Insight into the Structure and Activity of Surface-Engineered Lipase Biofluids.

Despite a successful application of solvent-free liquid protein (biofluids) concept to a number of commercial enzymes, the technical advantages of enzyme biofluids as hyperthermal stable biocatalysts cannot be fully utilized as up to 90-99% of native activities are lost when enzymes were made into biofluids. With a two-step strategy (site-directed mutagenesis and synthesis of variant biofluids) on Bacillus subtilis lipase A (BsLA), we elucidated a strong dependency of structure and activity on the number and distribution of polymer surfactant binding sites on BsLA surface. Here, it is demonstrated that improved BsLA variants can be engineered via site-mutagenesis by a rational design, either with enhanced activity in aqueous solution in native form, or with improved physical property and increased activity in solvent-free system in the form of a protein liquid. This work answered some fundamental questions about the surface characteristics for construction of biofluids, useful for identifying new strategies for developing advantageous biocatalysts.

Electron-Induced Reactions in 3-Bromopyruvic Acid.

3-Bromopyruvic acid (3BP) is a potential anti-cancer drug, the action of which on cellular metabolism is not yet entirely clear. The presence of a bromine atom suggests that it is also reactive towards low-energy electrons, which are produced in large quantities during tumour radiation therapy. Detailed knowledge of the interaction of 3BP with secondary electrons is a prerequisite to gain a complete picture of the effects of 3BP in different forms of cancer therapy. Herein, dissociative electron attachment (DEA) to 3BP in the gas phase has been studied both experimentally by using a crossed-beam setup and theoretically through scattering and quantum chemical calculations. These results are complemented by a vacuum ultraviolet absorption spectrum. The main fragmentation channel is the formation of Br- close to 0 eV and within several resonant features at 1.9 and 3-8 eV. At low electron energies, Br- formation proceeds through σ* and π* shape resonances, and at higher energies through core-excited resonances. It is found that the electron-capture cross-section is clearly increased compared with that of non-brominated pyruvic acid, but, at the same time, fragmentation reactions through DEA are significantly altered as well. The 3BP transient negative ion is subject to a lower number of fragmentation reactions than those of pyruvic acid, which indicates that 3BP could indeed act by modifying the electron-transport chains within oxidative phosphorylation. It could also act as a radio-sensitiser.

The valence and Rydberg states of difluoromethane: A combined experimental vacuum ultraviolet spectrum absorption and theoretical study by ab initio configuration interaction and density functional computations.

The vacuum ultraviolet (VUV) spectrum for CH2F2 from a new synchrotron study has been combined with earlier data and subjected to detailed scrutiny. The onset of absorption, band I and also band IV, is resolved into broad vibrational peaks, which contrast with the continuous absorption previously claimed. A new theoretical analysis, using a combination of time dependent density functional theory (TDDFT) calculations and complete active space self-consistent field, leads to a major new interpretation. Adiabatic excitation energies (AEEs) and vertical excitation energies, evaluated by these methods, are used to interpret the spectra in unprecedented detail using theoretical vibronic analysis. This includes both Franck-Condon (FC) and Herzberg-Teller (HT) effects on cold and hot bands. These results lead to the re-assignment of several known excited states and the identification of new ones. The lowest calculated AEE sequence for singlet states is 11B1 ∼ 11A2 < 21B1 < 11A1 < 21A1 < 11B2 < 31A1 < 31B1. These, together with calculated higher energy states, give a satisfactory account of the principal maxima observed in the VUV spectrum. Basis sets up to quadruple zeta valence with extensive polarization are used. The diffuse functions within this type of basis generate both valence and low-lying Rydberg excited states. The optimum position for the site of further diffuse functions in the calculations of Rydberg states is shown to lie on the H-atoms. The routine choice on the F-atoms is shown to be inadequate for both CHF3 and CH2F2. The lowest excitation energy region has mixed valence and Rydberg character. TDDFT calculations show that the unusual structure of the onset arises from the near degeneracy of 11B1 and 11A2 valence states, which mix in symmetric and antisymmetric combinations. The absence of fluorescence in the 10.8-11 eV region contrasts with strong absorption. This is interpreted by the 21B1 and 11A1 states where no fluorescence is calculated for these two states, which are only active in absorption. The nature of the two states, 11B1 and 21B1, is fundamentally different, but both are complex owing to the presence of FC and HT effects occurring in different ways. The two most intense bands, close to 12.5 and 15.5 eV, contain valence states as expected; the onset of the 15.5 eV band shows a set of vibrational peaks, but the vibration frequency does not correspond to any of the photoelectron spectral (PES) structure and is clearly valence in nature. The routine use of PES footprints to detect Rydberg states in VUV spectra is shown to be inadequate. The combined effects of FC and HT in the VUV spectral bands lead to additional vibrations when compared with the PES.

Combined theoretical and experimental study of the valence, Rydberg and ionic states of fluorobenzene.

New photoelectron spectra (PES) and ultra violet (UV) and vacuum UV (VUV) absorption spectra of fluorobenzene recorded at higher resolution than previously, have been combined with mass-resolved (2 + 1) and (3 + 1) resonance enhanced multiphoton ionization (REMPI) spectra; this has led to the identification of numerous Rydberg states. The PES have been compared with earlier mass-analyzed threshold ionization and photoinduced Rydberg ionization (PIRI) spectra to give an overall picture of the ionic state sequence. The analysis of these spectra using both equations of motion with coupled cluster singles and doubles (EOM-CCSD) configuration interaction and time dependent density functional theory (TDDFT) calculations have been combined with vibrational analysis of both the hot and cold bands of the spectra, in considerable detail. The results extend several earlier studies on the vibronic coupling leading to conical intersections between the X(2)B1 and A(2)A2 states, and a further trio (B, C, and D) of states. The conical intersection of the X and A states has been explicitly identified, and its structure and energetics evaluated. The energy sequence of the last group is only acceptable to the present study if given as B(2)B2

Combined theoretical and experimental study of the valence, Rydberg, and ionic states of chlorobenzene.

