by (a) an expansion of the FG-CC’ cleft, (b) the formation of a strand-liberating salt bridge, and (c) the burial of a solvent-exposed tyrosine residue. The observed “electrostatic switching/hydrophobic anchoring” motif suggests a possible structural mechanism through which hTIM3 could be activated, highlighting a stable strand rearrangement in the IgV domain that could send signals downstream and perhaps facilitate changes in the phosphorylation state in the extracellular region of hTIM3.

Results

Conclusion