Dynamics of Allosteric Transitions in Dynein

1SummaryCytoplasmic 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.

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Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin

10.1101/183590 ◽

2017 ◽

Author(s):

Zhechun Zhang ◽

Yonathan Goldtzvik ◽

D. Thirumalai

Keyword(s):

Conformational Changes ◽

Critical Role ◽

Molecular Simulations ◽

Single Step ◽

Motor Domain ◽

Coarse Grained ◽

Power Stroke ◽

Stochastic Motion ◽

Correct Orientation ◽

Motor Head

Kinesin walks processively on microtubules (MTs) in an asymmetric hand-over-hand manner consuming one ATP molecule per 16 nm step. The contributions due to docking of the approximately thirteen residue neck linker to the leading head (deemed to be the power stroke), and diffusion of the trailing head contribute in propelling the motor by 16 nm have not been quantified. We use molecular simulations by creating a new coarse-grained model of the microtubule-kinesin complex, which reproduces the measured stall force as well as the force required to dislodge the motor head from the MT, to show that nearly three quarters of the step occurs by bidirectional stochastic motion of the TH. However, docking of the neck linker to the leading head constrains the extent of diffusion and minimizes the probability that kinesin takes side steps implying that both the events are necessary in the motility of kinesin, and for the maintenance of processivity. Surprisingly, we find that during a single step the trailing head stochastically hops multiple times between the geometrically accessible neighboring sites on the MT prior to forming a stable interaction with the target binding site with correct orientation between the motor head and the α/ß tubulin dimer.Significance StatementLike all motors, the stepping of the two headed conventional Kinesin on the microtubule is facilitated by conformational changes in the motor domain upon ATP binding and hydrolysis. Numerous experiments have revealed that docking of the thirteen residue neck linker (NL) to the motor domain of the leading plays a critical role in propelling the trailing head towards the plus end of the microtubule by nearly 16 nm in a single step. Surprisingly our molecular simulations reveal that nearly three quarters of the step occurs by stochastic diffusion of the trailing head. Docking of the NL restricts the extent of diffusion, thus forcing the motor to walk with overwhelming probability on a single protofilament of the MT.

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Kinematics of the lever arm swing in myosin VI

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1615708114 ◽

2017 ◽

Vol 114 (22) ◽

pp. E4389-E4398 ◽

Cited By ~ 11

Author(s):

Mauro L. Mugnai ◽

D. Thirumalai

Keyword(s):

Rotational Diffusion ◽

Quantitative Agreement ◽

Motor Domain ◽

Coarse Grained ◽

Power Stroke ◽

Myosin Vi ◽

Step Size ◽

Arm Swing ◽

Coarse Grained Model ◽

Lever Arm

Myosin VI (MVI) is the only known member of the myosin superfamily that, upon dimerization, walks processively toward the pointed end of the actin filament. The leading head of the dimer directs the trailing head forward with a power stroke, a conformational change of the motor domain exaggerated by the lever arm. Using a unique coarse-grained model for the power stroke of a single MVI, we provide the molecular basis for its motility. We show that the power stroke occurs in two major steps. First, the motor domain attains the poststroke conformation without directing the lever arm forward; and second, the lever arm reaches the poststroke orientation by undergoing a rotational diffusion. From the analysis of the trajectories, we discover that the potential that directs the rotating lever arm toward the poststroke conformation is almost flat, implying that the lever arm rotation is mostly uncoupled from the motor domain. Because a backward load comparable to the largest interhead tension in a MVI dimer prevents the rotation of the lever arm, our model suggests that the leading-head lever arm of a MVI dimer is uncoupled, in accord with the inference drawn from polarized total internal reflection fluorescence (polTIRF) experiments. Without any adjustable parameter, our simulations lead to quantitative agreement with polTIRF experiments, which validates the structural insights. Finally, in addition to making testable predictions, we also discuss the implications of our model in explaining the broad step-size distribution of the MVI stepping pattern.

