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Here, we have constructed neural network-based models that predict atomic partial charges with high accuracy at low computational cost. The models were trained using high-quality data acquired from quantum mechanics calculations using the fragment molecular orbital method. We have succeeded in obtaining highly accurate atomic partial charges for three representative molecular systems of proteins, including one large biomolecule (approx. 2000 atoms). The novelty of our approach is the ability to take into account the electronic polarization in the system, which is a system-dependent phenomenon, being important in the field of drug design. Our high-precision models are useful for the prediction of atomic partial charges and expected to be widely applicable in structure-based drug designs such as structural optimization, high-speed and high-precision docking, and molecular dynamics calculations.

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.

We have performed dynamic docking between a prototypic G-protein-coupled receptor (GPCR) system, the β2-adrenergic receptor, and its antagonist, alprenolol, using one of the enhanced conformation sampling methods, multicanonical molecular dynamics (McMD), which does not rely on any prior knowledge for the definition of the reaction coordinate. Although we have previously applied our McMD-based dynamic docking protocol to various globular protein systems, its application to GPCR systems would be difficult because of their complicated design, which include a lipid bilayer, and because of the difficulty in sampling the configurational space of a binding site that exists deep inside the GPCR. Our simulations sampled a wide array of ligand-bound and ligand-unbound structures, and we measured 427 binding events during our 48 μs production run. Analysis of the ensemble revealed several stable and meta-stable structures, where the most stable structure at the global free energy minimum matches the experimental one. Additional canonical MD simulations were used for refinement and validation of the structures, revealing that most of the intermediates are sufficiently stable to trap the ligand in these intermediary states and furthermore validated our prediction results. Given the difficulty in reaching the orthosteric binding site, chemical optimization of the compound for the second ranking configuration, which binds near the pocket's entrance, might lead to a high-affinity allosteric inhibitor. Accordingly, we show that the application of our methodology can be used to provide crucial insights for the rational design of drugs that target GPCRs.

A medium-sized and highly flexible inhibitor to the enzyme β-secretase 1 (BACE), which produces the amyloid β-peptide by cleavage of its precursor protein, was dynamically docked into the large and wide catalytic cleft of BACE that binds to the amyloid-precursor by employing multicanonical molecular dynamics (McMD) simulations. We applied our method to predict the native binding configuration and sample the intermediary structures connecting this natively bound state to the unbound one. Representative structures located at free energy minima obtained from McMD were taken and subjected to canonical simulations to refine and validate them, reproducing the native complex structure in agreement with the experimental data in the most stable structure, i.e., the one at the global minimum. In addition, the binding free energy was estimated by umbrella sampling (US) simulations along representative pathways obtained from the McMD ensemble, followed by weighted histogram analysis to estimate the affinity, which also reproduced the experimental inhibitory affinity. Interestingly, the loss of interactions between the two molecules along the pathway was clearly shown in the free energy landscape, reiterating the fundamental importance of atomistic interactions to the binding affinity between receptor and drug compound. The sampled ensemble by the US simulations smoothly connected the bound and unbound states, refining the binding pathway while staying true to the McMD ensemble.

We verified that the matrix method, a process analysis method used mainly for life cycle inventory analysis, has several advantages in the analysis of power systems, which have recently become more complex to enhance efficiency and to reduce CO2 emissions. While designing a conceptual thermodynamic model of a complex power system, the matrix method provides a definite procedure and facilitates calculations, even if there is a recursive loop between the upstream and downstream processes. Similarly, in the case of partial modification to the constructed model, the matrix method can potentially reduce the time and effort required to calculate the thermodynamic balances, even if the constructed model is designed by others. In this study, we obtained mass flow and energy balances of example model power systems by the matrix method from the common thermodynamic conditions including temperatures and pressures which are set on the basis of an existing industrial steam power system. While analyzing the environmental impact of complex multiproduct power systems, such as carbon emissions, the matrix method can be used to easily derive the environmental impact of each final product. We could verify the efficacy of the matrix method in accurately deriving that of an example model power system.

