Multistep orthophosphate release tunes actomyosin energy transduction

Characterizing the concentration and load dependence of phosphate binding to rabbit fast skeletal actomyosin

Intensely contracting fast skeletal muscle rapidly loses the ability to generate force, due in part to the accumulation of phosphate (Pi) inhibiting myosin's force-generating capacity, in a process that is strain dependent. Crucial aspects of the mechanism underlying this inhibition remain unclear. Therefore, we directly determined the effects of increasing [Pi] on rabbit psoas muscle myosin's ability to generate force against progressively higher resistive loads in a laser trap assay, with the requisite spatial and temporal resolution to discern the mechanism of inhibition. Myosin's force-generating capacity decreased with increasing [Pi], an effect that became more pronounced at higher resistive loads. The decrease in force resulted from myosin's accelerated detachment from actin, which also increased at higher resistive forces. These data are well fit by a cross-bridge model in which Pi rebinds to actomyosin in a postpowerstroke, ADP-bound state before accelerating myosin's detachment from actin. Thus, these findings provide important molecular insight into the mechanism underlying the Pi-induced loss of force during muscle fatigue from intense contractile activity.

Mechanistic insights into effects of the cardiac myosin activator omecamtiv mecarbil from mechanokinetic modelling

Introduction

Small molecular compounds that affect the force, and motion-generating actin-myosin interaction in the heart have emerged as alternatives to treat or alleviate symptoms in severe debilitating conditions, such as cardiomyopathies and heart failure. Omecamtiv mecarbil (OM) is such a compound developed to enhance cardiac contraction. In addition to potential therapeutic use, its effects may help to elucidate myosin energy transduction mechanisms in health and disease and add insights into how the molecular properties govern contraction of large myosin ensembles in cardiac cells. Despite intense studies, the effects of OM are still incompletely understood.

Methods

Here we take an in silico approach to elucidate the issue. First, we modify a model, previously used in studies of skeletal muscle, with molecular parameter values for human ventricular β-myosin to make it useful for studies of both myosin mutations and drugs. Repeated tests lead to at a set of parameter values that allow faithful reproduction of range of functional variables of cardiac myocytes. We then apply the model to studies of OM.

Results and discussion

The results suggest that major effects of OM such as large reduction of the maximum velocity with more limited effects on maximum isometric force and slowed actin-activated ATPase can be accounted for by two key molecular effects. These encompass a reduced difference in binding free energy between the pre- and post-power-stroke states and greatly increased activation energy for the lever arm swing during the power-stroke. Better quantitative agreement, e.g., isometric force minimally changed from the control value by OM is achieved by additional changes in model parameter values previously suggested by studies of isolated proteins.

Phosphate rebinding induces force reversal via slow backward cycling of cross-bridges

Objective

Previous studies on muscle fibers, myofibrils, and myosin revealed that the release of inorganic phosphate (Pi) and the force-generating step(s) are reversible, with cross-bridges also cycling backward through these steps by reversing force-generating steps and rebinding Pi. The aim was to explore the significance of force redevelopment kinetics (rate constant k TR) in cardiac myofibrils for the coupling between the Pi binding induced force reversal and the rate-limiting transition f - for backward cycling of cross-bridges from force-generating to non-force-generating states.

Methods

k TR and force generation of cardiac myofibrils from guinea pigs were investigated at 0.015-20 mM Pi. The observed force-[Pi], force-log [Pi], k TR-[Pi], and k TR-force relations were assessed with various single-pathway models of the cross-bridge cycle that differed in sequence and kinetics of reversible Pi release, reversible force-generating step and reversible rate-limiting transition. Based on the interpretation that k TR reflects the sum of rate-limiting transitions in the cross-bridge cycle, an indicator, the coupling strength, was defined to quantify the contribution of Pi binding induced force reversal to the rate-limiting transition f - from the [Pi]-modulated k TR-force relation.

