Structure and Dynamics of the Integrin LFA-1 I-Domain in the Inactive State Underlie its Inside-Out/Outside-In Signaling and Allosteric Mechanisms

Abstract

SummaryLymphocyte function-associated antigen 1 (LFA-1) is an integrin that transmits information in two directions across the plasma membrane of leukocytes, in so-called outside-in and inside-out signaling mechanisms. To investigate the structural basis of these mechanisms, we studied the conformational space of the apo I-domain using replica-averaged metadynamics simulations in combination with nuclear magnetic resonance chemical shifts. We thus obtained a free energy landscape that reveals the existence of three conformational substates of this domain. The three substates include conformations similar to existing crystallographic structures of the low-affinity I-domain, the inactive I-domain with an allosteric antagonist inhibitor bound underneath α helix 7, and an intermediate affinity state of the I-domain. The multiple substates were validated with residual dipolar coupling measurements. These results suggest that the presence of three substates in the apo I-domain enables the precise regulation of the binding process that is essential for the physiological function of LFA-1.

Integrin‐associated molecules and signalling cross talking in osteoclast cytoskeleton regulation

“…The receptor aggregation induced by the ‘outside‐in’ signal after the occupation of the integrin cell's external distributor further increases the affinity of integrin to ligand. Another essential mode of activation is ‘inside‐out’ signal cascades, including signal cascades induced by secondary receptors (such as: cytokine receptors) that transmit conformational variations in the interior cellular portion of integrin to the exterior cellular domain . Integrins are thus prepared for ligand binding and for signalling outside the cell, further regulate cytoskeleton reorganization .…”

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

“…Traditional methods, including molecular dynamics (MD) and Monte Carlo (MC) simulations, are often inadequate to explore, in an affordable computational time, complex free energy landscapes in which relevant states are separated by high free-energy barriers. To accelerate sampling, metadynamics 6 (MetaD) has been proved to be particularly effective 7 , also in combination with replica-averaged modelling 8 9 10 (RAM). MetaD is based on the introduction of a time-dependent bias potential on selected descriptors of the system, or collective variables (CVs), that ideally should include all those degrees of freedom that are difficult to sample in an affordable computational time.…”

The free energy landscape of the oncogene protein E7 of human papillomavirus type 16 reveals a complex interplay between ordered and disordered regions

“…In this view, the generated ensemble is the most probable one given both the force field and the experimental data used. The RAM method has been previously shown to accurately characterise the free energy landscape of folded proteins 31,32 and, what is more challenging, the free energy landscape of denatured states 26,33,34 and intrinsically disordered proteins 35–37 .…”