Fig. 1: Evaluation of energetics and hydrogen bond (H-bond) properties between F-actin and Vt.
From: Molecular basis and cellular functions of vinculin-actin directional catch bonding
a Schematic representation of pulling forces imposed on Vt in different directions during MD simulations. b Quantification of Vt:F-actin binding strength through potential of mean force (PMF) calculations. The X-axis represents the reaction coordinate (ξ), and the Y-axis represents the PMF. The graph displays PMF profiles for three pulling directions: along the Fpointed, Fbarbed, and Fnormal directions, as Vt is pulled away from the actin filament. c A circular plot depicting Vt and F-actin interactions in the Fpointed direction to probe Vt:F-actin engagement. The occupancy percentages of inter-molecular H-bonds between F-actin and Vt as quantified from constant-force pulling DMD simulations were used to create the circular plot. A scatter plot was used to illustrate the occupancies of H-bonds, allowing for a detailed analysis of the H-bond occupancies at specific forces. Each dot on the plot represents the existence of H-bonds at different pulling forces, color-coded according to force magnitude. The size of each dot indicates the occupancy percentage of the corresponding H-bond during the pulling simulation at a specific force. Native H-bonds observed in the cryo-EM structure of the Vt:F-actin complex (PDB: 3JBI) are represented as black triangles. DAFS H-bonds that signify directional catch bonding between Vt and F-actin are illustrated as blue ribbons while normal H-bonds are represented by grey ribbons.