Results

Increasing [Pi] decreased force by a bi-linear force-log [Pi] relation, increased k TR in a slightly downward curved dependence with [Pi], and altered k TR almost reciprocally to force reflected by the k TR-force relation. Force-[Pi] and force-log [Pi] relations provided less selectivity for the exclusion of models than the k TR-[Pi] and k TR-force relations. The k TR-force relation observed in experiments with cardiac myofibrils yielded the coupling strength +0.84 ± 0.08 close to 1, the maximum coupling strength expected for the reciprocal k TR-force relationship. Single pathway models consisting of fast reversible force generation before or after rapid reversible Pi release failed to describe the observed k TR-force relation. Single pathway models consistent with the observed k TR-force relation had either slow Pi binding or slow force reversal, i.e., in the consistent single pathway models, f - was assigned to the rate of either Pi binding or force reversal.

Conclusion

Backward flux of cross-bridges from force-generating to non-force-generating states is limited by the rates of Pi binding or force reversal ruling out other rate-limiting steps uncoupled from Pi binding induced force reversal.

Mechanisms of myosin II force generation: insights from novel experimental techniques and approaches

Myosin II is a molecular motor that converts chemical energy derived from ATP hydrolysis into mechanical work. Myosin II isoforms are responsible for muscle contraction and a range of cell functions relying on the development of force and motion. When the motor attaches to actin, ATP is hydrolyzed and inorganic phosphate (Pi) and ADP are released from its active site. These reactions are coordinated with changes in the structure of myosin, promoting the so-called "power stroke" that causes the sliding of actin filaments. The general features of the myosin-actin interactions are well accepted, but there are critical issues that remain poorly understood, mostly due to technological limitations. In recent years, there has been a significant advance in structural, biochemical, and mechanical methods that have advanced the field considerably. New modeling approaches have also allowed researchers to understand actomyosin interactions at different levels of analysis. This paper reviews recent studies looking into the interaction between myosin II and actin filaments, which leads to power stroke and force generation. It reviews studies conducted with single myosin molecules, myosins working in filaments, muscle sarcomeres, myofibrils, and fibers. It also reviews the mathematical models that have been used to understand the mechanics of myosin II in approaches focusing on single molecules to ensembles. Finally, it includes brief sections on translational aspects, how changes in the myosin motor by mutations and/or posttranslational modifications may cause detrimental effects in diseases and aging, among other conditions, and how myosin II has become an emerging drug target.

Assembly and biological functions of metal-biomolecule network nanoparticles formed by metal-phosphonate coordination

Metal-organic networks have attracted widespread interest owing to their hybrid physicochemical properties. Natural biomolecules represent attractive building blocks for these materials because of their inherent biological function and high biocompatibility; however, assembling them into coordination network materials, especially nanoparticles (NPs), is challenging. Herein, we exploit the coordination between metal ions and phosphonate groups, which are present in many biomolecules, to form metal-biomolecule network (MBN) NPs in aqueous solution at room temperature. Various phosphonate-containing biomolecules, including plant phytate, DNA, and proteins, were used to assemble MBN NPs with tunable physicochemical properties (e.g., size). In addition to excellent biocompatibility and high cargo-loading efficiency (>95%), these two-component MBN NPs have various biological functionalities, including endosomal escape, immune regulation, and molecular recognition, thus offering advantages over nonbiomolecular-based coordination materials. This work expands our understanding of metal-organic chemistry with the emerging class of metal-biomolecule systems and provides a pathway for incorporating biofunctionalities into advanced coordination materials for diverse fields.

Probing actin-activated ATP turnover kinetics of human cardiac myosin II by single molecule fluorescence

