Biochemistry. Processive motor movement

Direct observation of intermediate states during the stepping motion of kinesin-1

The dimeric motor protein kinesin-1 walks along microtubules by alternatingly hydrolyzing ATP and moving two motor domains ('heads'). Nanometer-precision single-molecule studies demonstrated that kinesin takes regular 8-nm steps upon hydrolysis of each ATP; however, the intermediate states between steps have not been directly visualized. Here, we employed high-temporal resolution dark-field microscopy to directly visualize the binding and unbinding of kinesin heads to or from microtubules during processive movement. Our observations revealed that upon unbinding from microtubules, the labeled heads were displaced rightward and underwent tethered diffusive movement. Structural and kinetic analyses of wild-type and mutant kinesins with altered neck linker lengths provided evidence that rebinding of the unbound head to the rear-binding site is prohibited by a tension increase in the neck linker and that ATP hydrolysis by the leading head is suppressed when both heads are bound to the microtubule, thereby explaining how the two heads coordinate to move in a hand-over-hand manner.

The neck linker of kinesin 1 seems optimally designed to approach the largest stepping velocity: a simulation study of an ideal model

The neck linker is widely believed to play a critical role in the hand-over-hand walking of conventional kinesin 1. Experiments have shown that change of the neck linker length will significantly change the stepping velocity of the motor. In this paper, we studied this length effect based on a highly simplified chemically powered ratchet model. In this model, we assume that the chemical steps (ATP hydrolysis, ADP and P(i) release, ATP binding, neck linker docking) are fast enough under conditions far from equilibrium and the mechanical steps (detachment, diffusional search and re-attachment of the free head) are rate-limiting in kinesin walking. According to this model, and regarding the neck linker as a worm-like-chain polypeptide, we can calculate the steady state stepping velocity of the motor for different neck linker lengths. Our results show, under the actual values of binding energy between kinesin head and microtubule (~15k(B)T) and the persistence length of neck linker (~0.5 nm), that there is an optimal neck linker length (~14-16 a.a.) corresponding to the maximal velocity, which implies that the length of the wild-type neck linker (~15 a.a.) might be optimally designed for kinesin 1 to approach the largest stepping velocity.

Permanent electric dipole moments of carboxyamides in condensed media: what are the limitations of theory and experiment?

Electrostatic properties of proteins are crucial for their functionality. Carboxyamides are small polar groups that, as peptide bonds, are principal structural components of proteins that govern their electrostatic properties. We investigated the medium dependence of the molar polarization and of the permanent dipole moments of amides with different state of alkylation. The experimentally measured and theoretically calculated dipole moments manifested a solvent dependence that increased with the increase in the media polarity. We ascribed the observed enhancement of the amide polarization to the reaction fields in the solvated cavities. Chloroform, for example, caused about a 25% increase in the amide dipole moments determined for vacuum, as the experimental and theoretical results demonstrated. Another chlorinated solvent, 1,1,2,2-tetrachloroethane, however, caused an "abnormal" increase in the experimentally measured amide dipoles, which the theoretical approaches we used could not readily quantify. We showed and discussed alternatives for addressing such discrepancies between theory and experiment.

Structure and dynamics of the kinesin-microtubule interaction revealed by fluorescence polarization microscopy

Fluorescence polarization microscopy (FPM) is the analysis of the polarization of light in a fluorescent microscope in order to determine the angular orientation and rotational mobility of fluorescent molecules. Key advantages of FPM, relative to other structural analysis techniques, are that it allows the detection of conformational changes of fluorescently labeled macromolecules in real time in physiological conditions and at the single-molecule level. In this chapter we describe in detail the FPM experimental set-up and analysis methods we have used to investigate structural intermediates of the motor protein kinesin-1 associated with its walking mechanism along microtubules. We also briefly describe additional FPM methods that have been used to investigate other macromolecular complexes.

