The Synergic Role of Actomyosin Architecture and Biased Detachment in Muscle Energetics: Insights in Cross Bridge Mechanism Beyond the Lever-Arm Swing

Muscle energetics reflects the ability of myosin motors to convert chemical energy into mechanical energy. How this process takes place remains one of the most elusive questions in the field. Here, we combined experimental measurements of in vitro sliding velocity based on DNA-origami built filaments carrying myosins with different lever arm length and Monte Carlo simulations based on a model which accounts for three basic components: (i) the geometrical hindrance, (ii) the mechano-sensing mechanism, and (iii) the biased kinetics for stretched or compressed motors. The model simulations showed that the geometrical hindrance due to acto-myosin spatial mismatching and the preferential detachment of compressed motors are synergic in generating the rapid increase in the ATP-ase rate from isometric to moderate velocities of contraction, thus acting as an energy-conservation strategy in muscle contraction. The velocity measurements on a DNA-origami filament that preserves the motors’ distribution showed that geometrical hindrance and biased detachment generate a non-zero sliding velocity even without rotation of the myosin lever-arm, which is widely recognized as the basic event in muscle contraction. Because biased detachment is a mechanism for the rectification of thermal fluctuations, in the Brownian-ratchet framework, we predict that it requires a non-negligible amount of energy to preserve the second law of thermodynamics. Taken together, our theoretical and experimental results elucidate less considered components in the chemo-mechanical energy transduction in muscle.

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The synergic role of actomyosin architecture and biased detachment in muscle energetics: insights in cross bridge mechanism beyond the lever-arm swing

10.1101/2021.03.23.436693 ◽

2021 ◽

Author(s):

Lorenzo Marcucci ◽

Hiroki Fukunaga ◽

Toshio Yanagida ◽

Mitsuhiro Iwaki

Keyword(s):

Muscle Contraction ◽

Mechanical Energy ◽

Monte Carlo Model ◽

Thermal Fluctuations ◽

Dna Origami ◽

Conservation Strategy ◽

Sliding Velocity ◽

Muscle Energetics ◽

Lever Arm

AbstractMuscle energetics reflects the ability of myosin motors to convert chemical energy into mechanical energy. How this process takes place remains one of the most elusive questions in the field. Here we combined experimental measurements of in vitro sliding velocity based on DNA-origami built filaments carrying myosins with different lever arm length and simulations based on a Monte-Carlo model which accounts for three basic components: (i) the geometrical hindrance, (ii) the mechano-sensing mechanism, and (iii) the biased kinetics for stretched or compressed motors. The model simulations showed that the geometrical hindrance due to acto-myosin spatial mismatching and the preferential detachment of compressed motors are synergic in generating the rapid increase in the ATP-ase rate from isometric to moderate velocities of contraction, thus acting as an energy-conservation strategy in muscle contraction. The velocity measurements on a DNA-origami filament that preserves the motors’ distribution showed that geometrical hindrance and biased detachment generate a non-zero sliding velocity even without rotation of the myosin lever-arm, which is widely recognized as the basic event in muscle contraction. Because biased detachment is a mechanism for the rectification of thermal fluctuations, in the Brownian-ratchet framework, we predict that it requires a non-negligible amount of energy to preserve the second law of thermodynamics. Taken together, our theoretical and experimental results elucidate non-conventional components in the chemo-mechanical energy transduction in muscle.

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Pseudo-Rigid-Body Models of Compliant DNA Origami Mechanisms

Volume 5B: 39th Mechanisms and Robotics Conference ◽

10.1115/detc2015-46838 ◽

2015 ◽

Author(s):

Lifeng Zhou ◽

Alexander E. Marras ◽

Carlos E. Castro ◽

Hai-jun Su

Keyword(s):

Rigid Body ◽

Strain Energy ◽

Compliant Mechanisms ◽

Compliant Mechanism ◽

Mechanical Energy ◽

Energy Landscape ◽

Thermal Fluctuations ◽

Dna Origami ◽

Double Stranded Dna ◽

Flexible Parts

In this paper, we introduce the strategy of designing and analyzing compliant nanomechanisms fabricated with DNA origami which we call compliant DNA origami mechanism (CDOM). The rigid, compliant and flexible parts are constructed by a bunch of double-stranded DNA (dsDNA) helices, fewer dsDNA helices and single-stranded DNA (ssDNA) strands respectively. Just like in macroscopic compliant mechanisms, a CDOM generates its motion via deformation of at least one structural member. During the motion, strain energy is stored and released in the mechanism. These CDOM can suppress thermal fluctuations due to the internal mechanical energy barrier for motion. An example of compliant hinge joint and a bistable four-bar CDOM fabricated with DNA origami are discussed at the end of this paper. The classic pseudo-rigid-body (PRB) model for compliant mechanism is successfully employed to the analysis of these DNA origami nanomechanisms. This PRB model has been used to guide the design of a bistable CDOM for a desired energy landscape.

