YddV from Escherichia coli (Ec) is a novel globin-coupled heme-based oxygen sensor protein displaying diguanylate cyclase activity in response to oxygen availability. In this study, we quantified the turnover numbers of the active [Fe(III), 0.066 min(-1); Fe(II)-O(2) and Fe(II)-CO, 0.022 min(-1)] [Fe(III), Fe(III)-protoporphyrin IX complex; Fe(II), Fe(II)-protoporphyrin IX complex] and inactive forms [Fe(II) and Fe(II)-NO, <0.01 min(-1)] of YddV for the first time. Our data indicate that the YddV reaction is the rate-determining step for two consecutive reactions coupled with phosphodiesterase Ec DOS activity on cyclic di-GMP (c-di-GMP) [turnover number of Ec DOS-Fe(II)-O(2), 61 min(-1)]. Thus, O(2) binding and the heme redox switch of YddV appear to be critical factors in the regulation of c-di-GMP homeostasis. The redox potential and autoxidation rate of heme of the isolated heme domain of YddV (YddV-heme) were determined to be -17 mV versus the standard hydrogen electrode and 0.0076 min(-1), respectively. The Fe(II) complexes of Y43A and Y43L mutant proteins (residues at the heme distal side of the isolated heme-bound globin domain of YddV) exhibited very low O(2) affinities, and thus, their Fe(II)-O(2) complexes were not detected on the spectra. The O(2) dissociation rate constant of the Y43W protein was >150 s(-1), which is significantly larger than that of the wild-type protein (22 s(-1)). The autoxidation rate constants of the Y43F and Y43W mutant proteins were 0.069 and 0.12 min(-1), respectively, which are also markedly higher than that of the wild-type protein. The resonance Raman frequencies representing ν(Fe-O(2)) (559 cm(-1)) of the Fe(II)-O(2) complex and ν(Fe-CO) (505 cm(-1)) of the Fe(II)-CO complex of Y43F differed from those (ν(Fe-O(2)), 565 cm(-1); ν(Fe-CO), 495 cm(-1)) of the wild-type protein, suggesting that Tyr43 forms hydrogen bonds with both O(2) and CO molecules. On the basis of the results, we suggest that Tyr43 located at the heme distal side is important for the O(2) recognition and stability of the Fe(II)-O(2) complex, because the hydroxyl group of the residue appears to interact electrostatically with the O(2) molecule bound to the Fe(II) complex in YddV. Our findings clearly support a role of Tyr in oxygen sensing, and thus modulation of overall conversion from GTP to pGpG via c-di-GMP catalyzed by YddV and Ec DOS, which may be applicable to other globin-coupled oxygen sensor enzymes.

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Nonresonant optimal control simulation is applied to a CO molecule to design two-color phase-locked laser pulses (800 nm + 400 nm) with the aim of orienting the molecule under the field-free condition. The optimal pulse consists of two subpulses: the first subpulse aligns the molecule and the second one orients it. The molecular alignment induced by the first subpulse considerably enhances the degree of orientation, the value of which is close to an ideal value at temperature T = 0 K. To confirm the effectiveness of this alignment-enhanced orientation mechanism, we adopt a set of model Gaussian pulses and calculate the maximum degrees of orientation as a function of the delay time and the intensity. In finite-temperature (T = 3.0 K and T = 5.0 K) cases, although the alignment subpulse can improve the degree of orientation, the control achievement decreases with temperature rapidly; this decrease can be attributed to the initial-state-dependent (phase-shifted) rotational wave packet motion.

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Two types of pseudopolymorphs, 1·(2)3 and 1·(2)2, were obtained from Pd­(II) complex (1) with mesitylene (2), and the quantitative transformation into 1·(2)2 from 1·(2)3 was observed over 6 h after shaking for approximately 10 s. The transformation was observed in both a mesitylene-rich solution and under powder conditions. The guest release processes of 1·(2)3 and 1·(2)2 occurred in hexane to yield 1, and the guest insertion processes occurred in 2 to reproduce 1·(2)3 and 1·(2)2, whereas each crystal was constructed from the discrete molecules of each type. These crystals also selectively and repeatedly encapsulated three benzenes or one toluene in the uniform cavities of 1·(2)3 and 1·(2)2. In contrast, the corresponding nonfluorinated derivative, [Pd­(dbm)2] (dbm = dibenzoylmetanide), shows no guest encapsulation phenomena, indicating that the remarkable guest encapsulations are induced by fluorine substitutions. The dynamic crystal transformation and the reversible guest encapsulations of the two pseudopolymorphs were investigated by X-ray crystallographic and thermogravimetric studies for both single crystals and powder species.