Cyclic AMP-induced Conformational Changes in Mycobacterial Protein Acetyltransferases

The activities of a number of proteins are regulated by the binding of cAMP and cGMP to cyclic nucleotide binding (CNB) domains that are found associated with one or more effector domains with diverse functions. Although the conserved architecture of CNB domains has been extensively studied by x-ray crystallography, the key to unraveling the mechanisms of cAMP action has been protein dynamics analyses. Recently, we have identified a novel cAMP-binding protein from mycobacteria, where cAMP regulates the activity of an associated protein acetyltransferase domain. In the current study, we have monitored the conformational changes that occur upon cAMP binding to the CNB domain in these proteins, using a combination of bioluminescence resonance energy transfer and amide hydrogen/deuterium exchange mass spectrometry. Coupled with mutational analyses, our studies reveal the critical role of the linker region (positioned between the CNB domain and the acetyltransferase domain) in allosteric coupling of cAMP binding to activation of acetyltransferase catalysis. Importantly, major differences in conformational change upon cAMP binding were accompanied by stabilization of the CNB and linker domain alone. This is in contrast to other cAMP-binding proteins, where cyclic nucleotide binding has been shown to involve intricate and parallel allosteric relays. Finally, this powerful convergence of results from bioluminescence resonance energy transfer and hydrogen/deuterium exchange mass spectrometry reaffirms the power of solution biophysical tools in unraveling mechanistic bases of regulation of proteins in the absence of high resolution structural information.

Dynamo in protostars

In this paper, we estimate the magnetic Reynolds number of a typical protostar before and after deuterium burning, and claim for the existence of dynamo process in both the phases, because the magnetic Reynolds number of the protostar far exceeds the critical magnetic Reynolds number for dynamo action. Using the equipartition of kinetic and magnetic energies, we estimate the steady-state magnetic field of the protostar to be of the order of kilogauss, which is in good agreement with observations.

Titanium promoted reduction of imines with Grignards, silanes, and zinc: identification of a new mechanism with silanes

Aldimines react with reducing agents, such as Grignards, phenylsilane or zinc in the presence of titanium(IV) isopropoxide to form amines and reductively coupled imines (diamines). Using deuterium labeled reagents, the mechanism of reduction to form amines is described. Reducing agents, such as the Grignard and zinc result in the formation of low valent titanium (LVT), which in turn reduces the imine. On the other hand, phenylsilane reacts by a distinctly different mechanism and where a hydrogen atom from silicon is directly transferred to the titanium coordinated imine. (c) 2014 Elsevier Ltd. All rights reserved.

Rotational spectra of propargyl alcohol dimer: A dimer bound with three different types of hydrogen bonds

Pure rotational spectra of the propargyl alcohol dimer and its three deuterium isotopologues have been observed in the 4 to 13 GHz range using a pulsed-nozzle Fourier transform microwave spectrometer. For the parent dimer, a total of 51 transitions could be observed and fitted within experimental uncertainty. For two mono-substituted and one bi-substituted deuterium isotopologues, a total of 14, 17, and 19 transitions were observed, respectively. The observed rotational constants for the parent dimer A = 2321.8335(4) MHz, B = 1150.4774(2) MHz, and C = 1124.8898(2) MHz] are close to those of the most stable structure predicted by ab initio calculations. Spectra of the three deuterated isotopologues and Kraitchman analysis positively confirm this structure. Geometrical parameters and ``Atoms in Molecules'' analysis on the observed structure reveal that the two propargyl alcohol units in the dimer are bound by three different types of hydrogen bonds: O-H center dot center dot center dot O, O-H center dot center dot center dot pi, and C-H center dot center dot center dot pi. To the best of our knowledge, propargyl alcohol seems to be the smallest molecule forming a homodimer with three different points of contact. (C) 2014 AIP Publishing LLC.

Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond

In this discussion, we show that a static definition of a `bond' is not viable by looking at a few examples for both inter-and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate `hydrogen bonding' from `van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg center dot center dot center dot HX complexes (Rg = He/Ne/Ar and X = F/Cl/Br) and ethane-1,2-diol. Results for the Rg center dot center dot center dot HX/DX complexes show that Rg center dot center dot center dot DX could have a `deuterium bond' even when Rg center dot center dot center dot HX is not `hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an `intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the O center dot center dot center dot O stretching, though a `bond' is not found in the equilibrium structure. This dynamical `bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration `breaks' an existing bond and in the later case, a vibration leads to `bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this `hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition.