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Pseudorigid-Body Models of Compliant DNA Origami Mechanisms

Journal of Mechanisms and Robotics ◽

10.1115/1.4032213 ◽

2016 ◽

Vol 8 (5) ◽

Cited By ~ 9

Author(s):

Lifeng Zhou ◽

Alexander E. Marras ◽

Carlos E. Castro ◽

Hai-Jun Su

Keyword(s):

Self Assembly ◽

Strain Energy ◽

Compliant Mechanism ◽

Mechanical Energy ◽

Thermal Fluctuations ◽

Dna Origami ◽

Analysis Method ◽

Double Stranded Dna ◽

Compliant Joint ◽

Flexible Parts

In this paper, we introduce a strategy for the design and computational analysis of compliant DNA origami mechanisms (CDOMs), which are compliant nanomechanisms fabricated via DNA origami self-assembly. The rigid, compliant, and flexible parts are constructed by bundles of many double-stranded DNA (dsDNA) helices, bundles of a few dsDNA helices or a single dsDNA helix, and single-stranded DNA (ssDNA) strands, respectively. Similar to its macroscopic counterparts, a CDOM generates its motion via deformation of at least one structural member. During the motion, strain energy is stored and released in the compliant components. Therefore, these CDOMs have the advantage of suppressing thermal fluctuations due to the internal mechanical energy barrier for motion. Here, we show that classic pseudorigid-body (PRB) models for compliant mechanism are successfully employed to the analysis of these DNA origami nanomechanisms and can serve to guide the design and analysis method. An example of compliant joint and a bistable four-bar CDOM fabricated with DNA origami are presented.

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Direct visualization of human myosin II force generation using DNA origami-based thick filaments

10.1101/634287 ◽

2019 ◽

Author(s):

Keisuke Fujita ◽

Masashi Ohmachi ◽

Keigo Ikezaki ◽

Toshio Yanagida ◽

Mitsuhiro Iwaki

Keyword(s):

Muscle Contraction ◽

Single Molecule ◽

Dna Origami ◽

Force Generation ◽

Dynamic Features ◽

Forward Region ◽

Arm Swing ◽

Lever Arm ◽

Contraction Speed ◽

Thick Filaments

AbstractMuscle contraction can be explained by the swinging lever-arm model. However, the dynamic features of how the myosin head swings the lever-arm and its initial interactions with actin are not well understood even though they are essential for the muscle force generation, contraction speed, heat production, and response to mechanical perturbations. This is because myosin heads during force generation have not been directly visualized. Here, we engineered thick filaments composed of DNA origami and recombinant human muscle myosin, and directly visualized the heads during force generation using nanometer-precision single-molecule imaging. We found that when the head diffuses, it weakly interacts with actin filaments and then strongly binds preferentially to the forward region as a Brownian ratchet. Upon strong binding, the head two-step lever-arm swing dominantly halts at the first step and occasionally reverses direction. These results can explain all mechanical characteristics of muscle contraction and suggest that our DNA origami-based assay system can be used to dissect the mechanistic details of motor proteins.

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Cardioinotropic Effects in Subchronic Intoxication of Rats with Lead and/or Cadmium Oxide Nanoparticles

International Journal of Molecular Sciences ◽

10.3390/ijms22073466 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3466

Author(s):

Svetlana V. Klinova ◽

Boris A. Katsnelson ◽

Ilzira A. Minigalieva ◽

Oksana P. Gerzen ◽

Alexander A. Balakin ◽

...

