Contractile properties of rabbit psoas muscle fibres inhibited by beryllium fluoride

Inferring new drug indications using the complementarity between clinical disease signatures and drug effects

BACKGROUND

Drug repositioning is the process of finding new indications for existing drugs. Its importance has been dramatically increasing recently due to the enormous increase in new drug discovery cost. However, most of the previous molecular-centered drug repositioning work is not able to reflect the end-point physiological activities of drugs because of the inherent complexity of human physiological systems.

METHODS

Here, we suggest a novel computational framework to make inferences for alternative indications of marketed drugs by using electronic clinical information which reflects the end-point physiological results of drug's effects on the biological activities of humans. In this work, we use the concept of complementarity between clinical disease signatures and clinical drug effects. With this framework, we establish disease-related clinical variable vectors (clinical disease signature vectors) and drug-related clinical variable vectors (clinical drug effect vectors) by applying two methodologies (i.e., statistical analysis and literature mining). Finally, we assign a repositioning possibility score to each disease-drug pair by the calculation of complementarity (anti-correlation) and association between clinical states ("up" or "down") of disease signatures and clinical effects ("up", "down" or "association") of drugs. A total of 717 clinical variables in the electronic clinical dataset (NHANES), are considered in this study.

RESULTS

The statistical significance of our prediction results is supported through two benchmark datasets (Comparative Toxicogenomics Database and Clinical Trials). We discovered not only lots of known relationships between diseases and drugs, but also many hidden disease-drug relationships. For example, glutathione and edetic-acid may be investigated as candidate drugs for asthma treatment. We examined prediction results by using statistical experiments (enrichment verification, hyper-geometric and permutation test P<0.009 in Comparative Toxicogenomics Database and Clinical Trials) and presented evidences for those with already published literature.

CONCLUSION

The results show that electronic clinical information is a feasible data resource and utilizing the complementarity (anti-correlated relationships) between clinical signatures of disease and clinical effects of drugs is a potentially predictive concept in drug repositioning research. It makes the proposed approach useful to identity novel relationships between diseases and drugs that have a high probability of being biologically valid.

Phosphorylation of myosin regulatory light chain has minimal effect on kinetics and distribution of orientations of cross bridges of rabbit skeletal muscle

Force production in muscle results from ATP-driven cyclic interactions of myosin with actin. A myosin cross bridge consists of a globular head domain, containing actin and ATP-binding sites, and a neck domain with the associated light chain 1 (LC1) and the regulatory light chain (RLC). The actin polymer serves as a "rail" over which myosin translates. Phosphorylation of the RLC is thought to play a significant role in the regulation of muscle relaxation by increasing the degree of skeletal cross-bridge disorder and increasing muscle ATPase activity. The effect of phosphorylation on skeletal cross-bridge kinetics and the distribution of orientations during steady-state contraction of rabbit muscle is investigated here. Because the kinetics and orientation of an assembly of cross bridges (XBs) can only be studied when an individual XB makes a significant contribution to the overall signal, the number of observed XBs was minimized to ∼20 by limiting the detection volume and concentration of fluorescent XBs. The autofluorescence and photobleaching from an ex vivo sample was reduced by choosing a dye that was excited in the red and observed in the far red. The interference from scattering was eliminated by gating the signal. These techniques decrease large uncertainties associated with determination of the effect of phosphorylation on a few molecules ex vivo with millisecond time resolution. In spite of the remaining uncertainties, we conclude that the state of phosphorylation of RLC had no effect on the rate of dissociation of cross bridges from thin filaments, on the rate of myosin head binding to thin filaments, and on the rate of power stroke. On the other hand, phosphorylation slightly increased the degree of disorder of active cross bridges.

Contractility and kinetics of human fetal and human adult skeletal muscle

Little is known about the contraction and relaxation properties of fetal skeletal muscle, and measurements thus far have been made with non-human mammalian muscle. Data on human fetal skeletal muscle contraction are lacking, and there are no published reports on the kinetics of either fetal or adult human skeletal muscle myofibrils. Understanding the contractile properties of human fetal muscle would be valuable in understanding muscle development and a variety of muscle diseases that are associated with mutations in fetal muscle sarcomere proteins. Therefore, we characterised the contractile properties of developing human fetal skeletal muscle and compared them to adult human skeletal muscle and rabbit psoas muscle. Electron micrographs showed human fetal muscle sarcomeres are not fully formed but myofibril formation is visible. Isolated myofibril mechanical measurements revealed much lower specific force, and slower rates of isometric force development, slow phase relaxation, and fast phase relaxation in human fetal when compared to human adult skeletal muscle. The duration of slow phase relaxation was also significantly longer compared to both adult groups, but was similarly affected by elevated ADP. F-actin sliding on human fetal skeletal myosin coated surfaces in in vitro motility (IVM) assays was much slower compared with adult rabbit skeletal myosin, though the Km(app) (apparent (fitted) Michaelis-Menten constant) of F-actin speed with ATP titration suggests a greater affinity of human fetal myosin for nucleotide binding. Replacing ATP with 2 deoxy-ATP (dATP) increased F-actin speed for both groups by a similar amount. Titrations of ADP into IVM assays produced a similar inhibitory affect for both groups, suggesting ADP binding may be similar, at least under low load. Together, our results suggest slower but similar mechanisms of myosin chemomechanical transduction for human fetal muscle that may also be limited by immature myofilament structure.