Cyclic nucleotide binding and structural changes in the isolated GAF domain of Anabaena adenylyl cyclase, CyaB2

GAF domains are a large family of regulatory domains, and a subset are found associated with enzymes involved in cyclic nucleotide (cNMP) metabolism such as adenylyl cyclases and phosphodiesterases. CyaB2, an adenylyl cyclase from Anabaena, contains two GAF domains in tandem at the N-terminus and an adenylyl cyclase domain at the C-terminus. Cyclic AMP, but not cGMP, binding to the GAF domains of CyaB2 increases the activity of the cyclase domain leading to enhanced synthesis of cAMP. Here we show that the isolated GAFb domain of CyaB2 can bind both cAMP and cGMP, and enhanced specificity for cAMP is observed only when both the GAFa and the GAFb domains are present in tandem(GAFab domain). In silico docking and mutational analysis identified distinct residues important for interaction with either cAMP or cGMP in the GAFb domain. Structural changes associated with ligand binding to the GAF domains could not be detected by bioluminescence resonance energy transfer (BRET) experiments. However, amide hydrogen-deuterium exchange mass spectrometry (HDXMS) experiments provided insights into the structural basis for cAMP-induced allosteric regulation of the GAF domains, and differences in the changes induced by cAMP and cGMP binding to the GAF domain. Thus, our findings could allow the development of molecules that modulate the allosteric regulation by GAF domains present in pharmacologically relevant proteins.

Isotopic fractionation in proteins as a measure of hydrogen bond length

If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent, it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor (I) is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds, we calculate (I) as a function of the proton donor-acceptor distance R. For numerical results, we use a parameterization of the model for symmetric 0-H. ``.0 bonds R. H. McKenzie, Chem. Phys. Lett. 535, 196 (2012)]. We consider the relative contributions of the 0-H stretch vibration, O-H bend vibrations (both in plane and out of plane), tunneling splitting effects at finite temperature, and the secondary geometric isotope effect. We compare our total (I) as a function of R with NMR experimental results for enzymes, and in particular with an earlier model parametrization (D(R), used previously to determine bond lengths. (C) 2015 AIP Publishing LLC.

Study of H/D exchange rates to derive the strength of intramolecular hydrogen bonds in halo substituted organic building blocks: An NMR spectroscopic investigation

Rates of hydrogen/deuterium (H/D) exchange determined by H-1 NMR spectroscopy are utilized to derive the strength of hydrogen bonds and to monitor the electronic effects in the site-specific halogen substituted benzamides and anilines. The theoretical fitting of the time dependent variation of the integral areas of H-1 NMR resonances to the first order decay function permitted the determination of HID exchange rate constants (k) and their precise half-lives (t(1/2)) with high degree of reproducibility. The comparative study also permitted the unambiguous determination of relative strength of hydrogen bonds and the contribution from electronic effects on the HID exchange rate. (C) 2015 Elsevier B.V. All rights reserved.

Reagent-switch controlled metal-free intermolecular geminal diamination and aminooxygenation of vinylarenes

We report here the first general method for the geminal diamination and an intermolecular metal-free, geminal aminooxygenation of vinylarenes using hypervalent iodine reagent. A new m-CPBA mediated geminal aminooxygenation is also reported. A novel reagent-switch for the control of migrating group by controlling the two independent geminal addition paths is developed. Deuterium labelling studies and the control studies have provided unambiguous evidences for the phenyl migration and hydride migration in the oxidative geminal difunctionalization process mediated by Phl(OCOCF3)(2) and m-CPBA, respectively through a semi-pinacol rearrangement. (C) 2016 Elsevier Ltd. All rights reserved.

Non-Gravitational Effects with Density-Matching in Evaluating the Influence of Sedimentation on Colloidal Coagulation

The method of density matching between the solid and liquid phases is often adopted to effectively eliminate the effect of sedimentation of suspensions in studies on dynamic behaviour of a colloidal system. However, the associated changes in the solvent composition may bring side effects to the properties investigated and therefore might lead to a faulty conclusion if the relevant correction is not made. To illustrate the importance of this side effect, we present an example of the sedimentation influence on the coagulation rate of suspensions of 2 μm (diameter) polystyrene. The liquid mixtures, in the proper proportions of water (H2O), deuterium oxide (D2O) and methanol (MeOH) as the liquid phase, density-matched and unmatched experiments are performed. Besides the influence of viscosity, the presence of methanol in solvent media, used to enhance the sedimentation effect, causes significant changes (reduction) in rapid coagulation rates compared to that in pure water. Without the relevant corrections for those non-gravitational factors it seems that gravitational sedimentation would retard the coagulation. The magnitude of the contribution from the non-gravitational factor is quantitatively determined, making the relevant correction possible. After necessary corrections for all factors, our experiments show that the influence of the sedimentation on coagulation rates at the initial stage of the coagulation is not observable.