A novel method to correct a partial sampling effect, due to the hexagonal filament array of a statistical superlattice form, on the thick (myosin)-filament-based layer lines in X-ray diffraction patterns from higher-vertebrate striated muscle has been developed using the cylindrically averaged difference Patterson function [ΔQ(r, z)]. The method involves cutting off the inter-filament vector peaks that appear in the radial region beyond ∼32 nm on the ΔQ(r, z) map calculated from the observed layer-line intensities, and then deducing the single-myosin-filament transforms by inverse Fourier transformation of the truncated ΔQ(r, z). The accuracy of the cut-off method was tested using a single-myosin-filament model and a hexagonal filament-array model with a size of one superlattice unit cell. The layer-line intensities calculated from the truncated ΔQ(r, z) of the hexagonal filament-array model showed few sampling peaks, the layer lines being effectively coincident with those from the single-filament model except for the intensities close to the meridian. Some residual differences were caused by the face-to-face inter-crossbridge vectors between closest neighboring filaments, which correspond to ∼27.5% of the total number of crossbridge vectors in the truncated ΔQ(r, z) map, but the face-to-face inter-crossbridge vectors contributed mainly to the intensities close to the meridian. Their remnant off-meridional layer-line intensity components did not significantly affect a search for the optimum azimuthal orientation of myosin crossbridges in the resting state of muscle.

We propose a novel concept for power generation that involves the combination of a low-condition heat generator (LCHG), such as a light water nuclear reactor or a biomass combustion boiler, with an advanced closed-cycle oxy-fuel combustion gas turbine—a type of complex and efficient oxyfuel gas turbine plant, in accordance with our previous studies in combination with a simple oxy-fuel gas turbine plant. In this study, a LCHG is designed to heat water to saturated steam of a few MPa, to assist in the generation of the main working fluids, instead of a compressor used in the advanced oxy-fuel gas turbine. This saturated steam can have a lower pressure and temperature than those of an existing nuclear power plant or biomass-fired power plant. We estimated plant performances from a heat balance model based on a conceptual design of a plant for different gas turbine inlet pressures of 2.5–6.5 MPa and temperatures of 1300 and 1500°C, taking into account the work to produce O2 and capture CO2 . While the net power generating efficiencies of a reference advanced oxy-fuel gas turbine plant are estimated to be about 52.0% and 56.0% at 1300 and 1500°C, respectively, and conventional steam power generation is assumed to have an efficiency of about 35% or less for pressures of 2.5–6.5 MPa, the proposed hybrid plant achieved 42.8–44.7% at 1300°C and 47.8–49.2% for 1500°C. In the proposed plant, the power output contributed by a LCHG may be obtained by subtracting the LNG contribution from the whole net power output. Even supposing that the generation efficiency of the LNG system in the proposed plant remains equal to that of the reference plant (56.0% at 1500°C), some components used in the reference plant are omitted by installation of the LCHG. The efficiency of LCHG system can be estimated 37.4% for 6.5 MPa and 33.2% for 2.5 MPa, even though the LHCG system may be regarded as consisting of fewer plant facilities than a conventional LCHG power plant.Copyright © 2011 by ASME