Actin Sliding Velocities are Influenced by the Driving Forces of Actin-Myosin Binding

Unloaded shortening speeds, V, of muscle are thought to be limited by actin-bound myosin heads that resist shortening, or V = a·d·τon-1 where τon-1 is the rate at which myosin detaches from actin and d is myosin's step size. The a-term describes the efficiency of force transmission between myosin heads, and has been shown to become less than one at low myosin densities in a motility assay. Molecules such as inorganic phosphate, Pi, and blebbistatin inhibit both V and actin-myosin strong binding kinetics suggesting a link between V and attachment kinetics. To determine whether these small molecules slow V by increasing resistance to actin sliding or by decreasing the efficiency of force transmission, a, we determine how inhibition of V by Pi and blebbistatin changes the force exerted on actin filaments during an in vitro sliding assay, measured from changes in the rate, τbreak-1, at which actin filaments break. Upon addition of 30 mM Pi to a low (30 μM) [ATP] motility buffer V decreased from 1.8 to 1.3 μm·sec-1 and τbreak-1 from 0.029 to 0.018 sec-1. Upon addition of 50 μM blebbistatin to a low [ATP] motility buffer, V decreased from 1.0 to 0.7 μm·sec-1 and τbreak-1 from 0.059 to 0.022 sec-1. These results imply that blebbistatin and Pi slow V by decreasing force transmission, a, not by increasing resistive forces, implying that actin-myosin attachment kinetics influence V.

Myosin regulatory light chain phosphorylation inhibits shortening velocities of skeletal muscle fibers in the presence of the myosin inhibitor blebbistatin

Phosphorylation of skeletal myosin regulatory light chain (RLC) occurs in fatigue and may play a role in the inhibition of shortening velocities observed in vivo. Forces and shortening velocities were measured in permeabilized rabbit psoas fibers with either phosphorylated or dephosphorylated RLCs and in the presence or absence of the myosin inhibitor blebbistatin. Addition of 20 microM blebbistatin decreased tensions by approximately 80% in fibers, independent of phosphorylation. In blebbistatin maximal shortening velocities (V(max)) at 30 degrees C, were decreased by 45% (3.2 +/- 0.34 vs. 5.8 +/- 0.18 lengths/s) in phosphorylated fibers but were not inhibited in dephosphorylated fibers (6.0 +/- 0.30 vs. 5.4 +/- 0.30). In the presence of 20 microM blebbistatin, K(m) for V(max) as a function of [ATP] was lower for phosphorylated fibers than for dephosphorylated fibers (50 +/- 20 vs. 330 +/- 84 microM) indicating that the apparent binding of ATP is stronger in these fibers. Phosphorylation of RLC in situ during fiber preparation or by addition of myosin light chain kinase yielded similar data. RLC phosphorylation inhibited velocity in blebbistatin at both 30 and 10 degrees C, unlike previous reports where RLC phosphorylation only affected shortening velocities at higher temperatures.

An accelerated state of myosin-based actin motility

We use an in vitro motility assay to determine the biochemical basis for a hypermotile state of myosin-based actin sliding. It is widely assumed that the sole biochemical determinant of actin-sliding velocities, V, is actin-myosin detachment kinetics (1/tauon), yet we recently reported that, above a critical ATP concentration of approximately 100 microM, V exceeds the detachment limit by more than 2-fold. To determine the biochemical basis for this hypermotile state, we measure the effects of ATP and inorganic phosphate, Pi, on V and observe that at low [ATP] V decreases as ln [Pi], whereas above 100 microM ATP the hypermotile V is independent of Pi. The ln [Pi] dependence of V at low [ATP] is consistent with a macroscopic model of muscle shortening, similar to Hill's contractile component, which predicts that V varies linearly with an internal force (Hill's active state) that drives actin movement against the viscous drag of myosin heads strongly bound to actin (Hill's dashpot). At high [ATP], we suggest that the hypermotile V is caused by shear thinning of the resistive population of strongly bound myosin heads. Our data and analysis indicate that, in addition to contributions from tauon and myosin's step size, d, V is influenced by the biochemistry of myosin's working step as well as resistive properties of actin and myosin.