Ablation of hydrogen isotopic spherical pellet due to the impact of energetic ions of the respective isotopes

The ablation rate of a hydrogen isotopic spherical pellet G(is) due to the impact of energetic ions of the respective isotopes and its scaling law are obtained using the transsonic neutral-shielding model, where subscript s might refer to either hydrogen or deuterium. Numerical results show that if E0s/E0e2 greater-than-or-equal-to 1.5, G(is)/G(es) greater-than-or-equal-to 20%, where E0s and E0e are the energy of undisturbed ion and electron, respectively, and G(es) is the ablation rate of a pellet due to the impact of electrons. Hence, under the NBI heating, the effect of the impact of energetic ions on the pellet ablation should be taken into consideration. This result also gives an explanation of the observed enhancement of pellet ablation during NBIH.

Influence Of Gravity On Structure Of Colloidal Crystal Using Simulated Microgravity

Liquid mixtures of water and deuterium oxide as the liquid phase, were used to match the density of charged colloidal particles. Kossel diffraction method was used to detect the crystal structures. The experiments under the density-matched (g=0) and unmatched (g=1) conditions are compared to examine the influence of gravity on the crystal structures formed by self-assembly of 110 nm (in diameter) polystyrene microspheres. The result shows that die gravity tends to make the lattice constants of colloidal crystals smaller at lower positions, which indicates that the effect of gravity should be taken into account in the study of the colloidal crystals.

The diagnostics of density distribution for inhomogeneous dense DT plasmas using fast protons

The density distribution of inhomogeneous dense deuterium-tritium plasmas in laser fusion is revealed by the energy loss of fast protons going through the plasma. In our simulation of a plasma density diagnostics, the fast protons used for the diagnostics may be generated in the laser-plasma interaction. Dividing a two-dimensional area into grids and knowing the initial and final energies of the protons, we can obtain a large linear and ill-posed equation set. for the densities of all grids, which is solved with the Tikhonov regularization method. We find that the accuracy of the set plan with four proton sources is better than those of the set plans with less than four proton sources. Also we have done the density reconstruction especially. for four proton sources with and without assuming circularly symmetrical density distribution, and find that the accuracy is better for the reconstruction assuming circular symmetry. The error is about 9% when no noise is added to the final energy for the reconstruction of four proton sources assuming circular symmetry. The accuracies for different random noises to final proton energies with four proton sources are also calculated.

Laser-confined fusion

An approach for producing a large quantity of neutrons is proposed. It involves compression of a fuel foil and confinement of the resulting plasma between two intense laser pulses. It is shown that two circularly polarized laser pulses of amplitude a=7 illuminating a deuterium-tritium foil of areal density 3.3 X 10(18) cm(-2) can produce about 4.2 X 10(6) neutrons per joule of the input laser energy.

Mechanistic and kinetic studies of the surface chemistry of iridium and ruthenium

Quantitative investigations of the mechanisms and the kinetics of the surface-catalyzed activation of C-H, N-H, C-C, and C-N bonds on the close-packed surfaces of Ir(111) and Ru(001) have been performed. The interaction of CH_3NH_2 with Ru(001) was investigated in ultrahigh vacuum with the techniques of high-resolution electron energy loss spectroscopy and thermal desorption mass spectrometry. Activation of the central C-N bond is observed, but it is less favored than the competing channel of complete dehydrogenation, by a ratio between 2:1 to 3:1. The decomposition mechanism has been characterized with several surface intermediates and gas-phase products identified. A pronounced preference for the activation of C-H over N-H and C-N bonds has been established. Additionally, the kinetics of the initial dissociation of short chain alkanes on Ir(111) has been examined, and the rate parameters of the activation of C-C bonds and primary, secondary, and tertiary C-H bonds have been determined. The formation of primary alkyl products is favored, over most of the experimental temperature range, despite the thermodynamic preference for the activation of individual secondary and tertiary C-H bonds in comparison to individual primary C-H bonds. At higher surface temperatures, the activation of C-C bonds occurs at competitive rates to the C-H reaction channel. The measured deuterium kinetic isotope effect implicates substantial deformation of the terminal methyl group in the transition state of C-C bond cleavage. Finally, the surface structure sensitivity of C-H bond cleavage has been quantified for smooth (111) and corrugated (110) surfaces of iridium and platinum, as well as for step edge defect sites on Ir(111).