Fig. 7: MD simulation of Fv interactions with the GluN1b-GluN2B ATD dimer.
From: Development and characterization of functional antibodies targeting NMDA receptors
a–b A dynamical network representation of the interface contacts between Fv2 and the GluN2B ATD R1 lobe (panel a) and Fv5 and the GluN1b R2 and GluN2B ATD R1 lobes (panel b). The spheres correspond to Cα atoms, or nodes in the network, pairs of which are connected by a line (or edge) if the heavy atoms of their residues are within 6 Å for at least 75% of the trajectory. To highlight the most important interactions, we only show contact pairs present in at least 15/20 simulation windows and exhibit a correlation coefficient greater than 0.3. These selection criteria are used in all subsequent network representations unless indicated otherwise. The specific value of the correlation coefficient between each pair is indicated by the color of the line connecting them. c–d A dynamical network representation of the correlation of the GluN1b-GluN2B ATD interface residues bound to Fv2 (panel c) and Fv5 (panel d). The gray oval in panel c highlights the interaction between GluN1b ATD R1 and GluN2B ATD R2.
