Controllable molecular motors engineered from myosin and RNA

Application of Nanomaterials in Stem Cell-Based Therapeutics for Cardiac Repair and Regeneration

Cardiovascular disease is a leading cause of disability and death worldwide. Although the survival rate of patients with heart diseases can be improved with contemporary pharmacological treatments and surgical procedures, none of these therapies provide a significant improvement in cardiac repair and regeneration. Stem cell-based therapies are a promising approach for functional recovery of damaged myocardium. However, the available stem cells are difficult to differentiate into cardiomyocytes, which result in the extremely low transplantation efficiency. Nanomaterials are widely used to regulate the myocardial differentiation of stem cells, and play a very important role in cardiac tissue engineering. This study discusses the current status and limitations of stem cells and cell-derived exosomes/micro RNAs based cardiac therapy, describes the cardiac repair mechanism of nanomaterials, summarizes the recent advances in nanomaterials used in cardiac repair and regeneration, and evaluates the advantages and disadvantages of the relevant nanomaterials. Besides discussing the potential clinical applications of nanomaterials in cardiac therapy, the perspectives and challenges of nanomaterials used in stem cell-based cardiac repair and regeneration are also considered. Finally, new research directions in this field are proposed, and future research trends are highlighted.

Programmable molecular transport achieved by engineering protein motors to move on DNA nanotubes

Intracellular transport is the basis of microscale logistics within cells and is powered by biomolecular motors. Mimicking transport for in vitro applications has been widely studied; however, the inflexibility in track design and control has hindered practical applications. Here, we developed protein-based motors that move on DNA nanotubes by combining a biomolecular motor dynein and DNA binding proteins. The new motors and DNA-based nanoarchitectures enabled us to arrange the binding sites on the track, locally control the direction of movement, and achieve multiplexed cargo transport by different motors. The integration of these technologies realized microscale cargo sorters and integrators that automatically transport molecules as programmed in DNA sequences on a branched DNA nanotube. Our system should provide a versatile, controllable platform for future applications.

The C-terminal actin-binding domain of talin forms an asymmetric catch bond with F-actin

Talin is a mechanosensitive adaptor protein that links integrins to the actin cytoskeleton at cell–extracellular matrix adhesions. Although the C-terminal actin-binding domain ABS3 of talin is required for function, it binds weakly to actin in solution. We show that ABS3 binds actin strongly only when subjected to mechanical forces comparable to those generated by the cytoskeleton. Moreover, the interaction between ABS3 and actin depends strongly on the direction of force in a manner predicted to organize actin to facilitate adhesion growth and efficient cytoskeletal force generation. These characteristics can explain how force sensing by talin helps to nucleate adhesions precisely when and where they are required to transmit force between the cytoskeleton and the extracellular matrix.

Focal adhesions (FAs) are large, integrin-based protein complexes that link cells to the extracellular matrix (ECM). FAs form only when and where they are necessary to transmit force between the cellular cytoskeleton and the ECM, but how this occurs remains poorly understood. Talin is a 270-kDa adaptor protein that links integrins to filamentous (F)-actin and recruits additional components during FA assembly in a force-dependent manner. Cell biological and developmental data demonstrate that the third and C-terminal F-actin–binding site (ABS3) of talin is required for normal FA formation. However, purified ABS3 binds F-actin only weakly in solution. We used a single molecule optical trap assay to examine how and whether ABS3 binds F-actin under physiologically relevant mechanical loads. We find that ABS3 forms a catch bond with F-actin when force is applied toward the pointed end of the actin filament, with binding lifetimes >100-fold longer than when force is applied toward the barbed end. Long-lived bonds to F-actin under load require the ABS3 C-terminal dimerization domain, whose cleavage has been reported to regulate FA turnover. Our results support a mechanism in which talin ABS3 preferentially binds to and orients actin filaments with barbed ends facing the cell periphery, thus nucleating long-range order in the actin cytoskeleton. We suggest that talin ABS3 may function as a molecular AND gate that allows FA growth only when sufficient integrin density, F-actin polarization, and mechanical tension are simultaneously present.

Optical control of fast and processive engineered myosins in vitro and in living cells

Precision tools for spatiotemporal control of cytoskeletal motor function are needed to dissect fundamental biological processes ranging from intracellular transport to cell migration and division. Direct optical control of motor speed and direction is one promising approach, but it remains a challenge to engineer controllable motors with desirable properties such as the speed and processivity required for transport applications in living cells. Here, we develop engineered myosin motors that combine large optical modulation depths with high velocities, and create processive myosin motors with optically controllable directionality. We characterize the performance of the motors using in vitro motility assays, single-molecule tracking and live-cell imaging. Bidirectional processive motors move efficiently toward the tips of cellular protrusions in the presence of blue light, and can transport molecular cargo in cells. Robust gearshifting myosins will further enable programmable transport in contexts ranging from in vitro active matter reconstitutions to microfabricated systems that harness molecular propulsion.

