A structural model reveals energy transduction in dynein

Abstract

Intracellular active transport is driven by ATP-hydrolyzing motor proteins that move along cytoskeletal filaments. In particular, the microtubule-associated dynein motor is involved in the transport of organelles and vesicles, the maintenance of the Golgi, and mitosis. However, unlike kinesin and myosin, the mechanism by which dynein converts chemical energy into mechanical force remains largely a mystery, due primarily to the lack of a highresolution molecular structure. Using homology modeling and normal mode analysis, we propose a complete atomic structure and a mechanism for force generation by the motor protein dynein. In agreement with very recent electron microscopy (EM) reconstructions showing dynein as a ring-shaped heptamer, our model consists of six ATPases of the AAA (ATPases associated with various cellular activities) superfamily and a C-terminal domain, which is experimentally known to control motor function. Our model shows a coiled coil spanning the diameter of the motor that accounts for previously unidentified structures in EM studies and provides a potential mechanism for long-range communication between the AAA domains. Furthermore, normal mode analysis reveals that the subunits of the motor that contain the nucleotide binding sites exhibit minimal movement, whereas the rest of the motor is very mobile. Our analysis suggests the likely domain rearrangements of the motor unit that generate its power stroke. This study provides insights into the structure and function of dynein that can guide further experimental investigations into energy transduction in dynein.AAA ͉ homology modeling ͉ molecular motors ͉ electron microscopy ͉ ATP hydrolysis M otor proteins use energy derived from ATP hydrolysis to move along cytoskeletal filaments (1). In particular, the microtubule-associated molecular motor dynein is involved in the transport of organelles and vesicles, the maintenance of the Golgi, and mitosis (2, 3). Mutations in this protein have been implicated in neurodegenerative diseases (4) and polycystic kidney disease (5). Unlike the motor proteins kinesin and myosin, the mechanism by which dynein converts chemical energy into mechanical force remains largely a mystery. The primary reason for this is the lack of a high-resolution molecular structure. Cytoplasmic dynein is a large multisubunit complex (1.2 MDa) composed of two heavy chains (Ϸ0.5 MDa each) (6), making its structural characterization extremely challenging. In this study, we use homology modeling to propose a structure for the motor unit of the dynein heavy chain, which is the site for energy transduction and force generation (see Fig. 1a). Next, we perform normal mode analysis to determine the large-scale motions of the protein. Together, these results suggest a mechanism for both force generation and regulatory control in dynein.Sequence analysis of dynein's motor unit indicates that it consists of six concatenated AAA (ATPases associated with diverse cellular activities) subunits, an extended stalk that contains a microtubule bind...

The roles of noncatalytic ATP binding and ADP binding in the regulation of dynein motile activity in flagella

“…Dynein transduces the chemical energy of ATP hydrolysis into mechanical work, probably through its conformational changes [Burgess et al, 2003;Serohijos et al, 2006]. To generate the regular oscillatory movement of flagella, the activity of dynein arms in the flagellar axoneme should be controlled according to their position within the axoneme and the phase of the beating cycle.…”

Kinetic models for the coordinated stepping of cytoplasmic dynein

“…Several structural studies have shown that the dynein motor domain consists of six concatenated ATPases associated with diverse cellular activities ͑AAA+͒ subunits and a C-terminal domain that is twice the size of an AAA+ subunit. [1][2][3] Although dynein has four ATP-binding regions, the primary hydrolytic site is located between the AAA1 and AAA2 subunits. [4][5][6][7] In contrast to other cytoskeletal motors, such as kinesin and myosin, the mechanochemical cycle that drives dynein's unidirectional motion or the biophysical mechanisms that coordinate the motion of the two heads is less understood.…”

Multiscale approaches for studying energy transduction in dynein

“…To determine the tertiary organization of the various domains, we fit the model structures into the EM density 2. From the results of Koonce et al ., we assume that: (1) the seven lobe densities of the motor correspond to the six AAA+ units and the C-domain.…”

“…More specifically, we assumed that the smooth side consists of the more conserved AAA1-AAA4 domains while the rough side of the motor consists of AAA5, AAA6, and C-domain 14. Because the sequences of these domains are less conserved, they are not expected to follow the configuration of homomeric AAA complexes, and therefore break the symmetry of the motor ring 2,14. To preserve the functionally relevant interactions between the domains AAA1-AAA4 and to construct a regular tetramer for this portion of the motor, we further assume that: (2) the orientation of AAA1-AAA4 units follows the orientation of the σ54 RNA polymerase activator NtrCl (PDB ID: 1NY6) 15.…”