Mechanistic insights into myosin II energy transduction in striated muscle in health and disease would benefit from functional studies of a wide range of point-mutants. This approach is, however, hampered by the slow turnaround of myosin II expression that usually relies on adenoviruses for gene transfer. A recently developed virus-free method is more time effective but would yield too small amounts of myosin for standard biochemical analyses. However, if the fluorescent adenosine triphosphate (ATP) and single molecule (sm) total internal reflection fluorescence microscopy previously used to analyze basal ATP turnover by myosin alone, can be expanded to actin-activated ATP turnover, it would appreciably reduce the required amount of myosin. To that end, we here describe zero-length cross-linking of human cardiac myosin II motor fragments (sub-fragment 1 long [S1L]) to surface-immobilized actin filaments in a configuration with maintained actin-activated ATP turnover. After optimizing the analysis of sm fluorescence events, we show that the amount of myosin produced from C2C12 cells in one 60 mm cell culture plate is sufficient to obtain both the basal myosin ATP turnover rate and the maximum actin-activated rate constant (k cat). Our analysis of many single binding events of fluorescent ATP to many S1L motor fragments revealed processes reflecting basal and actin-activated ATPase, but also a third exponential process consistent with non-specific ATP-binding outside the active site.

Improved longevity of actomyosin in vitro motility assays for sustainable lab-on-a-chip applications

In the in vitro motility assay (IVMA), actin filaments are observed while propelled by surface-adsorbed myosin motor fragments such as heavy meromyosin (HMM). In addition to fundamental studies, the IVMA is the basis for a range of lab-on-a-chip applications, e.g. transport of cargoes in nanofabricated channels in nanoseparation/biosensing or the solution of combinatorial mathematical problems in network-based biocomputation. In these applications, prolonged myosin function is critical as is the potential to repeatedly exchange experimental solutions without functional deterioration. We here elucidate key factors of importance in these regards. Our findings support a hypothesis that early deterioration in the IVMA is primarily due to oxygen entrance into in vitro motility assay flow cells. In the presence of a typically used oxygen scavenger mixture (glucose oxidase, glucose, and catalase), this leads to pH reduction by a glucose oxidase-catalyzed reaction between glucose and oxygen but also contributes to functional deterioration by other mechanisms. Our studies further demonstrate challenges associated with evaporation and loss of actin filaments with time. However, over 8 h at 21-26 °C, there is no significant surface desorption or denaturation of HMM if solutions are exchanged manually every 30 min. We arrive at an optimized protocol with repeated exchange of carefully degassed assay solution of 45 mM ionic strength, at 30 min intervals. This is sufficient to maintain the high-quality function in an IVMA over 8 h at 21-26 °C, provided that fresh actin filaments are re-supplied in connection with each assay solution exchange. Finally, we demonstrate adaptation to a microfluidic platform and identify challenges that remain to be solved for real lab-on-a-chip applications.

Cost-Efficient Expression of Human Cardiac Myosin Heavy Chain in C2C12 Cells with a Non-Viral Transfection Reagent

Production of functional myosin heavy chain (MHC) of striated muscle myosin II for studies of isolated proteins requires mature muscle (e.g., C2C12) cells for expression. This is important both for fundamental studies of molecular mechanisms and for investigations of deleterious diseases like cardiomyopathies due to mutations in the MHC gene (MYH7). Generally, an adenovirus vector is used for transfection, but recently we demonstrated transfection by a non-viral polymer reagent, JetPrime. Due to the rather high costs of JetPrime and for the sustainability of the virus-free expression method, access to more than one transfection reagent is important. Here, we therefore evaluate such a candidate substance, GenJet. Using the human cardiac β-myosin heavy chain (β-MHC) as a model system, we found effective transfection of C2C12 cells showing a transfection efficiency nearly as good as with the JetPrime reagent. This was achieved following a protocol developed for JetPrime because a manufacturer-recommended application protocol for GenJet to transfect cells in suspension did not perform well. We demonstrate, using in vitro motility assays and single-molecule ATP turnover assays, that the protein expressed and purified from cells transfected with the GenJet reagent is functional. The purification yields reached were slightly lower than in JetPrime-based purifications, but they were achieved at a significantly lower cost. Our results demonstrate the sustainability of the virus-free method by showing that more than one polymer-based transfection reagent can generate useful amounts of active MHC. Particularly, we suggest that GenJet, due to its current ~4-fold lower cost, is useful for applications requiring larger amounts of a given MHC variant.

