Macromolecular Motors Research Articles

Synthesis and Direct Observation of Chiral Supramolecular Polymer of Porphyrin Having Cholesteryl Groups.

We report the synthesis and microscopic investigations of two chiral helical porphyrin supramolecular polymers with different coordinating metals that are expected to be capable of serving as synthetic macromolecular motors driven by thermal fluctuations. Furthermore, based on their microscopic images, we propose a stepwise process for the formation of higher-order structures. These porphyrins formed completely different association states, and this was reflected in the marked differences in the shapes of the supramolecular polymers. The Cu-TChOAlaCPP supramolecular polymers formed H-aggregate rods in diisopropyl ether, then grew into superhelices and then into ribbons. On the other hand, Zn-TChOAlaCPP supramolecular polymers formed aggregates based on van der Waals interactions in diethyl ether, then grew into fibers and then grew into multiple-helices and ribbons. In addition, we imaged the interaction between long and short chains of the Cu-TChOAlaCPP supramolecular polymer by fast-scanning atomic force microscopy, and we indicated the availability as a macromolecular motor driven by thermal fluctuations.

The Functions of Pt-DIC and Pt-Lamin B in Spermatogenesis of Portunus trituberculatus.

Cytoplasmic Dynein is a multiple-subunit macromolecular motor protein involved in the transport process of cells. The Dynein intermediate chain (DIC) is one of the subunits of Dynein-1. In our previous studies, we showed that Pt-DIC may play an important role in the nuclear deformation of spermiogenesis in Portunus trituberculatus. Lamin B is essential for maintaining nuclear structure and functions. Surprisingly, Pt-Lamin B was expressed not only in the perinucleus but also in the pro-acrosome during spermiogenesis in P. trituberculatus. Studies have also shown that Dynein-1 can mediate the transport of Lamin B in mammals. Thus, to study the relationship of Pt-DIC and Pt-Lamin B in the spermatogenesis of P. trituberculatus, we knocked down the Pt-DIC gene in P. trituberculatus by RNAi. The results showed that the distribution of Pt-DIC and Pt-Lamin B in spermiogenesis was abnormal, and the colocalization was weakened. Moreover, we verified the interaction of Pt-DIC and Pt-Lamin B via coimmunoprecipitation. Therefore, our results suggested that both Pt-DIC and Pt-Lamin B were involved in the spermatogenesis of P. trituberculatus, and one of the functions of Dynein-1 is to mediate the transport of Lamin B in the spermiogenesis of P. trituberculatus.

Chitosan/polypyrrole hybrid film as multistep electrochemical sensor: sensing electrical, thermal and chemical working ambient

The reactive sensing capabilities of a mechanically stable chitosan/polypyrrole hybrid film fabricated through an in situ chemical polymerization of pyrrole are presented. The sensing abilities studied as a function of applied current, working temperature and electrolyte concentration revealed that the film can act as a multi-step electrochemical macromolecular motor, replicating basic elements of biological functions. The electrical energy consumed is a linear function of working electrical and thermal condition and a logarithmic function of electrolyte concentration. The extension of reaction (coulovoltammetric charges) is a function of and senses the working chemical ambient. The conformational changes of polymer chains (multi-step sensing motors) during reaction through the cooperative actuation make the coulovoltammetric charge a self-sensor of the working energetic conditions. This similarity of cooperative actuation of polymeric chains in biological muscles in simultaneously sensing the working condition suggests the possibility of constructing biomimetic simultaneous sensing motors using flexible chitosan/polypyrrole film with only two connecting wires.

Spatial parameterization of attachment processes in molecular motor-cargo systems

Intracellular transport is conducted largely by molecular motor proteins which process along cytoskeletal filaments, from which they can attach or detach. We describe an analytical framework to characterize motor attachment or reattachment rates to microtubules as a function of the physical and geometric properties of the motor, the cargo to which it is attached, and possibly a second motor attached to the same cargo and a microtubule. The biophysical model is coarse-grained at the level of the macromolecular motors and formulated in terms of stochastic differential equations, allowing for rotation of the cargo and nonlinear force laws for the motor-cargo tether.