Muscle contraction occurs when the constitutive proteins, actin and myosin, interact via crossbridge formation, powered by the hydrolysis of adenosine triphosphate (ATP). It is a physical process that transduces chemical energy into mechanical work, producing directional motion. The central question is how force generation and movement in muscle contraction are associated with major conformational changes in contractile and regulatory proteins. The best available technique for such an approach is X-ray diffraction which can provide structural information with a submolecular resolution. X-ray diffraction with intense synchrotron radiation has demonstrated a structural basis for the molecular mechanism underlying muscle contraction with high spatial- and time-resolution. The structural alterations in vertebrate skeletal muscles undergoing contraction by synchrotron X-ray diffraction are outlined by putting a lot of weight on the thin filament as the locus of actomyosin interaction. Key Concepts: Muscle contraction occurs when constitutive proteins actin and myosin in muscle interact with each other, powered by the hydrolysis of adenosine triphosphate (ATP), leading to a force generation or a shortening of the sarcomere. Sliding filament theory is a proposal on the basis of the discovery that when a sarcomere shortens, two types of filaments slide each other with little change in their lengths, resulting in an overall shortening of muscle. Elastic elements sustaining the tension that muscle exerts during contraction are thought to be resided somewhere in a sarcomere. In the current hypothesis, the only elastic elements are assumed to reside somewhere around or within the myosin heads. Extensibility of the thin actin filament: The force is transmitted to the ends of the contractile unit through the thin actin filaments, which have been thought to contribute very little compliance to the mechanochemical machinery. Evidence that the thin actin filaments are purely elastic under active force generation has been obtained. Twisting of the thin actin filament suggests that the force acting at a myosin crossbridge contains torque components around the axis of the thin actin filament. X-ray diffraction is the interference of the X-rays scattered from the electron densities of the matter, and the Fourier transformation of the interference pattern yields the structure of the matter. Synchrotron radiations are electromagnetic waves that are emitted in the tangential direction of the orbit when electrons or positrons circulating near the speed of light in an accelerating ring (synchrotron). Synchrotron X-rays with high brilliance are an indispensable tool for muscle structural research. Keywords: muscle contraction; muscle regulation; thin filament; thick filament; extensibility of thin filament; twisting of thin filament; X-ray fibre diffraction; synchrotron radiation

Strong evidence has been accumulated that the conformational changes of the thin actin filaments are occurring and playing an important role in the entire process of muscle contraction. The conformational changes and the mechanical properties of the thin actin filaments we have found by X-ray fiber diffraction on skeletal muscle contraction are explored. Recent studies on the conformational changes of regulatory proteins bound to actin filaments upon activation and in the force generation process are also described. Finally, the roles of structural alterations and dynamics of the actin filaments are discussed in conjunction with the regulation mechanism and the force generation mechanism.

Strong evidence has been accumulated that the conformational changes of the thin actin filaments are occurring and playing an important role in the entire process of muscle contraction. The conformational changes and the mechanical properties of the thin actin filaments we have found by X-ray fiber diffraction on skeletal muscle contraction are explored. Recent studies on the conformational changes of regulatory proteins bound to actin filaments upon activation and in the force generation process are also described. Finally, the roles of structural alterations and dynamics of the actin filaments are discussed in conjunction with the regulation mechanism and the force generation mechanism.

X-ray diffraction patterns from live vertebrate striated muscles were analyzed to elucidate the detailed structural models of the myosin crown arrangement and the axial disposition of two-headed myosin crossbridges along the thick filaments in the relaxed and contracting states. The modeling studies were based upon the previous notion that individual myosin filaments had a mixed structure with two regions, a “regular” and a “perturbed”. In the relaxed state the distributions and sizes of the regular and perturbed regions on myosin filaments, each having its own axial periodicity for the arrangement of crossbridge crowns within the basic period, were similar to those reported previously. A new finding was that in the contracting state, this mixed structure was maintained but the length of each region, the periodicities of the crowns and the axial disposition of two heads of a crossbridge were altered. The perturbed regions of the crossbridge repeat shifted towards the Z-bands in the sarcomere without changing the lengths found in the relaxed state, but in which the intervals between three successive crowns within the basic period became closer to the regular 14.5-nm repeat in the contracting state. In high resolution modeling for a myosin head, the two heads of a crossbridge were axially tilted in opposite directions along the three-fold helical tracks of myosin filaments and their axial orientations were different from each other in perturbed and regular regions in both states. Under relaxing conditions, one head of a double-headed crossbridge pair appeared to be in close proximity to another head in a pair at the adjacent crown level in the axial direction in the regular region. In the perturbed region this contact between heads occurred only on the narrower inter-crown levels. During contraction, one head of a crossbridge oriented more perpendicular to the fiber axis and the partner head flared axially. Several factors that significantly influence the intensities of the myosin based-meridional reflections and their relative contributions are discussed.