Study of the Myosin Relay Helix Peptide by Molecular Dynamics Simulations, Pump-Probe and 2D Infrared Spectroscopy

The Davydov model was conjectured to describe how an amide I excitation created during ATP hydrolysis in myosin might be significant in providing energy to drive myosin's chemomechanical cycle. The free energy surfaces of the myosin relay helix peptide dissolved in 2,2,2-trifluoroethanol (TFE), determined by metadynamics simulations, demonstrate local minima differing in free energy by only ~2 kT, corresponding to broken and stabilized hydrogen bonds, respectively. Experimental pump-probe and 2D infrared spectroscopy were performed on the peptide dissolved in TFE. The relative heights of two peaks seen in the pump-probe data and the corresponding relative volumes of diagonal peaks seen in the 2D-IR spectra at time delays between 0.5 ps and 1 ps differ noticeably from what is seen at earlier or later time delays or in the linear spectrum, indicating that a vibrational excitation may influence the conformational state of this helix. Thus, it is possible that the presence of an amide I excitation may be a direct factor in the conformational state taken on by the myosin relay helix following ATP hydrolysis in myosin.

Modeling thick filament activation suggests a molecular basis for force depression

Multiscale models aiming to connect muscle's molecular and cellular function have been difficult to develop, in part due to a lack of self-consistent multiscale data. To address this gap, we measured the force response from single, skinned rabbit psoas muscle fibers to ramp shortenings and step stretches performed on the plateau region of the force-length relationship. We isolated myosin from the same muscles and, under similar conditions, performed single-molecule and ensemble measurements of myosin's ATP-dependent interaction with actin using laser trapping and in vitro motility assays. We fit the fiber data by developing a partial differential equation model that includes thick filament activation, whereby an increase in force on the thick filament pulls myosin out of an inhibited state. The model also includes a series elastic element and a parallel elastic element. This parallel elastic element models a titin-actin interaction proposed to account for the increase in isometric force after stretch (residual force enhancement). By optimizing the model fit to a subset of our fiber measurements, we specified seven unknown parameters. The model then successfully predicted the remainder of our fiber measurements and also our molecular measurements from the laser trap and in vitro motility. The success of the model suggests that our multiscale data are self-consistent and can serve as a testbed for other multiscale models. Moreover, the model captures the decrease in isometric force observed in our muscle fibers after active shortening (force depression), suggesting a molecular mechanism for force depression, whereby a parallel elastic element combines with thick filament activation to decrease the number of cycling cross-bridges.

Analysis of metabolite and strain effects on cardiac cross-bridge dynamics using model linearisation techniques

Multi-scale models of cardiac energetics are becoming crucial in better understanding the prevalent chronic diseases operating at the intersection of metabolic and cardiovascular dysfunction. Computationally efficient models of cardiac cross-bridge kinetics that are sensitive to changes in metabolite concentrations are necessary to simulate the effects of disease-induced changes in cellular metabolic state on cardiac mechanics across disparate spatial scales. While these models do currently exist, deeper analysis of how the modelling of metabolite effects and the assignment of strain dependence within the cross-bridge cycle affect the properties of the model is required. In this study, model linearisation techniques were used to simulate and interrogate the complex modulus of an ODE-based model of cross-bridge kinetics. Active complex moduli were measured from permeabilised rat cardiac trabeculae under five different metabolite conditions with varying ATP and Pi concentrations. Sensitivity to metabolites was incorporated into an existing three-state cross-bridge model using either a direct dependence or a rapid equilibrium approach. Combining the two metabolite binding methods with all possible locations of strain dependence within the cross-bridge cycle produced 64 permutations of the cross-bridge model. Using linear model analysis, these models were systematically explored to determine the effects of metabolite binding and their interaction with strain dependence on the frequency response of cardiac muscle. The results showed that the experimentally observed effects of ATP and Pi concentrations on the cardiac complex modulus could be attributed to their regulation of cross-bridge detachment rates. Analysis of the cross-bridge models revealed a mechanistic basis for the biochemical schemes which place Pi release following cross-bridge formation and ATP binding prior to cross-bridge detachment. In addition, placing strain dependence on the reverse rate of the cross-bridge power stroke produced the model which most closely matched the experimental data. From these analyses, a well-justified metabolite-sensitive model of rat cardiac cross-bridge kinetics is presented which is suitable for parameterisation with other data sets and integration with multi-scale cardiac models.