Conducting polymers as bio-mimetic multistep macromolecular sensors of working conditions: polyindole/polyvinyl alcohol hybrid film senses electrical and chemical working ambient

Conducting polymers can be considered as model materials for designing motors sensing working conditions while working without additional connectivity as they mimic the electrochemical reactions of biological muscles comprising macro molecular motors.

Exploring Brain Information Storage/Reading for Neuronal Connectivity Using Macromolecular Electrochemical Sensing Motors

Dense electroactive gels of conducting polymers, carbon nanotubes, or graphenes, constituted by multisensing macromolecular electrochemical motors, are presented herein as model materials to get a physicochemical characterization of the opening/closing cycles of ion protein channels in neurons. The conformational contracted energetic states of these macromolecular motors store both long‐term and short‐term information packages. Under a potential cycle, the energy of each ionic pulse generated during the channel opening reads the stored information, which is restored during the channel conformational closing. Simultaneously the motor actuation senses the working physical and chemical energetic conditions, transferring to the ionic pulse energy those sensing information packages. A quantitative description of the stored and read information packages is attained from basic electrochemical, mechanical, and polymeric concepts. Translated to ion channel proteins in brain dendrites, it can describe brain information storage mechanisms and the energetic information packages read and carried through each ionic pulse to the action potential. An unexplored way is opened to try to understand and describe how the different brain parts can use this information to originate brain functions. In parallel, the construction of new electrochemical devices and computers replicating biological functions will provide feedback quantitative information to decipher brain functions.

Macromolecular aging: ATP hydrolysis-driven functional and structural changes in Escherichia coli RecQ helicase

Aging has been considered a phenomenon that can be only applied to cells or organisms. Here, we show that RecQ helicase from E. coli displays an aging phenomenon: this macromolecular motor loses its structure and function after hydrolyzing a certain number of ATP molecules. The aging process was only triggered by repeated catalytic cycles. These observations lead to a new concept: macromolecule aging.

Electroactive macromolecular motors as model materials of ectotherm muscles.

The electrochemical reaction in liquid electrolytes of conducting polymers, carbon nanotubes, graphenes, among other materials, replicates the active components (macromolecular electro-chemical motors, ions and solvent) and volume variation of the sarcomere in any natural muscles during actuation, allowing the development of electro-chemo-mechanical artificial muscles. Materials, reactions and artificial muscles have been used as model materials, model reactions and model devices of the muscles from ectotherm animals. We present in this perspective the experimental results and a quantitative description of the thermal influence on the reaction extension and energetic achievements of those muscular models using different experimental methodologies. By raising the temperature for 40 °C keeping the extension of the muscular movement the cooperative actuation of the macromolecular motors harvest, saving chemical energy, up to 60% of the reaction energy from the thermal environment. The synergic thermal influence on either, the reaction rate (Arrhenius), the conformational movement rates of the motors (ESCR model) and the diffusion coefficients of ions across polymer matrix (WLF equation) can support the physical chemical foundations for the selection by nature of ectotherm muscles. Macromolecular motors act, simultaneously, as electro-chemo-mechanical and thermo-mechanical transducers. Technological and biological perspectives are presented.

Biochemical and Biophysical Characterization of the dsDNA Packaging Motor from the Lactococcus lactis Bacteriophage Asccphi28.

Double-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here, we describe the biochemical and biophysical characterization of the packaging ATPase from Lactococcus lactis phage asccφ28. Size-exclusion chromatography (SEC), analytical ultracentrifugation (AUC), small angle X-ray scattering (SAXS), and negative stain transmission electron microscopy (TEM) indicate that the ~45 kDa protein formed a 443 kDa cylindrical assembly with a maximum dimension of ~155 Å and radius of gyration of ~54 Å. Together with the dimensions of the crystallographic asymmetric unit from preliminary X-ray diffraction experiments, these results indicate that gp11 forms a decameric D5-symmetric complex consisting of two pentameric rings related by 2-fold symmetry. Additional kinetic analysis shows that recombinantly expressed gp11 has ATPase activity comparable to that of functional ATPase rings assembled on procapsids in other genome packaging systems. Hence, gp11 forms rings in solution that likely reflect the fully assembled ATPases in active virus-bound motor complexes. Whereas ATPase functionality in other double-stranded DNA (dsDNA) phage packaging systems requires assembly on viral capsids, the ability to form functional rings in solution imparts gp11 with significant advantages for high-resolution structural studies and rigorous biophysical/biochemical analysis.