Keyword(s):

Cadmium Oxide ◽

Male Rats ◽

Sliding Velocity ◽

Muscle Type ◽

In Vitro Motility Assay ◽

Thin Filaments ◽

In Vitro Motility ◽

Toxic Impact ◽

Cdo Nanoparticles

Subchronic intoxication was induced in outbred male rats by repeated intraperitoneal injections with lead oxide (PbO) and/or cadmium oxide (CdO) nanoparticles (NPs) 3 times a week during 6 weeks for the purpose of examining its effects on the contractile characteristics of isolated right ventricle trabeculae and papillary muscles in isometric and afterload contractions. Isolated and combined intoxication with these NPs was observed to reduce the mechanical work produced by both types of myocardial preparation. Using the in vitro motility assay, we showed that the sliding velocity of regulated thin filaments drops under both isolated and combined intoxication with CdO–NP and PbO–NP. These results correlate with a shift in the expression of myosin heavy chain (MHC) isoforms towards slowly cycling β–MHC. The type of CdO–NP + PbO–NP combined cardiotoxicity depends on the effect of the toxic impact, the extent of this effect, the ratio of toxicant doses, and the degree of stretching of cardiomyocytes and muscle type studied. Some indices of combined Pb–NP and CdO–NP cardiotoxicity and general toxicity (genotoxicity included) became fully or partly normalized if intoxication developed against background administration of a bioprotective complex.

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Evidence that a higher ATP cost of muscular contraction contributes to the lower mechanical efficiency associated with COPD: preliminary findings

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00835.2010 ◽

2011 ◽

Vol 300 (5) ◽

pp. R1142-R1147 ◽

Cited By ~ 27

Author(s):

Gwenael Layec ◽

Luke J. Haseler ◽

Jan Hoff ◽

Russell S. Richardson

Keyword(s):

Skeletal Muscle ◽

Muscle Contraction ◽

Energy Cost ◽

Plantar Flexion ◽

Mechanical Efficiency ◽

Exercise Intolerance ◽

Chronic Obstructive ◽

Small Subset ◽

Resonance Spectroscopy ◽

Muscle Energetics

Impaired metabolism in peripheral skeletal muscles potentially contributes to exercise intolerance in chronic obstructive pulmonary disease (COPD). We used 31P-magnetic resonance spectroscopy (31P-MRS) to examine the energy cost and skeletal muscle energetics in six patients with COPD during dynamic plantar flexion exercise compared with six well-matched healthy control subjects. Patients with COPD displayed a higher energy cost of muscle contraction compared with the controls (control: 6.1 ± 3.1% of rest·min−1·W−1, COPD: 13.6 ± 8.3% of rest·min−1·W−1, P = 0.01). Although, the initial phosphocreatine resynthesis rate was also significantly attenuated in patients with COPD compared with controls (control: 74 ± 17% of rest/min, COPD: 52 ± 13% of rest/min, P = 0.04), when scaled to power output, oxidative ATP synthesis was similar between groups (6.5 ± 2.3% of rest·min−1·W−1 in control and 7.8 ± 3.9% of rest·min−1·W−1 in COPD, P = 0.52). Therefore, our results reveal, for the first time that in a small subset of patients with COPD a higher ATP cost of muscle contraction may substantially contribute to the lower mechanical efficiency previously reported in this population. In addition, it appears that some patients with COPD have preserved mitochondrial function and normal energy supply in lower limb skeletal muscle.

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Internal Flow Losses: A Fresh Look at Old Concepts

Journal of Fluids Engineering ◽

10.1115/1.4003857 ◽

2011 ◽

Vol 133 (5) ◽

Cited By ~ 16

Author(s):

Bastian Schmandt ◽

Heinz Herwig

Keyword(s):

Flow Field ◽

Entropy Generation ◽

Mechanical Energy ◽

Internal Flow ◽

Second Law Of Thermodynamics ◽

Head Loss ◽

Local Entropy ◽

Flow Losses ◽

Loss Coefficients ◽

Local Entropy Generation

Losses in a flow field due to single conduit components often are characterized by experimentally determined head loss coefficients K. These coefficients are defined and determined with the pressure as the critical quantity. A thermodynamic definition, given here as an alternative, is closer to the physics of flow losses, however. This definition is based upon the dissipation of mechanical energy as main quantity. With the second law of thermodynamics this dissipation can be linked to the local entropy generation in the flow field. For various conduit components K values are determined and physically interpreted by determining the entropy generation in the component as well as upstream and downstream of it. It turns out that most of the losses occur downstream of the components what carefully has to be taken into account when several components are combined in a flow network.

