The origin of minus-end directionality and mechanochemistry of Ncd motors

Effects of Gold Nanoparticles on the Stepping Trajectories of Kinesin

A substantial increase in the temporal resolution of the stepping of dimeric molecular motors is possible by tracking the position of a large gold nanoparticle (GNP) attached to a labeled site on one of the heads. This technique was employed to measure the stepping trajectories of conventional kinesin (Kin1) using the time-dependent position of the GNP as a proxy. The trajectories revealed that the detached head always passes to the right of the head that is tightly bound to the microtubule (MT) during a step. In interpreting the results of such experiments, it is assumed that the GNP does not significantly alter the diffusive motion of the detached head. We used coarse-grained simulations of a system consisting of the MT-Kin1 complex with and without attached GNP to investigate how the stepping trajectories are affected. The two significant findings are: (1) The GNP does not faithfully track the position of the stepping head, and (2) the rightward bias is typically exaggerated by the GNP. Both these findings depend on the precise residue position to which the GNP is attached. Surprisingly, the stepping trajectories of kinesin are not significantly affected if, in addition to the GNP, a 1 μm diameter cargo is attached to the coiled coil. Our simulations suggest the effects of the large probe have to be considered when inferring the stepping mechanisms using GNP tracking experiments.

Computational modeling of dynein motor proteins at work

Along with various experimental methods, a combination of theoretical and computational methods is essential to explore different length-scale and time-scale processes in the biological system. The functional mechanism of a dynein, an ATP-fueled motor protein, working in a multiprotein complex, involves a wide range of length/time-scale events. It generates mechanical force from chemical energy and moves on microtubules towards the minus end direction while performing a large number of biological processes including ciliary beating, intracellular material transport, and cell division. Like in the cases of other conventional motor proteins, a combination of experimental techniques including X-crystallography, cryo-electron microscopy, and single molecular assay have provided a wealth of information about the mechanochemical cycle of a dynein. Dyneins have a large and complex structural architecture and therefore, computational modeling of different aspects of a dynein is extremely challenging. As the process of dynein movement involves varying length and timescales, it demands, like in experiments, a combination of computational methods covering such a wide range of processes for the comprehensive investigation of the mechanochemical cycle. In this review article, we will summarize how the use of state-of-the-art computational methods can provide a detailed molecular understanding of the mechanochemical cycle of the dynein. We implemented all-atom molecular dynamics simulations and hybrid quantum-mechanics/molecular-mechanics simulations to explore the ATP hydrolysis mechanisms at the primary ATPase site (AAA1) of dynein. To investigate the large-scale conformational changes we employed coarse-grained structure-based molecular dynamics simulations to capture the domain motions. Here we explored the conformational changes upon binding of ATP at AAA1, nucleotide state-dependent regulation of the mechanochemical cycle, and inter-head coordination by inter-head tension. Additionally, implementing a phenomenological theoretical model we explore the force-dependent detachment rate of a motorhead from the microtubule and the principle of multi-dynein cooperation during cargo transport.

Mechanistic basis of propofol-induced disruption of kinesin processivity

Propofol is a widely used general anesthetic to induce and maintain anesthesia, and its effects are thought to occur through impact on the ligand-gated channels including the GABA_A receptor. Propofol also interacts with a large number of proteins including molecular motors and inhibits kinesin processivity, resulting in significant decrease in the run length for conventional kinesin-1 and kinesin-2. However, the molecular mechanism by which propofol achieves this outcome is not known. The structural transition in the kinesin neck-linker region is crucial for its processivity. In this study, we analyzed the effect of propofol and its fluorine derivative (fropofol) on the transition in the neck-linker region of kinesin. Propofol binds at two crucial surfaces in the leading head: one at the microtubule-binding interface and the other in the neck-linker region. We observed in both the cases the order-disorder transition of the neck-linker was disrupted and kinesin lost its signal for forward movement. In contrast, there was not an effect on the neck-linker transition with propofol binding at the trailing head. Free-energy calculations show that propofol at the microtubule-binding surface significantly reduces the microtubule-binding affinity of the kinesin head. While propofol makes pi-pi stacking and H-bond interactions with the propofol binding cavity, fropofol is unable to make a suitable interaction at this binding surface. Therefore, the binding affinity of fropofol is much lower compared to propofol. Hence, this study provides a mechanism by which propofol disrupts kinesin processivity and identifies transitions in the ATPase stepping cycle likely affected.