Towards artificial proprioception from artificial muscles constituted by self-sensing multi-step electrochemical macromolecular motors

Many life functions emerge from bio-electro-chemical reactions involving macromolecular motors, exchange of ions and water triggered by nervous (electric) pulses. Muscles are natural electro-chemical motors sensing by themselves the working physical and chemical conditions: multi-sensing motors. Here we review how by electrochemical reactions conducting polymers and other electroactive materials give artificial muscles replicating both, the dense gel composition and multi-functionality of the muscle’ cell. They are Faradaic devices: the flowing current controls the movement rate and the consumed charge defines the displacement amplitude. The consumed energy (or any of its components: muscle potential, charge or current) responds to, adapts to and senses, at any time, the working mechanical, chemical, thermal and electrical conditions: multi-sensing or self-awareness. The equations describing self-awareness were attained from the basic chemical and electrochemical kinetics and checked by experimental results. Translated to Biology the sensing equations can describe: muscle's fatigue, the energy that coldblooded animals can extract from the ambient, why muscles only work by contraction, how muscles generate each nervous pulses and how many packages of quantitative information they translate to the brain. Only two connecting wires include, at any time, actuating and sensing signals: the system computer-potentiostat/two wires/artificial muscle replicates brain/motor neuron-sensory neuron/muscle. That multi-functionality is originated by only one reaction driving the cooperative actuation multi-sensing and multi-step electrochemical macromolecular motors. None similar multi-sensing motor exists in nowadays technology. The way is open to develop self-awareness devices and proprioceptive robots.

Multifunctionality of Polypyrrole Polyethyleneoxide Composites: Concurrent Sensing, Actuation and Energy Storage.

In films of conducting polymers, the electrochemical reaction(s) drive the simultaneous variation of different material properties (reaction multifunctionality). Here, we present a parallel study of actuation-sensing-energy storage triple functionality of polypyrrole (PPy) blends with dodecylbenzenesulfonate (DBS-), PPy/DBS, without and with inclusion of polyethyleneoxide, PPy-PEO/DBS. The characterization of the response of both materials in aqueous solutions of four different salts indicated that all of the actuating, sensing and charge storage responses were, independent of the electrolyte, present for both materials, but stronger for the PPy-PEO/DBS films: 1.4× higher strains, 1.3× higher specific charge densities, 2.5× higher specific capacitances and increased ion-sensitivity towards the studied counterions. For both materials, the reaction energy, the material potential and the strain variations adapt to and sense the electrical and chemical (exchanged cation) conditions. The driving and the response of actuation, sensing and charge can be controlled/read, simultaneously, via just two connecting wires. Only the cooperative actuation of chemical macromolecular motors from functional cells has such chemical multifunctionality.

Identification of cryptic subunits from an apicomplexan ATP synthase.

The mitochondrial ATP synthase is a macromolecular motor that uses the proton gradient to generate ATP. Proper ATP synthase function requires a stator linking the catalytic and rotary portions of the complex. However, sequence-based searches fail to identify genes encoding stator subunits in apicomplexan parasites like Toxoplasma gondii or the related organisms that cause malaria. Here, we identify 11 previously unknown subunits from the Toxoplasma ATP synthase, which lack homologs outside the phylum. Modeling suggests that two of them, ICAP2 and ICAP18, are distantly related to mammalian stator subunits. Our analysis shows that both proteins form part of the ATP synthase complex. Depletion of ICAP2 leads to aberrant mitochondrial morphology, decreased oxygen consumption, and disassembly of the complex, consistent with its role as an essential component of the Toxoplasma ATP synthase. Our findings highlight divergent features of the central metabolic machinery in apicomplexans, which may reveal new therapeutic opportunities.