Synthetic biology approaches to dissecting linear motor protein function: towards the design and synthesis of artificial autonomous protein walkers

Molecular motors and machines are essential for all cellular processes that together enable life. Built from proteins with a wide range of properties, functionalities and performance characteristics, biological motors perform complex tasks and can transduce chemical energy into mechanical work more efficiently than human-made combustion engines. Sophisticated studies of biological protein motors have provided many structural and biophysical insights and enabled the development of models for motor function. However, from the study of highly evolved, biological motors, it remains difficult to discern detailed mechanisms, for example, about the relative role of different force generation mechanisms, or how information is communicated across a protein to achieve the necessary coordination. A promising, complementary approach to answering these questions is to build synthetic protein motors from the bottom up. Indeed, much effort has been invested in functional protein design, but so far, the "holy grail" of designing and building a functional synthetic protein motor has not been realized. Here, we review the progress made to date, and we put forward a roadmap for achieving the aim of constructing the first artificial, autonomously running protein motor. Specifically, we propose to break down the task into (i) enzymatic control of track binding, (ii) the engineering of asymmetry and (iii) the engineering of allosteric control for internal communication. We also propose specific approaches for solving each of these challenges.

The energy landscape of -1 ribosomal frameshifting

Maintenance of translational reading frame ensures the fidelity of information transfer during protein synthesis. Yet, programmed ribosomal frameshifting sequences within the coding region promote a high rate of reading frame change at predetermined sites thus enriching genomic information density. Frameshifting is typically stimulated by the presence of 3' messenger RNA (mRNA) structures, but how these mRNA structures enhance -1 frameshifting remains debatable. Here, we apply single-molecule and ensemble approaches to formulate a mechanistic model of ribosomal -1 frameshifting. Our model suggests that the ribosome is intrinsically susceptible to frameshift before its translocation and this transient state is prolonged by the presence of a precisely positioned downstream mRNA structure. We challenged this model using temperature variation in vivo, which followed the prediction made based on in vitro results. Our results provide a quantitative framework for analyzing other frameshifting enhancers and a potential approach to control gene expression dynamically using programmed frameshifting.

Blind tests of RNA-protein binding affinity prediction

Interactions between RNA and proteins are pervasive in biology, driving fundamental processes such as protein translation and participating in the regulation of gene expression. Modeling the energies of RNA-protein interactions is therefore critical for understanding and repurposing living systems but has been hindered by complexities unique to RNA-protein binding. Here, we bring together several advances to complete a calculation framework for RNA-protein binding affinities, including a unified free energy function for bound complexes, automated Rosetta modeling of mutations, and use of secondary structure-based energetic calculations to model unbound RNA states. The resulting Rosetta-Vienna RNP-ΔΔG method achieves root-mean-squared errors (RMSEs) of 1.3 kcal/mol on high-throughput MS2 coat protein-RNA measurements and 1.5 kcal/mol on an independent test set involving the signal recognition particle, human U1A, PUM1, and FOX-1. As a stringent test, the method achieves RMSE accuracy of 1.4 kcal/mol in blind predictions of hundreds of human PUM2-RNA relative binding affinities. Overall, these RMSE accuracies are significantly better than those attained by prior structure-based approaches applied to the same systems. Importantly, Rosetta-Vienna RNP-ΔΔG establishes a framework for further improvements in modeling RNA-protein binding that can be tested by prospective high-throughput measurements on new systems.

All-in-One Synchronized DNA Nanodevices Facilitating Multiplexed Cell Imaging

Multifunctional DNA nanodevices perform ever more tasks with applications ranging from in vitro biomarker detection to in situ cell imaging. However, most developed ones consist of a series of split building blocks, which suffer from asynchronous behaviors in complicated cellular microenvironments (endocytosis pathway, diffusion-limited cytoplasm, etc.), causing the loss of stoichiometric information and additional postassembly processes. Herein, we constructed all-in-one DNA nanodevices to achieve synchronous multiplexed imaging. All DNA components, including two sets of probe modules (each containing target-specific walkers, i.e., hairpin tracks with chemically damaged bases), are modified on individual gold nanoparticles. This design not only enables their integrated internalization into cells, circumventing inhomogeneous distribution of different building blocks and increasing the local concentrations of the interacting modules, but also avoids the impact of stochastic diffusion in viscous cytoplasm. A couple of intracellular enzymes in situ actuate the synchronized motion of the modules, all on-particle, after specific recognition of intracellular targets (such as RNAs and proteins), thus facilitating synchronized, multiplexed cell imaging. Finally, the proposed all-in-one nanodevices were successfully applied to monitor intracellular microRNA-21 and telomerase expression levels. The flexible design can be extended to detect other cytoplasmic molecules and monitor related pathways by simply changing the sequences.