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Simulating the function of sodium/proton antiporters

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1516881112 ◽

2015 ◽

Vol 112 (40) ◽

pp. 12378-12383 ◽

Cited By ~ 14

Author(s):

Raphael Alhadeff ◽

Arieh Warshel

Keyword(s):

Conformational Changes ◽

Molecular Basis ◽

Molecular Level ◽

Structural Information ◽

Coarse Grained ◽

Charged State ◽

Transport Models ◽

Coarse Grained Model ◽

Effective Transport ◽

Molecular Origin

The molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function. This work explores the molecular origin of the function of the bacterial Na+/H+ antiporter NhaA by evaluating the energetics of the Na+ and H+ movement and then using the resulting landscape in Monte Carlo simulations that examine two transport models and explore which model can reproduce the relevant experimental results. The simulations reproduce the observed transport features by a relatively simple model that relates the protein structure to its transporting function. Focusing on the two key aspartic acid residues of NhaA, D163 and D164, shows that the fully charged state acts as an Na+ trap and that the fully protonated one poses an energetic barrier that blocks the transport of Na+. By alternating between the former and latter states, mediated by the partially protonated protein, protons, and Na+ can be exchanged across the membrane at 2:1 stoichiometry. Our study provides a numerical validation of the need of large conformational changes for effective transport. Furthermore, we also yield a reasonable explanation for the observation that some mammalian transporters have 1:1 stoichiometry. The present coarse-grained model can provide a general way for exploring the function of transporters on a molecular level.

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Molecular determinants of the interactions between proteins and ssDNA

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1416355112 ◽

2015 ◽

Vol 112 (16) ◽

pp. 5033-5038 ◽

Cited By ~ 18

Author(s):

Garima Mishra ◽

Yaakov Levy

Keyword(s):

Conformational Changes ◽

Protein Interactions ◽

Binding Pocket ◽

Dna Bases ◽

Coarse Grained ◽

Binding Modes ◽

Ssdna Binding ◽

Coarse Grained Model ◽

Molecular Determinants ◽

Ssdna Binding Proteins

ssDNA binding proteins (SSBs) protect ssDNA from chemical and enzymatic assault that can derail DNA processing machinery. Complexes between SSBs and ssDNA are often highly stable, but predicting their structures is challenging, mostly because of the inherent flexibility of ssDNA and the geometric and energetic complexity of the interfaces that it forms. Here, we report a newly developed coarse-grained model to predict the structure of SSB–ssDNA complexes. The model is successfully applied to predict the binding modes of six SSBs with ssDNA strands of lengths of 6–65 nt. In addition to charge–charge interactions (which are often central to governing protein interactions with nucleic acids by means of electrostatic complementarity), an essential energetic term to predict SSB–ssDNA complexes is the interactions between aromatic residues and DNA bases. For some systems, flexibility is required from not only the ssDNA but also, the SSB to allow it to undergo conformational changes and the penetration of the ssDNA into its binding pocket. The association mechanisms can be quite varied, and in several cases, they involve the ssDNA sliding along the protein surface. The binding mechanism suggests that coarse-grained models are appropriate to study the motion of SSBs along ssDNA, which is expected to be central to the function carried out by the SSBs.

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Searching for kinesin's mechanical amplifier

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2000.0586 ◽

2000 ◽

Vol 355 (1396) ◽

pp. 449-457 ◽

Cited By ~ 26

Author(s):

Ronald D. Vale ◽

Ryan Case ◽

Elena Sablin ◽

Cindy Hart ◽

Robert Fletterick

Keyword(s):

Amino Acids ◽

Conformational Changes ◽

Common Ancestor ◽

Atp Hydrolysis ◽

Power Stroke ◽

Catalytic Core ◽

Present Evidence ◽

Directional Motion ◽

Mechanical Element ◽

Mechanical Elements

Kinesin, a microtubule–based motor, and myosin, an actin–based motor, share a similar core structure, indicating that they arose from a common ancestor. However, kinesin lacks the long lever–arm domain that is believed to drive the myosin power stroke. Here, we present evidence that a much smaller region of ca . 10–40 amino acids serves as a mechanical element for kinesin motor proteins. These ‘neck regions’ are class conserved and have distinct structures in plus–end and minus–end–directed kinesin motors. Mutagenesis studies also indicate that the neck regions are involved in coupling ATP hydrolysis and energy into directional motion along the microtubule. We suggest that the kinesin necks drive motion by undergoing a conformational change in which they detach and re–dock onto the catalytic core during the ATPase cycle. Thus, kinesin and myosin have evolved unique mechanical elements that amplify small, nucleotide–dependent conformational changes that occur in their similar catalytic cores.

