Molecular dynamics simulations of Arp2/3 complex activation.

The Arp2/3 complex plays a role in forming branched actin networks during processes like endocytosis. Previous studies have shown the complex anchors new filaments to existing ones. Crystal structures reveal the inactive state of the complex. However, the transition from inactive to active remains unclear. Electron tomography has identified the active position of Arp2. The mechanism of this large-scale movement is not fully understood. This gap motivated the use of simulations to explore the conformational change. No prior work had resolved the detailed motion of Arp2 during activation. Understanding this change could clarify how the complex functions in vivo.

This study aimed to explore the structural transition of the Arp2/3 complex during activation. The goal was to model the movement of Arp2 from its inactive to active position. Researchers used molecular dynamics simulations to test this transition. They started with the inactive crystal structure as a basis. Forces were applied to Arp2 while Arp3 was restrained. The focus was on identifying the pivot point of the conformational change. The study sought to determine how the complex achieves its active state. This approach allowed for an atomistic-scale analysis of the structural shift.

The research team used atomistic-scale molecular dynamics simulations to model the Arp2/3 complex. They began with the inactive crystal structure of the complex as the starting point. Simulations applied forces to Arp2 to move it toward its active position. Arp3 was held in place to observe the resulting structural changes. The movement was analyzed to identify rotational components of the complex. A 30° counterclockwise rotation was observed around an α-helix in ARPC4. The pivot point was localized to Glu⁸¹-Asn¹⁰⁰ in this helix. The simulations tracked how subunits realigned during the transition.

The simulations revealed a 30° counterclockwise rotation of a structural block containing Arp2 and ARPC1. This rotation occurred around an α-helix in ARPC4 (Glu⁸¹-Asn¹⁰⁰). Arp2 moved to align next to Arp3 in a second structural block. The active conformation buried more surface area than the inactive state. The complex remained stable throughout the simulations. In most cases, subdomain 2 of Arp2 collided with Arp3 during the movement. These collisions slowed the transition to the active state. The results suggest a mechanical barrier to full activation.

The simulations showed a large-scale rotation of the Arp2/3 complex during activation. The pivot point for this movement was identified in an α-helix of ARPC4. Arp2 moved to align with Arp3 in the active conformation. The active state involved greater surface area burial than the inactive form. The complex remained stable during the transition. Subdomain collisions between Arp2 and Arp3 were observed in most simulations. These collisions may slow the activation process. The findings suggest a mechanical basis for the conformational change.