On DNA Motions under Action of Enzymes of Different Types. I

Different types of enzymes in rotational macromolecular motors of living cells are presented based on the data in the literature. Particular attention has been given to the restriction–modification enzymes and helicases, in which conformational changes in sites are physical reasons of linear motions and rotation of DNA molecules (caused by polar forces). It is shown that the structure and functioning of enzymes, similar to those in chiral smectic C-type liquid crystals, can be described within the formalism of generalized forces and currents. These forces include the membrane electrochemical gradient, the velocity of rotor mechanical motion, and the measure of change in free energy in the “fuel” adenosine triphosphate molecule.

Allostery and molecular machines.

Machines undergo repeated energy (fuel)-driven cycling between various functional and structural states. Such cycling involves motions of the machine parts, which take place in a highly coordinated manner in time and space. This description applies not only to man-made machines but also to the molecular machines that mediate many of the key processes in all forms of life [1]. Examples include protein synthesis by the ribosome, DNA unwinding by helicases during replication, protein degradation by the proteasome and protein folding by chaperones. The coordinated movements of most biomolecular machines are achieved by allosteric regulation of ATP binding and hydrolysis. Consequently, a molecular level understanding of how the essential machines of life work requires invoking and further developing allosteric theory. Hence, the motivation for the Royal Society Discussion Meeting entitled ‘Allostery and molecular machines' that took place in June 2017. The meeting brought together scientists interested in allostery, in general, with others who are studying specific biomolecular machines of interest. The meeting led to many interesting discussions and resulted in this special issue of the Philosophical Transactions B . In 1965, Monod, Wyman & Changeux published a seminal paper [2] that described a so-called ‘concerted model' (referred to here and generally as the MWC model) for cooperative ligand binding by oligomeric proteins. This issue contains a paper by one of the co-authors of this landmark paper in which the MWC model is explained in brief and its application to the nicotinic acetylcholine receptor is then described [3]. The MWC model remains important but its elegance has come at the price of several restrictive assumptions. One key assumption is that cooperativity is due to a shift in equilibrium between different quaternary …

Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases.

ATP synthase is the most prominent bioenergetic macromolecular motor in all life forms, utilizing the proton gradient across the cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, the precise molecular mechanism whereby vacuolar (V-type) ATP synthase fulfills its biological function remains largely fragmentary. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V1-ATPase. Employing a combination of transition-path sampling and high-performance free-energy methods, the sequence of conformational transitions involved in a functional cycle accompanying ATP hydrolysis has been investigated in unprecedented detail over an aggregate simulation time of 65 μs. Our simulated pathways reveal that the chemical energy produced by ATP hydrolysis is harnessed via the concerted motion of the protein-protein interfaces in the V1-ring, and is nearly entirely consumed in the rotation of the central stalk. Surprisingly, in an ATPase devoid of a central stalk, the interfaces of this ring are perfectly designed for inducing ATP hydrolysis. However, in a complete V1-ATPase, the mechanical property of the central stalk is a key determinant of the rate of ATP turnover. The simulations further unveil a sequence of events, whereby unbinding of the hydrolysis product (ADP + Pi) is followed by ATP uptake, which, in turn, leads to the torque generation step and rotation of the center stalk. Molecular trajectories also bring to light multiple intermediates, two of which have been isolated in independent crystallography experiments.