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Molecular mechanisms of the interhead coordination by interhead tension in cytoplasmic dyneins

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1806688115 ◽

2018 ◽

Vol 115 (40) ◽

pp. 10052-10057 ◽

Cited By ~ 6

Author(s):

Qian Wang ◽

Biman Jana ◽

Michael R. Diehl ◽

Margaret S. Cheung ◽

Anatoly B. Kolomeisky ◽

...

Keyword(s):

Binding Affinity ◽

Molecular Mechanisms ◽

Cytoplasmic Dynein ◽

Coarse Grained ◽

Cellular Transport ◽

Coarse Grained Model ◽

Detachment Rate ◽

The Moment ◽

Dynamics Simulations ◽

Molecular Picture

Cytoplasmic dyneins play a major role in retrograde cellular transport by moving vesicles and organelles along microtubule filaments. Dyneins are multidomain motor proteins with two heads that coordinate their motion via their interhead tension. Compared with the leading head, the trailing head has a higher detachment rate from microtubules, facilitating the movement. However, the molecular mechanism of such coordination is unknown. To elucidate this mechanism, we performed molecular dynamics simulations on a cytoplasmic dynein with a structure-based coarse-grained model that probes the effect of the interhead tension on the structure. The tension creates a torque that influences the head rotating about its stalk. The conformation of the stalk switches from the α registry to the β registry during the rotation, weakening the binding affinity to microtubules. The directions of the tension and the torque of the leading head are opposite to those of the trailing head, breaking the structural symmetry between the heads. The leading head transitions less often to the β registry than the trailing head. The former thus has a greater binding affinity to the microtubule than the latter. We measured the moment arm of the torque from a dynein structure in the simulations to develop a phenomenological model that captures the influence of the head rotating about its stalk on the differential detachment rates of the two heads. Our study provides a consistent molecular picture for interhead coordination via interhead tension.

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Communication between the AAA+ ring and microtubule-binding domain of dyneinThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process.

Biochemistry and Cell Biology ◽

10.1139/o09-127 ◽

2010 ◽

Vol 88 (1) ◽

pp. 15-21 ◽

Cited By ~ 21

Author(s):

Andrew P. Carter ◽

Ronald D. Vale

Keyword(s):

Conformational Changes ◽

Peer Review Process ◽

Coiled Coil ◽

Binding Domain ◽

Power Stroke ◽

Microtubule Binding ◽

Microtubule Motors ◽

Microtubule Binding Domain ◽

Mechanical Element ◽

Linker Domain

Dyneins are microtubule motors, the core of which consists of a ring of AAA+ domains. ATP-driven conformational changes of the AAA+ ring are used to drive the movement of a mechanical element (termed the linker domain) that provides the motor’s powerstroke and to change the affinity of the motor for microtubules (strong binding during the power stroke and weak binding to allow stepping and recocking of the linker domain). Dynein’s microtubule-binding domain (MTBD) is located at the end of a 10 nm long anti-parallel coiled coil (the stalk) and conformational changes that alter the affinity for microtubules must propagate through this coiled coil. A recent crystal structure of dynein’s MTBD sheds new light on how this long-range communication along a coiled coil might occur.

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A coarse-grained model of the expansion of the human rhinovirus 2 capsid reveals insights in genome release

Journal of The Royal Society Interface ◽

10.1098/rsif.2019.0044 ◽

2019 ◽

Vol 16 (157) ◽

pp. 20190044 ◽

Cited By ~ 1

Author(s):

Giuliana Indelicato ◽

Paolo Cermelli ◽

Reidun Twarock

Keyword(s):

Conformational Changes ◽

Minimum Energy ◽

Human Rhinovirus ◽

Coarse Grained ◽

Coarse Grained Model ◽

Transition Pathways ◽

Causative Agents ◽

The Common ◽

Minimum Energy Paths

Human rhinoviruses are causative agents of the common cold. In order to release their RNA genome into the host during a viral infection, these small viruses must undergo conformational changes in their capsids, whose detailed mechanism is strictly related to the process of RNA extrusion, which has been only partially elucidated. We study here a mathematical model for the structural transition between the native particle of human rhinovirus type 2 and its expanded form, viewing the process as an energy cascade, i.e. a sequence of metastable states with decreasing energy connected by minimum energy paths. We explore several transition pathways and discuss their implications for the RNA exit process.

