Paper Citing NAMD - Abstract
Xiang, Xue; Lee, Cho-yin; Li, Tian; Chen, Wei; Lou, Jizhong; Zhu, Cheng
Structural Basis and Kinetics of Force-Induced Conformational Changes of an alpha A Domain-Containing Integrin
PLOS ONE, 6 Art. No. e27946, NOV 28 2011
Background: Integrin alpha(L)beta(2) (lymphocyte function-associated antigen, LFA-1) bears force upon binding to its ligand intercellular adhesion molecule 1 (ICAM-1) when a leukocyte adheres to vascular endothelium or an antigen presenting cell (APC) during immune responses. The ligand binding propensity of LFA-1 is related to its conformations, which can be regulated by force. Three conformations of the LFA-1 alpha A domain, determined by the position of its alpha(7)-helix, have been suggested to correspond to three different affinity states for ligand binding. Methodology/Principal Findings: The kinetics of the force-driven transitions between these conformations has not been defined and dynamically coupled to the force-dependent dissociation from ligand. Here we show, by steered molecular dynamics (SMD) simulations, that the alpha A domain was successively transitioned through three distinct conformations upon pulling the C-terminus of its alpha(7)-helix. Based on these sequential transitions, we have constructed a mathematical model to describe the coupling between the alpha A domain conformational changes of LFA-1 and its dissociation from ICAM-1 under force. Using this model to analyze the published data on the force-induced dissociation of single LFA-1/ICAM-1 bonds, we estimated the force-dependent kinetic rates of interstate transition from the short-lived to intermediate-lived and from intermediate-lived to long-lived states. Interestingly, force increased these transition rates; hence activation of LFA-1 was accelerated by pulling it via an engaged ICAM-1. Conclusions/Significance: Our study defines the structural basis for mechanical regulation of the kinetics of LFA-1 alpha A domain conformational changes and relates these simulation results to experimental data of force-induced dissociation of single LFA-1/ICAM-1 bonds by a new mathematical model, thus provided detailed structural and kinetic characterizations for force-stabilization of LFA-1/ICAM-1 interaction.