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Compatibility between the entomopathogenic fungus Beauveria bassiana and insecticides used in coffee plantations

Scientia Agricola ◽

10.1590/s0103-90162003000400009 ◽

2003 ◽

Vol 60 (4) ◽

pp. 663-667 ◽

Cited By ~ 35

Author(s):

Carolina Natali de Oliveira ◽

Pedro Manuel Oliveira Janeiro Neves ◽

Lídio Sueki Kawazoe

Keyword(s):

Beauveria Bassiana ◽

Vegetative Growth ◽

Entomopathogenic Fungus ◽

Microbial Control ◽

Infection Process ◽

Conservation Strategy ◽

Coffee Plantations ◽

Conidia Germination ◽

Fungus Beauveria Bassiana

Microbial control in integrated pest management (IPM) programs of coffee plantations is an important factor for the reduction of pest population densities. The use of selective pesticides can be associated with entomopathogens, increasing the efficiency of the control and reducing the use of required insecticides. The in vitro fungitoxic effect of insecticide formulations of Thiamethoxam, Cyfluthrin, Deltamethrin, Alpha-Cypermethrin, Triazophos, Chlorpyrifos, Fenpropathrin and Endosulfan and Beauveria bassiana (CG 425 strain) was evaluated at three concentrations (FR = average field recommendation; 0.5 ´ FR and 2 ´ FR). Effects of these products on conidia germination, vegetative growth and sporulation were compared. Only five insecticides, at the FR concentration, promoted conidia viability higher than 60%. Viability should be considered the most important factor to be evaluated since it is the first step of the infection process. The insecticide formulations of Alpha-Cypermethrin, Thiamethoxam and Cyfluthrin caused the lower inhibition level on conidia germination at the two lower concentrations, with no difference in relation to the control. With respect to vegetative growth analysis, Thiamethoxam at the two lower concentrations was not found to cause radial growth inhibition. Thiamethoxam caused the smallest inhibition level with regard to conidia production. The use of Alpha-Cypermethrin and Thiamethoxam formulations in coffee IPM programs for a B. bassiana inoculum conservation strategy are recommended, since these products were compatible with the entomopathogenic fungus Beauveria bassiana (CG 425), an important natural control agent of the coffee berry borer, Hypothenemus hampei.

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Simulating the Intraoral Aging of Dental Bonding Agents: A Narrative Review

Dentistry Journal ◽

10.3390/dj10010013 ◽

2022 ◽

Vol 10 (1) ◽

pp. 13

Author(s):

Tomas Vilde ◽

Cameron A. Stewart ◽

Yoav Finer

Keyword(s):

Resin Composite ◽

Dental Materials ◽

Thermal Fluctuations ◽

Narrative Review ◽

Mechanical Degradation ◽

Hybrid Layer ◽

Bonding Agents ◽

Dental Bonding

Despite their popularity, resin composite restorations fail earlier and at higher rates than comparable amalgam restorations. One of the reasons for these rates of failure are the properties of current dental bonding agents. Modern bonding agents are vulnerable to gradual chemical and mechanical degradation from a number of avenues such as daily use in chewing, catalytic hydrolysis facilitated by salivary or bacterial enzymes, and thermal fluctuations. These stressors have been found to work synergistically, all contributing to the deterioration and eventual failure of the hybrid layer. Due to the expense and difficulty in conducting in vivo experiments, in vitro protocols meant to accurately simulate the oral environment’s stressors are important in the development of bonding agents and materials that are more resistant to these processes of degradation. This narrative review serves to summarize the currently employed methods of aging dental materials and critically appraise them in the context of our knowledge of the oral environment’s parameters.

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Role of the reaction-structure coupling in temperature compensation of the KaiABC circadian rhythm

10.1101/2021.10.11.464015 ◽

2021 ◽

Author(s):

Masaki Sasai

Keyword(s):

Temperature Compensation ◽

Oscillation Amplitude ◽

Thermal Fluctuations ◽

Reaction Rates ◽

System Level ◽

Single Amino Acid ◽

Structural Transitions ◽

Single Amino Acid Residue ◽

Residue Substitution

When the mixture solution of cyanobacterial proteins, KaiA, KaiB, and KaiC, is incubated with ATP in vitro, the phosphorylation level of KaiC shows stable oscillations with the temperature-compensated circadian period. We analyzed this temperature compensation by developing a theoretical model describing the feedback relations among reactions and structural transitions in the KaiC molecule. The model showed that the reduced structural cooperativity should weaken the negative feedback coupling among reactions and structural transitions, which enlarges the oscillation amplitude and period, explaining the observed significant period extension upon single amino-acid residue substitution. We propose that an increase in thermal fluctuations similarly attenuates the reaction-structure feedback, explaining the temperature compensation in the KaiABC clock. The model suggests that the ATPase reactions in the CI domain of KaiC affect the period depending on how the reaction rates are modulated. The KaiABC clock provides a unique opportunity to analyze how the reaction-structure coupling regulates the system-level synchronized oscillations of molecules.

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