Myosin light chain phosphorylation inhibits muscle fiber shortening velocity in the presence of vanadate

We have shown that myosin light chain phosphorylation inhibits fiber shortening velocity at high temperatures, 30 degrees C, in the presence of the phosphate analog vanadate. Vanadate inhibits tension by reversing the transition to force-generating states, thus mimicking a prepower stroke state. We have previously shown that at low temperatures vanadate also inhibits velocity, but at high temperatures it does not, with an abrupt transition in inhibition occurring near 25 degrees C (E. Pate, G. Wilson, M. Bhimani, and R. Cooke. Biophys J 66: 1554-1562, 1994). Here we show that for fibers activated in the presence of 0.5 mM vanadate, at 30 degrees C, shortening velocity is not inhibited in dephosphorylated fibers but is inhibited by 37 +/- 10% in fibers with phosphorylated myosin light chains. There is no effect of phosphorylation on fiber velocity in the presence of vanadate at 10 degrees C. The K(m) for ATP, defined by the maximum velocity of fibers partially inhibited by vanadate at 30 degrees C, is 20 +/- 4 microM for phosphorylated fibers and 192 +/- 40 microM for dephosphorylated fibers, showing that phosphorylation also affects the binding of ATP. Fiber stiffness is not affected by phosphorylation. Inhibition of velocity by phosphorylation at 30 degrees C depends on the phosphate analog, with approximately 12% inhibition in fibers activated in the presence of 5 mM BeF(3) and no inhibition in the presence of 0.25 mM AlF(4). Our results show that myosin phosphorylation can inhibit shortening velocity in fibers with large populations of myosin heads trapped in prepower stroke states, such as occurs during muscle fatigue.

Dynamics of the nucleotide pocket of myosin measured by spin-labeled nucleotides

We have used electron paramagnetic probes attached to the ribose of ATP (SL-ATP) to monitor conformational changes in the nucleotide pocket of myosin. Spectra for analogs bound to myosin in the absence of actin showed a high degree of immobilization, indicating a closed nucleotide pocket. In the Actin.Myosin.SL-AMPPNP, Actin.Myosin.SL-ADP.BeF(3), and Actin.Myosin.SL-ADP.AlF(4) complexes, which mimic weakly binding states near the beginning of the power stroke, the nucleotide pocket remained closed. The spectra of the strongly bound Actin.Myosin.SL-ADP complex consisted of two components, one similar to the closed pocket and one with increased probe mobility, indicating a more open pocket, The temperature dependence of the spectra showed that the two conformations of the nucleotide pocket were in equilibrium, with the open conformation more favorable at higher temperatures. These results, which show that opening of the pocket occurs only in the strongly bound states, appear reasonable, as this would tend to keep ADP bound until the end of the power stroke. This conclusion also suggests that force is initially generated by a myosin with a closed nucleotide pocket.

Dimethyl sulphoxide enhances the effects of P(i) in myofibrils and inhibits the activity of rabbit skeletal muscle contractile proteins

In the catalytic cycle of skeletal muscle, myosin alternates between strongly and weakly bound cross-bridges, with the latter contributing little to sustained tension. Here we describe the action of DMSO, an organic solvent that appears to increase the population of weakly bound cross-bridges that accumulate after the binding of ATP, but before P(i) release. DMSO (5-30%, v/v) reversibly inhibits tension and ATP hydrolysis in vertebrate skeletal muscle myofibrils, and decreases the speed of unregulated F-actin in an in vitro motility assay with heavy meromyosin. In solution, controls for enzyme activity and intrinsic tryptophan fluorescence of myosin subfragment 1 (S1) in the presence of different cations indicate that structural changes attributable to DMSO are small and reversible, and do not involve unfolding. Since DMSO depresses S1 and acto-S1 MgATPase activities in the same proportions, without altering acto-S1 affinity, the principal DMSO target apparently lies within the catalytic cycle rather than with actin-myosin binding. Inhibition by DMSO in myofibrils is the same in the presence or the absence of Ca(2+) and regulatory proteins, in contrast with the effects of ethylene glycol, and the Ca(2+) sensitivity of isometric tension is slightly decreased by DMSO. The apparent affinity for P(i) is enhanced markedly by DMSO (and to a lesser extent by ethylene glycol) in skinned fibres, suggesting that DMSO stabilizes cross-bridges that have ADP.P(i) or ATP bound to them.