Role of AAA3 Domain in Allosteric Communication of Dynein Motor Proteins

Abstract

Cytoplasmic dynein, an AAA+ motif containing motor, generates force and movement along the microtubule to execute important biological functions including intracellular material transport and cell division by hydrolyzing ATP. Among the six AAA+ domains, AAA1 is the primary ATPase site where a single ATP hydrolysis generates a single step. Nucleotide states in AAA3 gate dynein’s activity, suggesting that AAA3 acts as a regulatory switch. However, the comprehensive structural perspective of AAA3 in dynein’s mechanochemical cycle remains unclear. Here, we explored the allosteric transition path of dynein involving AAA3 using a coarse-grained structure-based model. ATP binding to the AAA1 domain creates a cascade of conformational changes through the other domains of the ring, which leads to the pre-power stroke formation. The linker domain, which is the mechanical element of dynein, shifts from a straight to a bent conformation during this process. In our present study, we observe that AAA3 gates the allosteric communication from AAA1 to the microtubule binding domain (MTBD) through AAA4 and AAA5. The MTBD is linked to the AAA+ ring via a coiled-coil stalk and a buttress domain, which are extended from AAA4 and AAA5, respectively. Further analysis also uncovers the role of AAA3 in the linker movement. The free energy calculation shows that the linker prefers the straight conformation when AAA3 remains in the ATP-bound condition. As AAA3 restricts the motion of AAA4 and AAA5, the linker/AAA5 interactions get stabilized, and the linker cannot move to the pre-power stroke state that halts the complete structural transition required for the mechanochemical cycle. Therefore, we suggest that AAA3 governs dynein’s mechanochemical cycle and motility by controlling the AAA4 and AAA5 domains that further regulate the linker movement and the power stroke formation.

Structures of human dynein in complex with the lissencephaly 1 protein, LIS1

“…The contact between the AAA3-AAA4 bridging loop and LIS1 ( Figure 2D ) is the pivot point about which the position of LIS1 ring rotates between the human and yeast systems ( Video 1 ). Given the conservation of this interaction between the two systems, an intriguing possibility is that this contact relays information about the nucleotide state of AAA3, a regulatory site in dynein ( Bhabha et al, 2014 ; DeSantis et al, 2017 ; DeWitt et al, 2015 ; Dutta and Jana, 2019 ; Nicholas et al, 2015 ; Qiu et al, 2021 ), to LIS1/Pac1. Although ATP hydrolysis at AAA1 is the main driver of dynein motility, AAA3 has been shown to play a major role in controlling the communication between AAA1 and dynein’s MTBD; AAA3:apo or ATP blocks communication, leading to tight microtubule binding, while AAA3:ADP restores dynein’s normal mechanochemical cycle ( DeWitt et al, 2015 ).…”

Structures of human cytoplasmic dynein in complex with the lissencephaly 1 protein, LIS1

“…The contact between the AAA3-AAA4 bridging loop and LIS1 (Figure 2D) is the pivot point about which the position of LIS1 ring rotates between the human and yeast systems (Video 1). Given the conservation of this interaction between the two systems, an intriguing possibility is that this contact relays information about the nucleotide state of AAA3, a regulatory site in dynein (DeSantis et al, 2017; Dewitt et al, 2015; Dutta and Jana, 2019; Nicholas et al, 2015; Qiu et al, 2021), to LIS1/Pac1. The loop forms a hydrophobic pocket with the small domain of AAA3 (AAA3 S ), and nucleotide-induced conformational changes in AAA3 may cause this loop and AAA3 S to shift together (Figure 2D).…”

Dynamical asymmetry exposes 2019-nCoV prefusion spike

“…A structure-based Hamiltonian of trimeric spike protein for SAR-CoV2 is derived using the super-symmetric contact map. In the current structure-based model amino acids are represented by single beads at the location of the C-α atom (15,25,31,32). The coarse-grained structurebased model, a well-established model, comprehends a novel way to investigate the mechanisms associated with protein folding and function (20-22, 24, 33-38).…”