From amino-acid to disease: the effects of oxidation on actin-myosin interactions in muscle

Actin-myosin interactions form the basis of the force-producing contraction cycle within the sarcomere, serving as the primary mechanism for muscle contraction. Post-translational modifications, such as oxidation, have a considerable impact on the mechanics of these interactions. Considering their widespread occurrence, the explicit contributions of these modifications to muscle function remain an active field of research. In this review, we aim to provide a comprehensive overview of the basic mechanics of the actin-myosin complex and elucidate the extent to which oxidation influences the contractile cycle and various mechanical characteristics of this complex at the single-molecule, myofibrillar and whole-muscle levels. We place particular focus on amino acids shown to be vulnerable to oxidation in actin, myosin, and some of their binding partners. Additionally, we highlight the differences between in vitro environments, where oxidation is controlled and limited to actin and myosin and myofibrillar or whole muscle environments, to foster a better understanding of oxidative modification in muscle. Thus, this review seeks to encompass a broad range of studies, aiming to lay out the multi layered effects of oxidation in in vitro and in vivo environments, with brief mention of clinical muscular disorders associated with oxidative stress.

Exploitation of Engineered Light-Switchable Myosin XI for Nanotechnological Applications

For certain nanotechnological applications of the contractile proteins actin and myosin, e.g., in biosensing and network-based biocomputation, it would be desirable to temporarily switch on/off motile function in parts of nanostructured devices, e.g., for sorting or programming. Myosin XI motor constructs, engineered with a light-switchable domain for switching actin motility between high and low velocities (light-sensitive motors (LSMs) below), are promising in this regard. However, they were not designed for use in nanotechnology, where longevity of operation, long shelf life, and selectivity of function in specific regions of a nanofabricated network are important. Here, we tested if these criteria can be fulfilled using existing LSM constructs or if additional developments will be required. We demonstrated extended shelf life as well as longevity of the actin-propelling function compared to those in previous studies. We also evaluated several approaches for selective immobilization with a maintained actin propelling function in dedicated nanochannels only. Whereas selectivity was feasible using certain nanopatterning combinations, the reproducibility was not satisfactory. In summary, the study demonstrates the feasibility of using engineered light-controlled myosin XI motors for myosin-driven actin transport in nanotechnological applications. Before use for, e.g., sorting or programming, additional work is however needed to achieve reproducibility of the nanofabrication and, further, optimize the motor properties.

New paradigms in actomyosin energy transduction: Critical evaluation of non-traditional models for orthophosphate release

Release of the ATP hydrolysis product ortophosphate (Pi) from the active site of myosin is central in chemo-mechanical energy transduction and closely associated with the main force-generating structural change, the power-stroke. Despite intense investigations, the relative timing between Pi-release and the power-stroke remains poorly understood. This hampers in depth understanding of force production by myosin in health and disease and our understanding of myosin-active drugs. Since the 1990s and up to today, models that incorporate the Pi-release either distinctly before or after the power-stroke, in unbranched kinetic schemes, have dominated the literature. However, in recent years, alternative models have emerged to explain apparently contradictory findings. Here, we first compare and critically analyze three influential alternative models proposed previously. These are either characterized by a branched kinetic scheme or by partial uncoupling of Pi-release and the power-stroke. Finally, we suggest critical tests of the models aiming for a unified picture.