Dynamic Asymmetry Exposes 2019-nCoV Prefusion Spike

The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this study, a symmetry-information-loaded structure-based Hamiltonian is developed using recent Cryo-EM structural data to explore the complete conformational energy landscape of the full-length prefusion spike protein. The study finds the 2019-nCoV prefusion spike to adopt a unique strategy by undertaking a dynamic conformational asymmetry that results in two prevalent asymmetric structures of spike where one or two spike heads rotate up to provide better exposure to the host-cell receptor. A few unique interchain interactions are identified at the interface of closely associated N-terminal domain (NTD) and receptor binding domain (RBD) playing a crucial role in the thermodynamic stabilization of the up conformation of the RBD in the case of the 2019-nCoV spike. The interaction-level information decoded in this study may provide deep insight into developing effective therapeutic targets.

Role of AAA3 Domain in Allosteric Communication of Dynein Motor Proteins

Cytoplasmic dynein, an AAA+ motif containing motor, generates force and movement along the microtubule to execute important biological functions including intracellular material transport and cell division by hydrolyzing ATP. Among the six AAA+ domains, AAA1 is the primary ATPase site where a single ATP hydrolysis generates a single step. Nucleotide states in AAA3 gate dynein's activity, suggesting that AAA3 acts as a regulatory switch. However, the comprehensive structural perspective of AAA3 in dynein's mechanochemical cycle remains unclear. Here, we explored the allosteric transition path of dynein involving AAA3 using a coarse-grained structure-based model. ATP binding to the AAA1 domain creates a cascade of conformational changes through the other domains of the ring, which leads to the pre-power stroke formation. The linker domain, which is the mechanical element of dynein, shifts from a straight to a bent conformation during this process. In our present study, we observe that AAA3 gates the allosteric communication from AAA1 to the microtubule binding domain (MTBD) through AAA4 and AAA5. The MTBD is linked to the AAA+ ring via a coiled-coil stalk and a buttress domain, which are extended from AAA4 and AAA5, respectively. Further analysis also uncovers the role of AAA3 in the linker movement. The free energy calculation shows that the linker prefers the straight conformation when AAA3 remains in the ATP-bound condition. As AAA3 restricts the motion of AAA4 and AAA5, the linker/AAA5 interactions get stabilized, and the linker cannot move to the pre-power stroke state that halts the complete structural transition required for the mechanochemical cycle. Therefore, we suggest that AAA3 governs dynein's mechanochemical cycle and motility by controlling the AAA4 and AAA5 domains that further regulate the linker movement and the power stroke formation.

Interactions between motor domains in kinesin-14 Ncd - a molecular dynamics study

Minus-end directed, non-processive kinesin-14 Ncd is a dimeric protein with C-terminally located motor domains (heads). Generation of the power-stroke by Ncd consists of a lever-like rotation of a long superhelical 'stalk' segment while one of the kinesin's heads is bound to the microtubule. The last ∼30 amino acids of Ncd head play a crucial but still poorly understood role in this process. Here, we used accelerated molecular dynamics simulations to explore the conformational dynamics of several systems built upon two crystal structures of Ncd, the asymmetrical T436S mutant in pre-stroke/post-stroke conformations of two partner subunits and the symmetrical wild-type protein in pre-stroke conformation of both subunits. The results revealed a new conformational state forming following the inward motion of the subunits and stabilized with several hydrogen bonds to residues located on the border or within the C-terminal linker, i.e. a modeled extension of the C-terminus by residues 675-683. Forming of this new, compact Ncd conformation critically depends on the length of the C-terminus extending to at least residue 681. Moreover, the associative motion leading to the compact conformation is accompanied by a partial lateral rotation of the stalk. We propose that the stable compact conformation of Ncd may represent an initial state of the working stroke.

Investigating role of conformational changes of microtubule in regulating its binding affinity to kinesin by all-atom molecular dynamics simulation

Changes of affinity of kinesin head to microtubule regulated by changes in the nucleotide state are essential to processive movement of kinesin on microtubule. Here, using all-atom molecular dynamics simulations we show that besides the nucleotide state, large conformational changes of microtubule-tubulin heterodimers induced by strong interaction with the head in strongly binding state are also indispensable to regulate the affinity of the head to the tubulin. In strongly binding state the high affinity of the head to microtubule arises largely from mutual conformational changes of the microtubule and head induced by the specific interaction between them via an induced-fit mechanism. Moreover, the ADP-head has a much weaker affinity to the local microtubule-tubulin, whose conformation is largely altered by the interaction with the head in strongly binding state, than to other unperturbed tubulins. This indicates that upon Pi release the ADP-head temporarily has a much weaker affinity to the local tubulin than to other tubulins.