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Kinematics of the Lever Arm Swing in Myosin VI

10.1101/078626 ◽

2016 ◽

Author(s):

M. L. Mugnai ◽

D. Thirumalai

Keyword(s):

Rotational Diffusion ◽

Quantitative Agreement ◽

Motor Domain ◽

Coarse Grained ◽

Power Stroke ◽

Myosin Vi ◽

Step Size ◽

Arm Swing ◽

Post Stroke ◽

Lever Arm

AbstractMyosin VI (MVI) is the only known member of the myosin superfamily that, upon dimerization, walks processively towards the pointed end of the actin filament. The leading head of the dimer directs the trailing head forward with a power stroke, a conformational change of the motor domain exaggerated by the lever arm. Using a new coarse-grained model for the power stroke of a single MVI, we provide the molecular basis for its motility. We show that the power stroke occurs in two major steps: first, the motor domain attains the post-stroke conformation without directing the lever arm forward; second, the lever arm reaches the post-stroke orientation by undergoing a rotational diffusion. From the analysis of the trajectories, we discover that the potential that directs the rotating lever arm towards the post-stroke conformation is almost flat, implying that the lever arm rotation is mostly un-coupled from the motor domain. Because a backward load comparable with the largest inter-head tension in a MVI dimer prevents the rotation of the lever arm, our model suggests that the leading-head lever arm of a MVI dimer is uncoupled, in accord with the inference drawn from polarized Total Internal Reflection Fluorescence (polTIRF) experiments. Our simulations are in quantitative agreement with polTIRF experiments, which validates our structural insights. Finally, we discuss the implications of our model in explaining the broad step-size distribution of MVI stepping pattern, and we make testable predictions.

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Multi-Scale Coarse Grained Model for the Stepping of Molecular Motors with application to Kinesin.

10.1101/2021.04.05.438476 ◽

2021 ◽

Author(s):

Yonathan Y Goldtzvik ◽

D Thirumalai

Keyword(s):

Molecular Motors ◽

Interaction Strength ◽

Accurate Method ◽

Significant Loss ◽

Coarse Grained ◽

Power Stroke ◽

Coarse Grained Model ◽

Multi Scale ◽

Walking Mechanism ◽

Conventional Kinesin

Conventional kinesin, a motor protein that transports cargo within cells, walks by taking multiple steps towards the plus end of the microtubule (MT). While significant progress has been made in understanding the details of the walking mechanism of kinesin there are many unresolved issues. From a computational perspective, a central challenge is the large size of the system, which limits the scope of time scales accessible in standard computer simulations. Here, we create a general multi-scale coarse-grained model for motors that enables us to simulate the stepping process of motors on polar tracks (actin and MT) with focus on kinesin. Our approach greatly shortens the computation times without a significant loss in detail, thus allowing us to better describe the molecular basis of the stepping kinetics. The small number of parameters, which are determined by fitting to experimental data, allows us to develop an accurate method that may be adopted to simulate stepping in other molecular motors. The model enables us to simulate a large number of steps, which was not possible previously. We show in agreement with experiments that due to the docking of the neck linker (NL) of kinesin, sometimes deemed as the power stroke, the space explored diffusively by the tethered head is severely restricted allowing the step to be in a tens of microseconds. We predict that increasing the interaction strength between the NL and the motor head, achievable by mutations in the NL, decreases the stepping time but reaches a saturation value. Furthermore, the full 3-dimensional dynamics of the cargo are fully resolved in our model, contributing to the predictive power and allowing us to study the important aspects of cargo-motor interactions.

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