Theoretical efficiency limits and speed-efficiency trade-off in myosin motors

Muscle myosin is a non-processive molecular motor generates mechanical work when cooperating in large ensembles. During its cyle, each individual motor keeps attaching and detaching from the actin filament. The random nature of attachment and detachment inevitably leads to losses and imposes theoretical limits on the energetic efficiency. Here, we numerically determine the theoretical efficiency limit of a classical myosin model with a given number of mechano-chemical states. All parameters that are not bounded by physical limits (like rate limiting steps) are determined by numerical efficiency optimization. We show that the efficiency is limited by the number of states, the stiffness and the rate-limiting kinetic steps. There is a trade-off between speed and efficiency. Slow motors are optimal when most of the available free energy is allocated to the working stroke and the stiffness of their elastic element is high. Fast motors, on the other hand, work better with a lower and asymmetric stiffness and allocate a larger fraction of free energy to the release of ADP. Overall, many features found in myosins coincide with the findings from the model optimization: there are at least 3 bound states, the largest part of the working stroke takes place during the first transition, the ADP affinity is adapted differently in slow and fast myosins and there is an asymmetry in elastic elements.

A mutation in switch I alters the load-dependent kinetics of myosin Va

Myosin Va is the molecular motor that drives intracellular vesicular transport, powered by the transduction of chemical energy from ATP into mechanical work. The coupling of the powerstroke and phosphate (Pi) release is key to understanding the transduction process, and crucial details of this process remain unclear. Therefore, we determined the effect of elevated Pi on the force-generating capacity of a mini-ensemble of myosin Va S1 (WT) in a laser trap assay. By increasing the stiffness of the laser trap we determined the effect of increasing resistive loads on the rate of Pi-induced detachment from actin, and quantified this effect using the Bell approximation. We observed that WT myosin generated higher forces and larger displacements at the higher laser trap stiffnesses in the presence of 30 mM Pi, but binding event lifetimes decreased dramatically, which is most consistent with the powerstroke preceding the release of Pi from the active site. Repeating these experiments using a construct with a mutation in switch I of the active site (S217A) caused a seven-fold increase in the load-dependence of the Pi-induced detachment rate, suggesting that the S217A region of switch I may help mediate the load-dependence of Pi-rebinding.

Protein dynamics by the combination of high-speed AFM and computational modeling

High-speed atomic force microscopy (HS-AFM) allows direct observation of biological molecules in dynamic action. However, HS-AFM has no atomic resolution. This article reviews recent progress of computational methods to infer high-resolution information, including the construction of 3D atomistic structures, from experimentally acquired resolution-limited HS-AFM images.

Conformational changes linked to ADP release from human cardiac myosin bound to actin-tropomyosin

Following binding to the thin filament, β-cardiac myosin couples ATP-hydrolysis to conformational rearrangements in the myosin motor that drive myofilament sliding and cardiac ventricular contraction. However, key features of the cardiac-specific actin-myosin interaction remain uncertain, including the structural effect of ADP release from myosin, which is rate-limiting during force generation. In fact, ADP release slows under experimental load or in the intact heart due to the afterload, thereby adjusting cardiac muscle power output to meet physiological demands. To further elucidate the structural basis of this fundamental process, we used a combination of cryo-EM reconstruction methodologies to determine structures of the human cardiac actin-myosin-tropomyosin filament complex at better than 3.4 Å-resolution in the presence and in the absence of Mg2+·ADP. Focused refinements of the myosin motor head and its essential light chains in these reconstructions reveal that small changes in the nucleotide-binding site are coupled to significant rigid body movements of the myosin converter domain and a 16-degree lever arm swing. Our structures provide a mechanistic framework to understand the effect of ADP binding and release on human cardiac β-myosin, and offer insights into the force-sensing mechanism displayed by the cardiac myosin motor.

Integrating comparative modeling and accelerated simulations reveals conformational and energetic basis of actomyosin force generation

Muscle contraction is performed by arrays of contractile proteins in the sarcomere. Serious heart diseases, such as cardiomyopathy, can often be results of mutations in myosin and actin. Direct characterization of how small changes in the myosin-actin complex impact its force production remains challenging. Molecular dynamics (MD) simulations, although capable of studying protein structure-function relationships, are limited owing to the slow timescale of the myosin cycle as well as a lack of various intermediate structures for the actomyosin complex. Here, employing comparative modeling and enhanced sampling MD simulations, we show how the human cardiac myosin generates force during the mechanochemical cycle. Initial conformational ensembles for different myosin-actin states are learned from multiple structural templates with Rosetta. This enables us to efficiently sample the energy landscape of the system using Gaussian accelerated MD. Key myosin loop residues, whose substitutions are related to cardiomyopathy, are identified to form stable or metastable interactions with the actin surface. We find that the actin-binding cleft closure is allosterically coupled to the myosin motor core transitions and ATP-hydrolysis product release from the active site. Furthermore, a gate between switch I and switch II is suggested to control phosphate release at the prepowerstroke state. Our approach demonstrates the ability to link sequence and structural information to motor functions.