Structural consequences of hereditary spastic paraplegia disease-related mutations in kinesin

A wide range of mutations in the kinesin motor Kif5A have been linked to a neuronal disorder called hereditary spastic paraplegia (HSP). The position of these mutations can vary, and a range of different motile behaviors have been observed, indicating that the HSP mutants can alter distinct aspects of kinesin mechanochemistry. While focusing on four key HSP-associated mutants, this study examined the structural and dynamic perturbations that arise from these mutations using a series of different computational methods, ranging from bioinformatics analyses to all-atom simulations, that account for solvent effects explicitly. We show that two catalytic domain mutations (R280S and K253N) reduce the microtubule (MT) binding affinity of the kinesin head domains appreciably, while N256S has a much smaller impact. Bioinformatics analysis suggests that the stalk mutation A361V perturbs motor dimerization. Subsequent integration of these effects into a coarse-grained structure-based model of dimeric kinesin revealed that the order-disorder transition of the neck linker is substantially affected, indicating a hampered directionality and processivity of kinesin. The present analyses therefore suggest that, in addition to kinesin-MT binding and coiled-coil dimerization, HSP mutations affecting motor stepping transitions and processivity can lead to disease.

Simulations Reveal Multiple Intermediates in the Unzipping Mechanism of Neuronal SNARE Complex

The assembling of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor protein complex is a fundamental step in neuronal exocytosis, and it has been extensively studied in the last two decades. Yet, many details of this process remain inaccessible with the current experimental space and time resolution. Here, we study the zipping mechanism of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor complex computationally by using a coarse-grained model. We explore the different pathways available and analyze their dependence on the computational model employed. We reveal and characterize multiple intermediate states, in agreement with previous experimental findings. We use our model to analyze the influence of single-residue mutations on the thermodynamics of the folding process.

Mechanochemical Model of the Power Stroke of the Single-Headed Motor Protein KIF1A

During the process of ATP binding to an apo-kinesin microtubule (MT), the kinesin core rotates on the MT, and the neck linker (NL) of the kinesin undergoes an undocked to docked transition. This has been suggested to be a power stroke of kinesin, on the basis of the structural analysis. Here, we developed a mesoscopic structure-based model and studied the power stroke of KIF1A. We quantified the underlying free energy landscape and showed the emergence of several states for the power stroke of KIF1A: UB-UR-UD (unbound, unrotating, undock), B-IR-UD (bound, initial rotating, undock), B-PR-UD (bound, partial rotating, undock), and B-R-D (bound, rotating, dock). We found that ATP binding triggered conformational fluctuations of key elements. We also explored the conformational change of key structural elements during the rotation of KIF1A and docking of the NL. In addition, we semiquantitatively and qualitatively estimated the free energy released by the ATP binding, and how much of this remains for the docking of the NL during the power stroke process at different temperatures. Finally, based on results from the thermodynamics landscape and conformational change of structural key elements, we proposed a mechanochemical model of the power stroke of KIF1A.

Energetic Costs, Precision, and Transport Efficiency of Molecular Motors

An efficient molecular motor would deliver cargo to the target site at a high speed and in a punctual manner while consuming a minimal amount of energy. According to a recently formulated thermodynamic principle, referred to as the thermodynamic uncertainty relation, the travel distance of a motor and its variance are, however, constrained by the free energy being consumed. Here we use the principle underlying the uncertainty relation to quantify the transport efficiency of molecular motors for varying ATP concentration ([ATP]) and applied load (f). Our analyses of experimental data find that transport efficiencies of the motors studied here are semioptimized under the cellular condition. The efficiency is significantly deteriorated for a kinesin-1 mutant that has a longer neck-linker, which underscores the importance of molecular structure. It is remarkable to recognize that, among many possible directions for optimization, biological motors have evolved to optimize the transport efficiency in particular.