Programming in situ accelerated DNA walkers in diffusion-limited microenvironments

Macromolecule diffusion in cellular microenvironments dictates the kinetics of biochemical processes, yet inevitably limiting the assembly and operation of biomimetic motors. Herein we program in situ accelerated DNA walkers in diffusion-limited microenvironments such as molecularly crowded solutions and cytoplasm. All DNA components, including single-foot walkers, chemically damaged tracks and calibration elements, are anchored on individual gold nanoparticles. Two endogenous enzymes participating in base repair pathways are used to actuate on-particle walking via a base excision/hydrolyzation coupled reaction. The walkers are in situ driven without requiring external drivers and accelerated several times. They also avoid low-efficiency diffusion/assembly procedures and respond to heterogeneous cellular milieus with calibration function. We further regulated the walking kinetics via DNA densities and sets of enzymes, and demonstrated cytoplasmic behaviors of three kinds of walkers. They were utilized to profile DNA repair pathways and monitor enzyme catalysis in living cells.

Switchable DNA-origami nanostructures that respond to their environment and their applications

Structural DNA nanotechnology, in which Watson-Crick base pairing drives the formation of self-assembling nanostructures, has rapidly expanded in complexity and functionality since its inception in 1981. DNA nanostructures can now be made in arbitrary three-dimensional shapes and used to scaffold many other functional molecules such as proteins, metallic nanoparticles, polymers, fluorescent dyes and small molecules. In parallel, the field of dynamic DNA nanotechnology has built DNA circuits, motors and switches. More recently, these two areas have begun to merge-to produce switchable DNA nanostructures, which change state in response to their environment. In this review, we summarise switchable DNA nanostructures into two major classes based on response type: molecular actuation triggered by local chemical changes such as pH or concentration and external actuation driven by light, electric or magnetic fields. While molecular actuation has been well explored, external actuation of DNA nanostructures is a relatively new area that allows for the remote control of nanoscale devices. We discuss recent applications for DNA nanostructures where switching is used to perform specific functions-such as opening a capsule to deliver a molecular payload to a target cell. We then discuss challenges and future directions towards achieving synthetic nanomachines with complexity on the level of the protein machinery in living cells.

Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity

Despite extensive scrutiny of the myosin superfamily, the lack of high-resolution structures of actin-bound states has prevented a complete description of its mechanochemical cycle and limited insight into how sequence and structural diversification of the motor domain gives rise to specialized functional properties. Here we present cryo-EM structures of the unique minus-end directed myosin VI motor domain in rigor (4.6 Å) and Mg-ADP (5.5 Å) states bound to F-actin. Comparison to the myosin IIC-F-actin rigor complex reveals an almost complete lack of conservation of residues at the actin-myosin interface despite preservation of the primary sequence regions composing it, suggesting an evolutionary path for motor specialization. Additionally, analysis of the transition from ADP to rigor provides a structural rationale for force sensitivity in this step of the mechanochemical cycle. Finally, we observe reciprocal rearrangements in actin and myosin accompanying the transition between these states, supporting a role for actin structural plasticity during force generation by myosin VI.

Like miniature motors, proteins called myosins generate the forces needed for cells to move and for muscles to contract. Myosins use the energy stored in a chemical called ATP to move along filaments made from another protein called actin and produce force. The same part of the myosin protein that binds to and uses ATP also contacts actin. As a myosin protein consumes ATP, it cycles through a series of shape changes to drive the motor protein forward, altering how it interacts with the actin filament in the process.

Although all myosins use ATP in fundamentally the same way, individual members of this protein family have specialized properties that enable them to carry out different roles. It is not clear whether each type of myosin makes unique contacts with the actin filament, which could help determine these properties. Furthermore, mechanical forces can control the activity of myosin motors in ways that are poorly understood.

Gurel et al. have now looked at a family member called myosin VI, which moves in the opposite direction along actin filaments relative to other myosins, to better understand the properties of these proteins. An imaging technique called cryo-electron microscopy (cryo-EM) was used to determine the three-dimensional structure of myosin VI bound to actin at two steps in its cycle. Gurel et al. found that myosin VI formed specific interactions with actin that were very different from another myosin family member called myosin IIc, whose structure bound to actin was already known. In addition, the structural changes observed between the two stages of myosin VI’s cycle provided insight into how force could be used to control the motor.

Together these findings give a more detailed picture of how myosins work. They suggest that the surface of myosin that contacts actin can evolve to change the properties of a specific myosin. Studies of other myosins bound to actin will provide further insight into how distinct interactions relate to motor-specific properties. Future studies could also help scientists to understand how mutations in genes for myosins – which have been linked to a number of diseases in humans – alter the way in which myosins interact with actin filaments. This in turn could give insight into how these mutations disrupt the proteins’ activities.