Strain through the neck linker ensures processive runs: a DNA-kinesin hybrid nanomachine study

The motor protein kinesin has two heads and walks along microtubules processively using energy derived from ATP. However, how kinesin heads are coordinated to generate processive movement remains elusive. Here we created a hybrid nanomachine (DNA-kinesin) using DNA as the skeletal structure and kinesin as the functional module. Single molecule imaging of DNA-kinesin hybrid allowed us to evaluate the effects of both connect position of the heads (N, C-terminal or Mid position) and sub-nanometer changes in the distance between the two heads on motility. Our results show that although the native structure of kinesin is not essential for processive movement, it is the most efficient. Furthermore, forward bias by the power stroke of the neck linker, a 13-amino-acid chain positioned at the C-terminus of the head, and internal strain applied to the rear of the head through the neck linker are crucial for the processive movement. Results also show that the internal strain coordinates both heads to prevent simultaneous detachment from the microtubules. Thus, the inter-head coordination through the neck linker facilitates long-distance walking.

Alternating-site mechanism of kinesin-1 characterized by single-molecule FRET using fluorescent ATP analogues

Kinesin-1 motor proteins move along microtubules in repetitive steps of 8 nm at the expense of ATP. To determine nucleotide dwell times during these processive runs, we used a Förster resonance energy transfer method at the single-molecule level that detects nucleotide binding to kinesin motor heads. We show that the fluorescent ATP analog used produces processive motility with kinetic parameters altered <2.5-fold compared with normal ATP. Using our confocal fluorescence kinesin motility assay, we obtained fluorescence intensity time traces that we then analyzed using autocorrelation techniques, yielding a time resolution of approximately 1 ms for the intensity fluctuations due to fluorescent nucleotide binding and release. To compare these experimental autocorrelation curves with kinetic models, we used Monte-Carlo simulations. We find that the experimental data can only be described satisfactorily on the basis of models assuming an alternating-site mechanism, thus supporting the view that kinesin's two motor domains hydrolyze ATP and step in a sequential way.

Basic mechanisms for recognition and transport of synaptic cargos

Synaptic cargo trafficking is essential for synapse formation, function and plasticity. In order to transport synaptic cargo, such as synaptic vesicle precursors, mitochondria, neurotransmitter receptors and signaling proteins to their site of action, neurons make use of molecular motor proteins. These motors operate on the microtubule and actin cytoskeleton and are highly regulated so that different cargos can be transported to distinct synaptic specializations at both pre- and post-synaptic sites. How synaptic cargos achieve specificity, directionality and timing of transport is a developing area of investigation. Recent studies demonstrate that the docking of motors to their cargos is a key control point. Moreover, precise spatial and temporal regulation of motor-cargo interactions is important for transport specificity and cargo recruitment. Local signaling pathways - Ca2+ influx, CaMKII signaling and Rab GTPase activity - regulate motor activity and cargo release at synaptic locations. We discuss here how different motors recognize their synaptic cargo and how motor-cargo interactions are regulated by neuronal activity.

Properties of tug-of-war model for cargo transport by molecular motors

Molecular motors are essential components for the biophysical functions of the cell. Current quantitative understanding of how multiple motors move along a single track is not complete, even though models and theories for a single motor mechanochemistry abound. Recently, Müller et al. have developed a tug-of-war model to describe the bidirectional movement of the cargo [Proc. Natl. Acad. Sci. U.S.A. 105, 4609 (2008)]. They found that the tug-of-war model exhibits several qualitative different motility regimes, which depend on the precise value of single motor parameters, and they suggested that the sensitivity can be used by a cell to regulate its cargo traffic. In the present paper, we will carry out a detailed theoretical analysis of a special case of tug-of-war model: in which the numbers of the two different motor species which bound to the cargo tend to infinite. Through the analysis, all the stable, i.e., biophysically observable, steady states and their stability domains can be obtained. Depending on values of the several parameters, the tug-of-war model exhibits uni-, bi-, or tristability. The steady-state movement of the cargo, which is transported by two different molecular motor species, is determined by the initial numbers of the motors which bound to the track.