Working stroke of the kinesin-14, ncd, comprises two substeps of different direction

Single-molecule experiments have been used with great success to explore the mechanochemical cycles of processive motor proteins such as kinesin-1, but it has proven difficult to apply these approaches to nonprocessive motors. Therefore, the mechanochemical cycle of kinesin-14 (ncd) is still under debate. Here, we use the readout from the collective activity of multiple motors to derive information about the mechanochemical cycle of individual ncd motors. In gliding motility assays we performed 3D imaging based on fluorescence interference contrast microscopy combined with nanometer tracking to simultaneously study the translation and rotation of microtubules. Microtubules gliding on ncd-coated surfaces rotated around their longitudinal axes in an [ATP]- and [ADP]-dependent manner. Combined with a simple mechanical model, these observations suggest that the working stroke of ncd consists of an initial small movement of its stalk in a lateral direction when ADP is released and a second, main component of the working stroke, in a longitudinal direction upon ATP binding.

Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity

A structure-based model of myosin motor is built in the same spirit of our early work for kinesin-1 and Ncd towards physical understanding of its mechanochemical cycle. We find a structural adaptation of the motor head domain in post-powerstroke state that signals faster ADP release from it compared to the same from the motor head in the pre-powerstroke state. For dimeric myosin, an additional forward strain on the trailing head, originating from the postponed powerstroke state of the leading head in the waiting state of myosin, further increases the rate of ADP release. This coordination between the two heads is the essence of the processivity of the cycle. Our model provides a structural description of the powerstroke step of the cycle as an allosteric transition of the converter domain in response to the P_i release. Additionally, the variation in structural elements peripheral to catalytic motor domain is the deciding factor behind diverse directionalities of myosin motors (myosin V & VI). Finally, we observe that there are general rules for functional molecular motors across the different families. Allosteric structural adaptation of the catalytic motor head in different nucleotide states is crucial for mechanochemistry. Strain-mediated coordination between motor heads is essential for processivity and the variation of peripheral structural elements is essential for their diverse functionalities.

Molecular motors are perhaps the most important proteins present in the cell. The importance specifically lies with the fact that these proteins use the chemical energy source (such as ATP) of the cell to generate mechanical work and perform a wide range of functionalities. In this article, we generalize the idea of using structure-based models to explore the mechanochemistry of myosin molecular motors in structural terms. We find that a structural adaptation of the motor head domain in post-powerstroke state signals faster ADP release from the trailing head to maintain its processivity while directionality arises from a careful design of peripheral structural elements. These results along with our earlier results on other motors provide a general rule for motor activity.

SMOG 2: A Versatile Software Package for Generating Structure-Based Models

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.

Exploring the mechanochemical cycle of dynein motor proteins: structural evidence of crucial intermediates

Exploration of the biologically relevant pathways of dynein's mechanochemical cycle using structure based models.

Drosophila Ncd reveals an evolutionarily conserved powerstroke mechanism for homodimeric and heterodimeric kinesin-14s

Drosophila melanogaster kinesin-14 Ncd cross-links parallel microtubules at the spindle poles and antiparallel microtubules within the spindle midzone to play roles in bipolar spindle assembly and proper chromosome distribution. As observed for Saccharomyces cerevisiae kinesin-14 Kar3Vik1 and Kar3Cik1, Ncd binds adjacent microtubule protofilaments in a novel microtubule binding configuration and uses an ATP-promoted powerstroke mechanism. The hypothesis tested here is that Kar3Vik1 and Kar3Cik1, as well as Ncd, use a common ATPase mechanism for force generation even though the microtubule interactions for both Ncd heads are modulated by nucleotide state. The presteady-state kinetics and computational modeling establish an ATPase mechanism for a powerstroke model of Ncd that is very similar to those determined for Kar3Vik1 and Kar3Cik1, although these heterodimers have one Kar3 catalytic motor domain and a Vik1/Cik1 partner motor homology domain whose interactions with microtubules are not modulated by nucleotide state but by strain. The results indicate that both Ncd motor heads bind the microtubule lattice; two ATP binding and hydrolysis events are required for each powerstroke; and a slow step occurs after microtubule collision and before the ATP-promoted powerstroke. Note that unlike conventional myosin-II or other processive molecular motors, Ncd requires two ATP turnovers rather than one for a single powerstroke-driven displacement or step. These results are significant because all metazoan kinesin-14s are homodimers, and the results presented show that despite their structural and functional differences, the heterodimeric and homodimeric kinesin-14s share a common evolutionary structural and mechanochemical mechanism for force generation.