Identification of the T-complex protein as a binding partner for newly synthesized cytoplasmic dynein intermediate chain 2

Cytoplasmic dynein is a macromolecular motor complex with diverse functions in eukaryotic cells. Dynein plays essential roles in intracellular transport of organelles and mitosis, mediated in part by interactions between the dynein intermediate chain 2 (IC-2) subunits and adapter proteins that bind specific cargos. In experiments to identify phosphorylation-dependent binding partners for IC-2 we instead identified a phosphorylation-independent binding partner, the cytosolic chaperonin containing T complex protein 1 (CCT). CCT consists of eight subunits (CCT1-8) and facilitates folding of a subset of newly synthesized proteins. We confirmed interactions between IC-2 and CCT5 and CCT8 in co-immunoprecipitation experiments and determined that the C-terminal half of IC-2 is necessary and sufficient to bind CCT8. Interestingly, co-immunoiprecipitation of IC-2 and CCT is abolished by prior cycloheximide treatment of cells, suggesting that CCT participates in folding of nascent IC-2. In vitro translation experiments employing recombinant CCT complex demonstrated that CCT is able to bind newly synthesized IC-2 after release from the ribosome consistent with a role in folding of IC-2.

Dynein light chain interaction with the peroxisomal import docking complex modulates peroxisome biogenesis in yeast

Dynein is a large macromolecular motor complex that moves cargo along microtubules. A motor-independent role for the light chain of dynein, Dyn2p, in peroxisome biology in Saccharomyces cerevisiae was suggested from its interaction with Pex14p, a component of the peroxisomal matrix protein import docking complex. Here we show that cells of the yeast Yarrowia lipolytica deleted for the gene encoding the homologue of Dyn2p are impaired in peroxisome function and biogenesis. These cells exhibit compromised growth on medium containing oleic acid as the carbon source, the metabolism of which requires functional peroxisomes. Their peroxisomes have abnormal morphology, atypical matrix protein localization, and an absence of proteolytic processing of the matrix enzyme thiolase, which normally occurs upon its import into the peroxisome. We also show physical and genetic interactions between Dyn2p and members of the docking complex, particularly Pex17p. Together, our results demonstrate a role for Dyn2p in the assembly of functional peroxisomes and provide evidence that Dyn2p acts in cooperation with the peroxisomal matrix protein import docking complex to effect optimal matrix protein import.

Molecular, Supramolecular, and Macromolecular Motors and Artificial Muscles

AbstractRecent developments in chemical synthesis, nanoscale assembly, and molecular-scale measurements enable the extension of the concept of macroscopic machines to the molecular and supramolecular levels. Molecular machines are capable of performing mechanical movements in response to external stimuli. They offer the potential to couple electrical or other forms of energy to mechanical action at the nano- and molecular scales. Working hierarchically and in concert, they can form actuators referred to as artificial muscles, in analogy to biological systems. We describe the principles behind driven motion and assembly at the molecular scale and recent advances in the field of molecular-level electromechanical machines, molecular motors, and artificial muscles. We discuss the challenges and successes in making these assemblies work cooperatively to function at larger scales.

Step-by-step rotation of a molecule-gear mounted on an atomic-scale axis

Gears are microfabricated down to diameters of a few micrometres. Natural macromolecular motors, of tens of nanometres in diameter, also show gear effects. At a smaller scale, the random rotation of a single-molecule rotor encaged in a molecular stator has been observed, demonstrating that a single molecule can be rotated with the tip of a scanning tunnelling microscope (STM). A self-assembled rack-and-pinion molecular machine where the STM tip apex is the rotation axis of the pinion was also tested. Here, we present the mechanics of an intentionally constructed molecule-gear on a Au(111) surface, mounting and centring one hexa-t-butyl-pyrimidopentaphenylbenzene molecule on one atom axis. The combination of molecular design, molecular manipulation and surface atomic structure selection leads to the construction of a fundamental component of a planar single-molecule mechanical machine. The rotation of our molecule-gear is step-by-step and totally under control, demonstrating nine stable stations in both directions.

Surface-Bound Soft Matter Gradients

This feature article describes the progress realized over the past half century in the field of surface-bound gradient structures created on or from soft materials (oligomers and/or polymers), or those enabling the study of the behavior of soft materials. By highlighting our work in the field and accounting for the contribution of other groups, we emphasize the exceptional versatility of gradient assemblies in facilitating fast screening of physicochemical phenomena, acting as "recording media" for monitoring a process, and playing a key role in the design and fabrication of surface-bound molecular and macromolecular motors capable of directing a transport phenomenon.