Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation

Reversible phosphorylation of proteins is a post‐translational modification that regulates diverse biological processes. The molecular mechanism underlying phosphoryl transfer catalyzed by enzymes remains a subject of active debate. In particular, the nature of transition state (TS), whether it has an associative or dissociative character, has been one of the most controversial issues. Structural evidence supports associative TS, whereas physical organic studies point to a dissociative character. Here we perform hybrid quantum mechanics/molecular mechanics simulations for the reversible phosphorylation of phosphoserine phosphatase (PSP) to study the nature of the TS. Both phosphorylation and dephosphorylation reactions are investigated based on the two‐dimensional energy surfaces along phosphoryl and proton transfer coordinates. The structures of the active site at TS in both reactions reveal compact geometries, consistent with crystal structures of PSP with phosphate analogues. However, the electron density of the phosphoryl group in both TS structures slightly decreases compared with that in the reactant states. These findings suggest that the TS of PSP has a geometrically associative yet electronically dissociative character and strongly depends on proton transfer being coupled with phosphoryl transfer. Structure and literature database, which searches on phosphotransferases, suggest that such a hybrid TS is consistent with many structures and physical organic studies and likely holds for most enzymes catalyzing phosphoryl transfer. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Geometrical Excess Entropy Production in Nonequilibrium Quantum Systems

For open systems described by the quantum Markovian master equation, we study a possible extension of the Clausius equality to quasistatic operations between nonequilibrium steady states (NESSs). We investigate the excess heat divided by temperature (i.e., excess entropy production) which is transferred into the system during the operations. We derive a geometrical expression for the excess entropy production, which is analogous to the Berry phase in unitary evolution. Our result implies that in general one cannot define a scalar potential whose difference coincides with the excess entropy production in a thermodynamic process, and that a vector potential plays a crucial role in the thermodynamics for NESSs. In the weakly nonequilibrium regime, we show that the geometrical expression reduces to the extended Clausius equality derived by Saito and Tasaki (J. Stat. Phys. 145:1275, 2011). As an example, we investigate a spinless electron system in quantum dots. We find that one can define a scalar potential when the parameters of only one of the reservoirs are modified in a non-interacting system, but this is no longer the case for an interacting system.     

Interferometric thickness measurement of glass plate by phase-shifting analysis using wavelength scanning with elimination of bias phase error

Optical Review - Phase-shifting fringe analysis using wavelength scanning has been broadly applied to the interferometric profiling of the thickness variation of glass plates. However, the...     

Simultaneous measurement of surface shape and absolute optical thickness of a glass plate by wavelength tuning phase-shifting interferometry

The absolute optical thickness and the surface shape of a glass plate of 7-in. square and 3.1mm thick was simultaneously measured by three-surface interferometry using a wavelength tuning Fizeau interferometer. The wavelength of a tunable diode laser is scanned linearly from 632 to 642 nm, at which the initial and the final phases of the interference fringes for the surface shape and for the optical thickness were separated and measured by a tunable phase-shifting technique. The number of phase variations in the interference fringes during the scanning is counted by discrete Fourier analysis, in which systematic errors caused by a nonlinearity in the wavelength scanning is corrected by a correlation analysis between the observed and theoretical interference fringes. Experimental results demonstrate that the systematic errors in the measured value were 15 nm for the surface shape and 0.6 μm for the absolute optical thickness.     

Arrayed-waveguide grating with uniform loss properties over the entire range of wavelength channels

We propose an arrayed-waveguide grating that shows uniform loss properties over the entire range of wavelength channels by combining two light waves with adjacent diffraction orders at its output. We applied this configuration to an arrayed-waveguide grating with 32 channels and a 50 GHz spacing and were able to reduce the deviations in loss to less than 1.0 and 1.8 dB over one and three free spectral ranges, respectively.     

Anomalous resistivity at the initial stage of a theta pinch

It is found that an anomalous resistivity exists even before the implosion phase, that is, it exists already at the so-called plasma formation stage of the theta pinch in the low-pressure regime.     

31%-efficient blue second-harmonic generation in a periodically poled MgO:LiNbO3 waveguide by frequency doubling of an AlGaAs laser diode

We present a method of controlling the shape of the domain-inverted structure in an off-cut MgO:LiNbO(3) crystal by utilizing a two-dimensional high-voltage application. With this technique a periodically domain-inverted structure with a period of 3.2mum and a thickness of 2.0mum was fabricated over a 10-mm interaction length. This structure has made possible sufficient overlaps between propagation modes and domain inversion in the waveguide. Using this structure, we demonstrated cw blue second-harmonic generation of 17.3 mW of power at a wavelength of 426 nm with single-pass 55-mW cw AlGaAs laser diode input, which corresponded to 31% power-conversion efficiency.     

Photochemistry of ketone polymers. XII. Studies of ring-substituted phenyl isopropenyl ketones and their styrene copolymers

The synthesis of a number of ring-substituted phenyl isopropenyl ketones and their polymerization with styrene is reported. The ultraviolet absorption spectra of the polymers are analogous to those of ring-substituted acetophenones and valerophenones. The quantum yields of the Norrish type II photoreaction were estimated in 1,2-dichloroethane solution at 364 nm by automatic viscometry. These quantum yields are comparable to those of substituted butyrophenones and valerophenones, in that relatively high quantum yields were obtained for the unsubstituted and p-chloro-substituted compounds with low yields for p-amino and p-hydroxy compounds. The p-nitro-substituted compound gives no type II reaction, presumably because the excitation becomes localized on the nitro groups which photolyzes by a mechanism which does not involve chain scission. The implications of these studies on possible applications to photoimaging are discussed.     

Replica state exchange metadynamics for improving the convergence of free energy estimates

Metadynamics (MTD) is a powerful enhanced sampling method for systems with rugged energy landscapes. It constructs a bias potential in a predefined collective variable (CV) space to overcome barriers between metastable states. In bias‐exchange MTD (BE‐MTD), multiple replicas approximate the CV space by exchanging bias potentials (replica conditions) with the Metropolis–Hastings (MH) algorithm. We demonstrate that the replica‐exchange rates and the convergence of free energy estimates of BE‐MTD are improved by introducing the infinite swapping (IS) or the Suwa‐Todo (ST) algorithms. Conceptually, IS and ST perform transitions in a replica state space rather than exchanges in a replica condition space. To emphasize this, the proposed scheme is called the replica state exchange MTD (RSE‐MTD). Benchmarks were performed with alanine polypeptides in vacuum and water. For the systems tested in this work, there is no significant performance difference between IS and ST. © 2015 Wiley Periodicals, Inc.     

Visualization of how light changes affect ion movement in rice plants using a real-time radioisotope imaging system

Journal of Radioanalytical and Nuclear Chemistry - We developed a real-time radioisotope imaging system (RRIS) technique that can nondestructively visualize the element absorption and transport...