Analysis of the myosin-based meridional intensity data in the X-ray diffraction patterns of live frog skeletal muscles was performed to propose a more precise model for a myosin crown periodicity and an axial disposition of two-headed crossbridges along the thick filament in a sarcomere. Modeling studies revealed that the thick filament has a mixed structure of two different periodicities of the myosin crossbridge crown arrangement and that the crown periodicity and the axial disposition of crossbridges are altered when muscle goes from the relaxed state to the contracting state. Factors that primarily affect the meridional intensities were examined.

Analysis of the myosin-based meridional intensity data in the X-ray diffraction patterns of live frog skeletal muscles was performed to propose a more precise model for a myosin crown periodicity and an axial disposition of two-headed crossbridges along the thick filament in a sarcomere. Modeling studies revealed that the thick filament has a mixed structure of two different periodicities of the myosin crossbridge crown arrangement and that the crown periodicity and the axial disposition of crossbridges are altered when muscle goes from the relaxed state to the contracting state. Factors that primarily affect the meridional intensities were examined.

The intensities of the myosin-based layer lines in the x-ray diffraction patterns from live resting frog skeletal muscles with full thick-thin filament overlap from which partial lattice sampling effects had been removed were analyzed to elucidate the configurations of myosin crossbridges around the thick filament backbone to nanometer resolution. The repeat of myosin binding protein C (C-protein) molecules on the thick filaments was determined to be 45.33 nm, slightly longer than that of myosin crossbridges. With the inclusion of structural information for C-proteins and a pre-powerstroke head shape, modeling in terms of a mixed population of regular and perturbed regions of myosin crown repeats along the filament revealed that the myosin filament had azimuthal perturbations of crossbridges in addition to axial perturbations in the perturbed region, producing pseudo-six-fold rotational symmetry in the structure projected down the filament axis. Myosin crossbridges had a different organization about the filament axis in each of the regular and perturbed regions. In the regular region that lacks C-proteins, there were inter-molecular interactions between the myosin heads in axially adjacent crown levels. In the perturbed region that contains C-proteins, in addition to inter-molecular interactions between the myosin heads in the closest adjacent crown levels, there were also intra-molecular interactions between the paired heads on the same crown level. Common features of the interactions in both regions were interactions between a portion of the 50-kDa-domain and part of the converter domain of the myosin heads, similar to those found in the phosphorylation-regulated invertebrate myosin. These interactions are primarily electrostatic and the converter domain is responsible for the head-head interactions. Thus multiple head-head interactions of myosin crossbridges also characterize the switched-off state and have an important role in the regulation or other functions of myosin in thin filament-regulated muscles as well as in the thick filament-regulated muscles.

A novel method using the cylindrically averaged difference Patterson function was applied to correct a sampling effect due to the hexagonal filament array on the thick filament-based layer-line intensities from frog skeletal muscles at the full-filament overlap length. Using the corrected intensity data and the mixed structural model of a thick filament with two different axial periodicities of the myosin crossbridges, we performed an optimum search of azimuthal orientation of two heads of a myosin crossbridge and compared the optimum orientation to that from muscles stretched beyond filament overlap reported previously. The result showed that the myosin crossbriges in the regular repeating region had a similar configuration in both muscles. Two heads of a myosin crossbridge formed a windmill-shape when seen from the top of the filament and one head of a myosin crossbridge seemed to be almost in contact with another head in a pair at an adjacent crown level along the filament axis. One head was toward the converter domain of the other head, similar to regulated myosin heads in Tarantula muscles in which the intramolecular head-head interaction occurs. In the perturbed region, however, myosin crossbridges had different configurations in these muscles. In top view, two heads of a myosin crossbridge showed a U-shape structure in the overstreched muscles while a cross-shape structure in muscles with the full-filament overlap. One myosin head seemed to be in contact with the other head at the same axial crown level. The models suggest that the disposition of two-headed myosin crossbridges is stabilized by the head-head interaction at same or different axial crown levels. Probably this would be related to the inhibition mechanism of actomyosin interaction in the relaxed muscles.