A mobile kinesin-head intermediate during the ATP-waiting state

Kinesin1 is a motor protein that uses the energy from ATP hydrolysis to move intracellular cargoes along microtubules. It contains 2 identical motor domains, or heads, that coordinate their mechano-chemical cycles to move processively along microtubules. The molecular mechanism of coordination between head domains remains unclear, partly because of the lack of structural information on critical intermediates of the kinesin1 mechano-chemical cycle. A point of controversy has been whether before ATP binding, in the so called ATP-waiting state, 1 or 2 motor domains are bound to the microtubule. To address this issue, here we use ensemble and single molecule fluorescence polarization microscopy (FPM) to determine the mobility and orientation of the kinesin1 heads at different ATP concentrations and in heterodimeric constructs with microtubule binding impaired in 1 head. We found evidence for a mobile head during the ATP-waiting state. We incorporate our results into a model for kinesin translocation that accounts well for many reported experimental results.

Kinesin's walk: springy or gated head coordination?

Conventional kinesin (kinesin-1) is a motor protein that performs a vital function in the eukaryotic cell: it actively transports cargo to required destinations. Kinesin pulls cargo along microtubule tracks using twin linked motor domains (heads) that bind the microtubule, hydrolyse ATP, and alternately step forward. The detail of the kinesin walk has yet to be discovered but a prominent theory is that the mechanism is rectified Brownian motion (RBM) biased by linker zippering. There is evidence that an ATP binding gate coordinates the heads. The hypothesis proposed here is that the gate is unnecessary, that entropic linker strain is sufficient to enable procession. An agent-based computer simulation has been devised to explore head coordination in the RBM model. Walking was found to emerge in silico without a gate to synchronise the heads. Further investigation of the model by applying a range of hindering loads resulted in backstepping or detachment with similar characteristics to behaviour observed in vitro. It is unclear whether kinesin waits at an obstacle but adding an ATP hydrolysis gate to the model in order to force waiting resulted in the model behaving less realistically under load. It is argued here that an RBM model free of gating is a good candidate for explaining kinesin procession.

Intramolecular strain coordinates kinesin stepping behavior along microtubules

Kinesin advances 8 nm along a microtubule per ATP hydrolyzed, but the mechanism responsible for coordinating the enzymatic cycles of kinesin's two identical motor domains remains unresolved. Here, we have tested whether such coordination is mediated by intramolecular tension generated by the "neck linkers," mechanical elements that span between the motor domains. When tension is reduced by extending the neck linkers with artificial peptides, the coupling between ATP hydrolysis and forward stepping is impaired and motor's velocity decreases as a consequence. However, speed recovers to nearly normal levels when external tension is applied by an optical trap. Remarkably, external load also induces bidirectional stepping of an immotile kinesin that lacks its mechanical element (neck linker) and fuel (ATP). Our results indicate that the kinesin motor domain senses and responds to strain in a manner that facilitates its plus-end-directed stepping and communication between its two motor domains.

Processive movement by a kinesin heterodimer with an inactivating mutation in one head

A single molecule of the motor enzyme kinesin-1 keeps a tight grip on its microtubule track, making tens or hundreds of discrete, unidirectional 8 nm steps before dissociating. This high duty ratio processive movement is thought to require a mechanism in which alternating stepping of the two head domains of the kinesin dimer is driven by alternating, overlapped cycles of ATP hydrolysis by the two heads. The R210K point mutation in Drosophila kinesin heavy chain was reported to disrupt the ability of the enzyme active site to catalyze ATP P-O bond cleavage. We expressed R210K homodimers as well as isolated R210K heads and confirmed that both are essentially inactive. We then coexpressed tagged R210K subunits with untagged wild-type subunits and affinity purified R210K/wild-type heterodimers together with the inactive R210K homodimers. In contrast to the R210K head or homodimer, the heterodimer was a highly active (>50% of wild-type) microtubule-stimulated ATPase, and the heterodimer displayed high duty ratio processive movement in single-molecule motility experiments. Thus, dimerization of a subunit containing the inactivating mutation with a functional subunit can complement the mutation; this must occur either by lowering or by bypassing kinetic barriers in the ATPase or mechanical cycles of the mutant head. The observations provide support for kinesin-1 gating mechanisms in which one head stimulates the rate of essential processes in the other.