Decrypting the structural, dynamic, and energetic basis of a monomeric kinesin interacting with a tubulin dimer in three ATPase states by all-atom molecular dynamics simulation

We have employed molecular dynamics (MD) simulation to investigate, with atomic details, the structural dynamics and energetics of three major ATPase states (ADP, APO, and ATP state) of a human kinesin-1 monomer in complex with a tubulin dimer. Starting from a recently solved crystal structure of ATP-like kinesin-tubulin complex by the Knossow lab, we have used flexible fitting of cryo-electron-microscopy maps to construct new structural models of the kinesin-tubulin complex in APO and ATP state, and then conducted extensive MD simulations (total 400 ns for each state), followed by flexibility analysis, principal component analysis, hydrogen bond analysis, and binding free energy analysis. Our modeling and simulation have revealed key nucleotide-dependent changes in the structure and flexibility of the nucleotide-binding pocket (featuring a highly flexible and open switch I in APO state) and the tubulin-binding site, and allosterically coupled motions driving the APO to ATP transition. In addition, our binding free energy analysis has identified a set of key residues involved in kinesin-tubulin binding. On the basis of our simulation, we have attempted to address several outstanding issues in kinesin study, including the possible roles of β-sheet twist and neck linker docking in regulating nucleotide release and binding, the structural mechanism of ADP release, and possible extension and shortening of α4 helix during the ATPase cycle. This study has provided a comprehensive structural and dynamic picture of kinesin's major ATPase states, and offered promising targets for future mutational and functional studies to investigate the molecular mechanism of kinesin motors.

CK2 activates kinesin via induction of a conformational change

Kinesin is the canonical plus-end microtubule motor and has been the focus of intense study since its discovery in 1985. We previously demonstrated a time-dependent inactivation of kinesin in vitro that was fully reversible by the addition of purified casein kinase 2 (CK2) and showed that this inactivation/reactivation pathway was relevant in cells. Here we show that kinesin inactivation results from a conformational change that causes the neck linker to be positioned closer to the motor domain. Furthermore, we show that treatment of kinesin with CK2 prevents and reverses this repositioning. Finally, we demonstrate that CK2 treatment facilitates ADP dissociation from the motor, resulting in a nucleotide-free state that promotes microtubule binding. Thus, we propose that kinesin inactivation results from neck-linker repositioning and that CK2-mediated reactivation results from CK2's dual ability to reverse this repositioning and to promote ADP release.

From structure to function: the convergence of structure based models and co-evolutionary information

Understanding protein folding and function is one of the most important problems in biological research. Energy landscape theory and the folding funnel concept have provided a framework to investigate the mechanisms associated to these processes. Since protein energy landscapes are in most cases minimally frustrated, structure based models (SMBs) have successfully determined the geometrical features associated with folding and functional transitions. However, structural information is limited, particularly with respect to different functional configurations. This is a major limitation for SBMs. Alternatively, statistical methods to study amino acid co-evolution provide information on residue-residue interactions useful for the study of structure and function. Here, we show how the combination of these two methods gives rise to a novel way to investigate the mechanisms associated with folding and function. We use this methodology to explore the mechanistic aspects of protein translocation in the integral membrane protease FtsH. Dual basin-SBM simulations using the open and closed state of this hexameric motor reveals a functionally important paddling motion in the catalytic cycle. We also find that Direct Coupling Analysis (DCA) predicts physical contacts between AAA and peptidase domains of the motor, which are crucial for the open to close transition. Our combined method, which uses structural information from the open state experimental structure and co-evolutionary couplings, suggests that this methodology can be used to explore the functional landscape of complex biological macromolecules previously inaccessible to methods dependent on experimental structural information. This efficient way to sample the conformational space of large systems creates a theoretical/computational framework capable of better characterizing the functional landscape in large biomolecular assemblies.

Mechanism and regulation of kinesin-5, an essential motor for the mitotic spindle

Mitotic cell division is the most fundamental task of all living cells. Cells have intricate and tightly regulated machinery to ensure that mitosis occurs with appropriate frequency and high fidelity. A core element of this machinery is the kinesin-5 motor protein, which plays essential roles in spindle formation and maintenance. In this review, we discuss how the structural and mechanical properties of kinesin-5 motors uniquely suit them to their mitotic role. We describe some of the small molecule inhibitors and regulatory proteins that act on kinesin-5, and discuss how these regulators may influence the process of cell division. Finally, we touch on some more recently described functions of kinesin-5 motors in non-dividing cells. Throughout, we highlight a number of open questions that impede our understanding of both this motor's function and the potential utility of kinesin-5 inhibitors.