New photoelectron (PE) and ultra violet (UV) and vacuum UV (VUV) spectra have been obtained for chlorobenzene by synchrotron study with higher sensitivity and resolution than previous work and are subjected to detailed analysis. In addition, we report on the mass-resolved (2 + 1) resonance enhanced multiphoton ionization (REMPI) spectra of a jet-cooled sample. Both the VUV and REMPI spectra have enabled identification of a considerable number of Rydberg states for the first time. The use of ab initio calculations, which include both multi-reference multi-root doubles and singles configuration interaction (MRD-CI) and time dependent density functional theoretical (TDDFT) methods, has led to major advances in interpretation of the vibrational structure of the ionic and electronically excited states. Franck-Condon (FC) analyses of the PE spectra, including both hot and cold bands, indicate much more complex envelopes than previously thought. The sequence of ionic states can be best interpreted by our multi-configuration self-consistent field computations and also by comparison of the calculated vibrational structure of the B and C ionic states with experiment; these conclusions suggest that the leading sequence is the same as that of iodobenzene and bromobenzene, namely: X(2)B1(3b1 (-1)) < A(2)A2(1a2 (-1)) < B(2)B2(6b2 (-1)) < C(2)B1(2b1 (-1)). The absorption onset near 4.6 eV has been investigated using MRD-CI and TDDFT calculations; the principal component of this band is (1)B2 and an interpretation based on the superposition of FC and Herzberg-Teller contributions has been performed. The other low-lying absorption band near 5.8 eV is dominated by a (1)A1 state, but an underlying weak (1)B1 state (πσ(∗)) is also found. The strongest band in the VUV spectrum near 6.7 eV is poorly resolved and is analyzed in terms of two ππ(∗) states of (1)A1 (higher oscillator strength) and (1)B2 (lower oscillator strength) symmetries, respectively. The calculated vertical excitation energies of these two states are critically dependent upon the presence of Rydberg functions in the basis set, since both manifolds are strongly perturbed by the Rydberg states in this energy range. A number of equilibrium structures of the ionic and singlet excited states show that the molecular structure is less subject to variation than corresponding studies for iodobenzene and bromobenzene.

Amyloid-like Hfq interaction with single-stranded DNA: involvement in recombination and replication in Escherichia coli.

Interactions between proteins and single-stranded DNA (ssDNA) are crucial for many fundamental biological processes, including DNA replication and genetic recombination. Thus, understanding detailed mechanisms of these interactions is necessary to uncover regulatory rules occurring in all living cells. The RNA-binding Hfq is a pleiotropic bacterial regulator that mediates many aspects of nucleic acid metabolism. The protein notably mediates mRNA stability and translation efficiency by using stress-related small regulatory RNA as cofactors. In addition, Hfq helps to compact double-stranded DNA. In this paper, we focused on the action of Hfq on ssDNA. A combination of experimental methodologies, including spectroscopy and molecular imaging, has been used to probe the interactions of Hfq and its amyloid C-terminal region with ssDNA. Our analysis revealed that Hfq binds to ssDNA. Moreover, we demonstrate for the first time that Hfq drastically changes the structure and helical parameters of ssDNA, mainly due to its C-terminal amyloid-like domain. The formation of the nucleoprotein complexes between Hfq and ssDNA unveils important implications for DNA replication and recombination.

The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment.

The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin. Its precise role in DNA structuration is, however, unclear and whether Hfq plays a direct role in DNA-related processes such as replication or recombination is controversial. In previous works, we showed that Escherichia coli Hfq, or more precisely its amyloid-like C-terminal region (CTR), induces DNA compaction into a condensed form. In this paper, we evidence a new property for Hfq; precisely we show that its CTR influences double helix structure and base tilting, resulting in a strong local alignment of nucleoprotein Hfq:DNA fibers. The significance of this alignment is discussed in terms of chromatin structuration and possible functional consequences on evolutionary processes and adaptation to environment.

On the formation of the double helix between adenine single strands at acidic pH from synchrotron radiation circular dichroism experiments.

Here, we present synchrotron radiation circular dichroism spectra for a series of DNA adenine strands, (dA)(n) , n = 2-10, 15, at acidic pH. Reference spectra of a protonated single strand, (dAH(+) )(n) , and a protonated double helix, (dAH(+) )(n) :(dAH(+) )(n) , are provided in the wavelength region from 175 to 330 nm. The largest spectral difference between single and double strands is in the vacuum ultraviolet, where a band changes sign. This new spectral feature that characterizes double helix formation may be useful for analytical purposes but also for shedding light on the underlying complexation mechanism. Furthermore, we find that a minimum of eight or nine bases in a strand is needed for two (dAH(+) )(n) strands to form a duplex. This is a relatively high number as compared with guanine quadruplex and cytosine i-motif formation, which is likely linked to the significant Coulomb repulsion between the all-protonated bases. Finally, spectra recorded as a function of time after sample preparation indicates that the equilibrium is slowly reached, in certain cases taking an hour or more.