A cool look at the structural changes in kinesin motor domains

Recently, several 3D images of kinesin-family motor domains interacting with microtubules have been obtained by analysis of electron microscope images of frozen hydrated complexes at much higher resolutions (9-12 A) than in previous reports (15-30 A). The high-resolution maps show a complex interaction interface between kinesin and tubulin, in which kinesin's switch II helix alpha4 is a central feature. Differences due to the presence of ADP, as compared with ATP analogues, support previously determined crystal structures of kinesins alone in suggesting that alpha4 is part of a pathway linking the nucleotide-binding site and the neck that connects to cargo. A 3D structure of the microtubule-bound Kar3 motor domain in a nucleotide-free state has revealed dramatic changes not yet reported for any crystal structure, including melting of the switch II helix, that may be part of the mechanism by which information is transmitted. A nucleotide-dependent movement of helix alpha6, first seen in crystal structures of Kif1a, appears to bring it into contact with tubulin and may provide another communication link. A microtubule-induced movement of loop L7 and a related distortion of the central beta-sheet, detected only in the empty state, may also send a signal to the region of the motor core that interacts with the neck. Earlier images of a kinesin-1 dimer in the empty state, showing a close interaction between the two motor heads, can now be interpreted in terms of a communication route from the active site of the directly bound head via its central beta-sheet to the tethered head.

Kinesin steps do not alternate in size

Kinesin is a two-headed motor protein that transports cargo inside cells by moving stepwise on microtubules. Its exact trajectory along the microtubule is unknown: alternative pathway models predict either uniform 8-nm steps or alternating 7- and 9-nm steps. By analyzing single-molecule stepping traces from "limping" kinesin molecules, we were able to distinguish alternate fast- and slow-phase steps and thereby to calculate the step sizes associated with the motions of each of the two heads. We also compiled step distances from nonlimping kinesin molecules and compared these distributions against models predicting uniform or alternating step sizes. In both cases, we find that kinesin takes uniform 8-nm steps, a result that strongly constrains the allowed models.

How kinesin waits between steps

Kinesin-1 (conventional kinesin) is a dimeric motor protein that carries cellular cargoes along microtubules by hydrolysing ATP and moving processively in 8-nm steps. The mechanism of processive motility involves the hand-over-hand motion of the two motor domains ('heads'), a process driven by a conformational change in the neck-linker domain of kinesin. However, the 'waiting conformation' of kinesin between steps remains controversial-some models propose that kinesin adopts a one-head-bound intermediate, whereas others suggest that both the kinesin heads are bound to adjacent tubulin subunits. Addressing this question has proved challenging, in part because of a lack of tools to measure structural states of the kinesin dimer as it moves along a microtubule. Here we develop two different single-molecule fluorescence resonance energy transfer (smFRET) sensors to detect whether kinesin is bound to its microtubule track by one or two heads. Our FRET results indicate that, while moving in the presence of saturating ATP, kinesin spends most of its time bound to the microtubule with both heads. However, when nucleotide binding becomes rate-limiting at low ATP concentrations, kinesin waits for ATP in a one-head-bound state and makes brief transitions to a two-head-bound intermediate as it walks along the microtubule. On the basis of these results, we suggest a model for how transitions in the ATPase cycle position the two kinesin heads and drive their hand-over-hand motion.