Resistance to a tyrosine kinase inhibitor mediated by changes to the conformation space of the kinase

Gilteritinib is a highly selective and effective inhibitor of the FLT3/ITD mutated protein, and is used successfully in treating acute myeloid leukaemia (AML). Unfortunately, tumour cells gradually develop resistance to gilteritinib due to mutations in the molecular drug target. The atomistic details behind this observed resistance are not clear, since the protein structure of the complex is only available in the inactive state, while the drug binds better to the active state. To overcome this limitation, we used a computer-aided approach where we docked gilteritinib to the active site of FLT3/ITD and calculated the Gibbs free energy difference between the binding energies of the parental and mutant enzymes. These calculations agreed with experimental estimations for one mutation (F691L) but not the other (D698N). To further understand how these mutations operate, we used metadynamics simulations to study the conformational landscape of the activation process. Both mutants show a lower activation energy barrier which suggests that they are more likely to adopt an active state until inhibited, making the mutant enzymes more active. This suggests that a higher efficiency of tyrosine kinases contributes to resistance not only against type 2 but also against type 1 kinase inhibitors.

BioAFMviewer software for simulation atomic force microscopy of molecular structures and conformational dynamics

Atomic force microscopy (AFM) and high-speed scanning have significantly advanced real time observation of biomolecular dynamics, with applications ranging from single molecules to the cellular level. To facilitate the interpretation of resolution-limited imaging, post-experimental computational analysis plays an increasingly important role to understand AFM measurements. Data-driven simulation of AFM, computationally emulating experimental scanning, and automatized fitting has recently elevated the understanding of measured AFM topographies by inferring the underlying full 3D atomistic structures. Providing an interactive user-friendly interface for simulation AFM, the BioAFMviewer software has become an established tool within the Bio-AFM community, with a plethora of applications demonstrating how the obtained full atomistic information advances molecular understanding beyond topographic imaging. This graphical review illustrates the BioAFMviewer capacities and further emphasizes the importance of simulation AFM to complement experimental observations.

Insights into Muscle Contraction Derived from the Effects of Small-Molecular Actomyosin-Modulating Compounds

Bottom-up mechanokinetic models predict ensemble function of actin and myosin based on parameter values derived from studies using isolated proteins. To be generally useful, e.g., to analyze disease effects, such models must also be able to predict ensemble function when actomyosin interaction kinetics are modified differently from normal. Here, we test this capability for a model recently shown to predict several physiological phenomena along with the effects of the small molecular compound blebbistatin. We demonstrate that this model also qualitatively predicts effects of other well-characterized drugs as well as varied concentrations of MgATP. However, the effects of one compound, amrinone, are not well accounted for quantitatively. We therefore systematically varied key model parameters to address this issue, leading to the increased amplitude of the second sub-stroke of the power stroke from 1 nm to 2.2 nm, an unchanged first sub-stroke (5.3−5.5 nm), and an effective cross-bridge attachment rate that more than doubled. In addition to better accounting for the effects of amrinone, the modified model also accounts well for normal physiological ensemble function. Moreover, a Monte Carlo simulation-based version of the model was used to evaluate force−velocity data from small myosin ensembles. We discuss our findings in relation to key aspects of actin−myosin operation mechanisms causing a non-hyperbolic shape of the force−velocity relationship at high loads. We also discuss remaining limitations of the model, including uncertainty of whether the cross-bridge elasticity is linear or not, the capability to account for contractile properties of very small actomyosin ensembles (<20 myosin heads), and the mechanism for requirements of a higher cross-bridge attachment rate during shortening compared to during isometric contraction.