scholarly journals 3P166 Free energy simulations for the conformational change of the αβ subunits in F_1-ATPase after the ATP hydrolysis(11. Molecular motor,Poster)

2013 ◽  
Vol 53 (supplement1-2) ◽  
pp. S239
Author(s):  
Yuko Ito ◽  
Mitsunori Ikeguchi
Keyword(s):  
Free Energy ◽  
Conformational Change ◽  
Atp Hydrolysis ◽  
Molecular Motor ◽  
Energy Simulations

scholarly journals Coupling of ATPase activity, microtubule binding and mechanics in the dynein motor domain

2018 ◽  
Author(s):  
Stefan Niekamp ◽  
Nicolas Coudray ◽  
Nan Zhang ◽  
Ronald D. Vale ◽  
Gira Bhabha
Keyword(s):  
Atpase Activity ◽  
Conformational Change ◽  
Conformational Changes ◽  
Large Scale ◽  
Atp Hydrolysis ◽  
Molecular Motor ◽  
Coiled Coil ◽  
Microtubule Binding ◽  
Dynein Motor ◽  
In The Wild

The movement of a molecular motor protein along a cytoskeletal track requires communication between enzymatic, polymer-binding, and mechanical elements. Such communication is particularly complex and not well understood in the dynein motor, an ATPase that is comprised of a ring of six AAA domains, a large mechanical element (linker) spanning over the ring, and a microtubule-binding domain (MTBD) that is separated from the AAA ring by a ~135 Å coiled-coil stalk. We identified mutations in the stalk that disrupt directional motion, have microtubule-independent hyperactive ATPase activity, and nucleotide-independent low affinity for microtubules. Cryo-electron microscopy structures of a mutant that uncouples ATPase activity from directional movement reveal that nucleotide-dependent conformational changes occur normally in one half of the AAA ring, but are disrupted in the other half. The large-scale linker conformational change observed in the wild-type protein is also inhibited, revealing that this conformational change is not required for ATP hydrolysis. These results demonstrate an essential role of the stalk in regulating motor activity and coupling conformational changes across the two halves of the AAA ring.

scholarly journals Diverse stepping motions of cytoplasmic dynein revealed by kinetic modeling

2019 ◽  
Author(s):  
Shintaroh Kubo ◽  
Tomohiro Shima ◽  
Shoji Takada
Keyword(s):  
Experimental Data ◽  
Monte Carlo ◽  
Free Energy ◽  
Kinetic Model ◽  
Monte Carlo Simulations ◽  
Molecular Mechanisms ◽  
Atp Hydrolysis ◽  
Molecular Motor ◽  
Cytoplasmic Dynein ◽  
Power Stroke

AbstractCytoplasmic dynein is a two-headed molecular motor that moves to the minus end of microtubule (MT) using ATP hydrolysis free energy. By employing its two heads (motor domains), cytoplasmic dynein shows various bipedal stepping motions; the inchworm and hand-over-hand motions, as well as non-alternate steps of one head. However, the molecular basis to achieve such diverse stepping manners remains obscure. Here, we propose a kinetic model for bipedal motions of cytoplasmic dynein and performed Gillespie Monte Carlo simulations that reproduces most experimental data obtained to date. The model represents status of each motor domain as five states according to conformations, nucleotide- and MT-binding conditions of the domain. Also, the relative positions of the two domains were approximated by three discrete states. Accompanied by ATP hydrolysis cycles, the model dynein stochastically and processively moved forward in multiple steps via diverse pathways, including inchworm and hand-over-hand motions, same as experimental data. The model reproduced key experimental motility-related parameters including velocity and run-length as functions of ATP concentration and external force. Our model reveals that, in a typical inchworm motion, the leading domain moves via the ATP-dependent power-stroke of the linker coupled with a small change in the stalk angle, whereas the lagging domain moves via diffusion dragged by the leading domain. Moreover, the hand-over-hand motion in the model dynein clearly differs from that of kinesin by the usage of the power-stroke.Author SummaryCytoplasmic dynein is a two-headed molecular motor, which moves linearly and transports intra-cellar organelles along microtubules driven by ATP hydrolysis free energy. In contrast to other better-known molecular motors, such as kinesin, dynein is known to take various stepping motions including motions akin to human walking and inchworm-like motions. However, molecular mechanisms underpinning the diverse stepping motions are unclear. Here, based on recent high-resolution structure information and single-molecule motility assay data, we designed a kinetic model that explicitly include two heads, each of which makes ATP hydrolysis cycles and moves along the microtubules. Using the model, we performed Monte Carlo simulations. The simulation reproduced most of currently available experimental results. More importantly, the simulation suggested molecular mechanisms of various stepping motions. While stepping motions apparently resemble to those proposed before, once looking into details, we found the resulting mechanisms distinct from previously proposed ones in the usage of ATP and protein conformation changes coupled with stepping motions.

scholarly journals A rotary molecular motor that can work at near 100% efficiency

2000 ◽  
Vol 355 (1396) ◽  
pp. 473-489 ◽  
Author(s):  
Kazuhiko Kinosita ◽  
Ryohei Yasuda ◽  
Hiroyuki Noji ◽  
Kengo Adachi
Keyword(s):  
Free Energy ◽  
Actin Filament ◽  
Single Molecule ◽  
High Efficiency ◽  
Atp Hydrolysis ◽  
Molecular Motor ◽  
Constant Torque ◽  
Γ Subunit ◽  
Work Done

A single molecule of F 1 –ATPase is by itself a rotary motor in which a central γ–subunit rotates against a surrounding cylinder made of α 3 β 3 –subunits. Driven by the three βs that sequentially hydrolyse ATP, the motor rotates in discrete 120° steps, as demonstrated in video images of the movement of an actin filament bound, as a marker, to the central γ–subunit. Over a broad range of load (hydrodynamic friction against the rotating actin filament) and speed, the F motor produces a constant torque of ca . 40 pN nm. The work done in a 120° step, or the work per ATP molecule, is thus ca . 80 pN nm. In cells, the free energy of ATP hydrolysis is ca . 90 pN nm per ATP molecule, suggesting that the F 1 motor can work at near 100% efficiency. We confirmed in vitro that F 1 indeed does ca . 80 pN nm of work under the condition where the free energy per ATP is 90 pN nm. The high efficiency may be related to the fully reversible nature of the F 1 motor: the ATP synthase, of which F 1 is a part, is considered to synthesize ATP from ADP and phosphate by reverse rotation of the F motor. Possible mechanisms of F 1 rotation are discussed.

Prediction of Alkanolamine pKa Values by Combined Molecular Dynamics Free Energy Simulations and ab initio Calculations

2019 ◽  
Author(s):  
Javad Noroozi ◽  
William Smith
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio Calculations ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Phase Reaction ◽  
Pka Values ◽  
Gas Phase Reaction ◽  
Reaction Free Energy ◽  
Energy Simulations

We use molecular dynamics free energy simulations in conjunction with quantum chemical calculations of gas phase reaction free energy to predict alkanolamines pka values. <br>

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