Motor proteins and molecular motors: how to operate machines at the nanoscale

Several classes of biological molecules that transform chemical energy into mechanical work are known as motor proteins or molecular motors. These nanometer-sized machines operate in noisy stochastic isothermal environments, strongly supporting fundamental cellular processes such as the transfer of genetic information, transport, organization and functioning. In the past two decades motor proteins have become a subject of intense research efforts, aimed at uncovering the fundamental principles and mechanisms of molecular motor dynamics. In this review, we critically discuss recent progress in experimental and theoretical studies on motor proteins. Our focus is on analyzing fundamental concepts and ideas that have been utilized to explain the non-equilibrium nature and mechanisms of molecular motors.

Mapping the structural and dynamical features of kinesin motor domains

Kinesin motor proteins drive intracellular transport by coupling ATP hydrolysis to conformational changes that mediate directed movement along microtubules. Characterizing these distinct conformations and their interconversion mechanism is essential to determining an atomic-level model of kinesin action. Here we report a comprehensive principal component analysis of 114 experimental structures along with the results of conventional and accelerated molecular dynamics simulations that together map the structural dynamics of the kinesin motor domain. All experimental structures were found to reside in one of three distinct conformational clusters (ATP-like, ADP-like and Eg5 inhibitor-bound). These groups differ in the orientation of key functional elements, most notably the microtubule binding α4–α5, loop8 subdomain and α2b-β4-β6-β7 motor domain tip. Group membership was found not to correlate with the nature of the bound nucleotide in a given structure. However, groupings were coincident with distinct neck-linker orientations. Accelerated molecular dynamics simulations of ATP, ADP and nucleotide free Eg5 indicate that all three nucleotide states could sample the major crystallographically observed conformations. Differences in the dynamic coupling of distal sites were also evident. In multiple ATP bound simulations, the neck-linker, loop8 and the α4–α5 subdomain display correlated motions that are absent in ADP bound simulations. Further dissection of these couplings provides evidence for a network of dynamic communication between the active site, microtubule-binding interface and neck-linker via loop7 and loop13. Additional simulations indicate that the mutations G325A and G326A in loop13 reduce the flexibility of these regions and disrupt their couplings. Our combined results indicate that the reported ATP and ADP-like conformations of kinesin are intrinsically accessible regardless of nucleotide state and support a model where neck-linker docking leads to a tighter coupling of the microtubule and nucleotide binding regions. Furthermore, simulations highlight sites critical for large-scale conformational changes and the allosteric coupling between distal functional sites.

Kinesin motor proteins transport cargo along microtubule tracks to support essential cellular functions including cell growth, axonal signaling and the separation of chromosomes during cell division. All kinesins contain one or more conserved motor domains that modulate binding and movement along microtubules via cycles of ATP hydrolysis. Important conformational transitions occurring during this cycle have been characterized with extensive crystallographic studies. However, the link between the observed conformations and the mechanisms involved in conformational change and microtubule interaction modulation remain unclear. Here we describe a comprehensive principal component analysis of available motor domain crystallographic structures supplemented with extensive unbiased conventional and accelerated molecular dynamics simulations that together characterize the response of kinesin motor domains to ATP binding and hydrolysis. Our studies reveal atomic details of conformational transitions, as well as novel nucleotide-dependent dynamical couplings, of distal regions and residues potentially important for the allosteric link between nucleotide and microtubule binding sites.

Molecular machines

Molecular machines (MM) are essential components of living cells. They conduct mechanical work, transport materials into and out of cells, assist in processing enzymatic reactions, and more. Their operations are frequently combined with significant conformational transitions. Computational studies of these conformational transitions and their coupling to molecular functions are discussed. It is argued that coarse descriptions of these molecules which are based on mass density and shape provide useful information on directions of action. It is further argued that MM are likely to have well focused and narrow reaction pathways. The proposal for such pathways is supported by evolutionary analyses of homologous machines. Finally, these observations are used to build atomically detailed models of these systems that are making the link from structure to functions (kinetics and thermodynamics). For that purpose enhanced sampling techniques are required.