Dynamics of Allosteric Transitions in Dynein

Abstract

SummaryCytoplasmic Dynein, a motor with an unusual architecture made up of a motor domain belonging to the AAA+ family, walks on microtubule towards the minus end. Prompted by the availability of structures in different nucleotide states, we performed simulations based on a new coarse-grained model to illustrate the molecular details of the dynamics of allosteric transitions in the motor. The simulations show that binding of ATP results in the closure of the cleft between the AAA1 and AAA2, which in turn triggers conformational changes in the rest of the motor domain, thus poising dynein in the pre-power stroke state. Interactions with the microtubule, which are modeled implicitly, substantially enhances the rate of ADP release, and formation of the post-power stroke state.The dynamics associated with the key mechanical element, the linker (LN) domain, which changes from a straight to a bent state and vice versa, are highly heterogeneous suggestive of multiple routes in the pre power stroke to post power stroke transition. We show that persistent interactions between the LN and the insert loops in the AAA2 domain prevent the formation of pre-power stroke state when ATP is bound to AAA3, thus locking dynein in a non-functional repressed state. Motility in such a state may be rescued by applying mechanical force to the LN domain. Taken together, these results show how the intricate signaling dynamics within the motor domain facilitate the stepping of dynein. IntroductionMolecular motors are spectacular nanomachines that transport cargos by moving processively along filamentous actin and microtubules (MT). 1-3 Of the three motor families, kinesins and dyneins walk along MTs whereas myosins step on filamentous actin. Although a number of questions still remain unanswered, it is fair to say that the mechanism of processive motion of kinesin-1 and myosin V is fairly well understood, thanks to remarkable experimental studies conducted over the last twenty five years. 2,[4][5][6][7][8][9][10][11][12][13][14][15][16] In contrast, the characterization of the motility of cytoplasmic dynein has lagged behind.Although discovered over fifty years ago, 17 it is only in the last decade the complexity 2 and variations in the architecture of dyneins have been revealed, raising various questions that challenge our views of information processing in nanoscale biological machines. Even though this issue, which relates to to allosteric communication in protein complexes, is most interesting, our focus here is to provide quantitative insights into the molecular basis of the dynamics of allosteric transitions between distinct functional states in the motility of dynein, a most intriguing molecular motor.Cytoplasmic dynein transports cargo along MTs, and is a minus end-directed motor. Among dyne's different cargoes are endosomes, lysosomes, and mitochondria. [18][19][20] Additionally, cytoplasmic dynein (or dynein from now on) is involved in the process of positioning of the spindle during cell division. 21 In almost all respects, dynein...

Self-organized networks: Darwinian evolution of dynein rings, stalks, and stalk heads

“…The complexity of the architecture of dynein and the difficulties in carrying out atomically detailed simulations, both due to the long time scales and inaccuracies in the force fields (especially water), have led to the creation of coarse grained (CG) models. Such models with 7 multiple parameters based on crystal structures from several species have been used to analyze AAA and linker interactions separately [31]. The methods used here on dynein have previously been tested on other cytoskeleton proteins [7][8][9], as well as many other proteins [3,10,24], and have consistently yielded new insights into positive Darwinian evolution of protein functions from sequences alone.…”

Role of AAA3 Domain in Allosteric Communication of Dynein Motor Proteins

“…Recent studies of Goldtzvik et al have shown that the AAA2 insert loop (AAA2-IL) has an important role in stabilizing the linker in the straight conformation as the interaction between AAA2-IL and the linker prevents the linker from bending. 40 However, from contact map analysis (Figure 2), we understand that the linker makes contact with AAA5 along with AAA2-IL in its straight conformations. Thirumalai and his group have elucidated the underlying mechanism using a coarse-grained self-organized polymer model.…”

“…Thirumalai and his group have elucidated the underlying mechanism using a coarse-grained self-organized polymer model. 40 They found that the ATP-bound state of AAA3 stabilizes the linker/AAA2-IL interactions that prevent the linker bending. However, what happens to the linker/AAA5 interactions or how important those interactions are for the regulation of switching function is not very clear from this study.…”

“…Previously, Thirumalai and his group investigated the molecular mechanism behind this AAA3 regulatory switching function. 40 Their computational study using a self-organized polymer model proposed that the ATP binding to the AAA3 stabilizes linker/AAA2-IL interactions that prevent linker bending. We already know that the linker makes contact with AAA5 along with AAA2-IL in the straight conformation.…”

Diverse stepping motions of cytoplasmic dynein revealed by kinetic modeling

“…This ATP-dependent change in the affinity of MTBD must be critical, because dynein needs to bind tightly with MT when it exerts force against MT but needs to dissociate from MT during recovery-stroke to avoid backward movement [27,28]. In addition to these specific parts of the motor domain, allosteric conformational changes in the entire motor domain may play an important role for the dynein movement [29,30]. The dimeric dynein state.…”