Computational studies on the interaction of ABO-active saccharides with the norovirus VA387 capsid protein can explain experimental binding data

Norovirus strains are known to cause recurring epidemics of winter vomiting disease. The crystal structure of the capsid protein of VA387, a representative of the clinically important GII.4 genocluster, was recently solved in complex with histo-blood group A- and B-trisaccharides. However, the VA387 strain is known to bind also to other natural carbohydrates for which detailed structural information of the complexes is not available. In this study we have computationally explored the fit of the VA387 with a set of naturally occurring carbohydrate ligands containing a terminal α1,2-linked fucose. MD simulations both with explicit and implicit solvent models indicate that type 1 and 3 extensions of the ABO-determinant including ALe^b and BLe^b pentasaccharides can be well accommodated in the site. Scoring with Glide XP indicates that the downstream extensions of the ABO-determinants give an increase in binding strength, although the α1,2-linked fucose is the single strongest interacting residue. An error was discovered in the geometry of the GalNAc-Gal moiety of the published crystal structure of the A-trisaccharide/VA387 complex. The present modeling of the complexes with histo-blood group A-active structures shows some contacts which provide insight into mutational data, explaining the involvement of I389 and Q331. Our results can be applicable in structure-based design of adhesion inhibitors of noroviruses.     

Downfield proton chemical shifts are not reliable aromaticity indicators

[structure: see text] The downfield chemical shifts of arene hydrogens (delta (1)H) are due only in part to the pi ring current contribution [sigma(//)(pi)]; local framework effects are equally important. Neither proton chemical shifts nor even sigma(||)(pi) tensor elements, per se, are reliable aromaticity indicators. Unsaturated polycyclic hydrocarbons with nonaromatic quinoid structures have delta (1)H and sigma(//)(pi) values in the "aromatic range". Conversely, numerous aromatic protons, including those in five-membered ring heterocycles, resonate in the "nonaromatic range".     

On the stability of large [4n]annulenes

[reaction: see text] The stabilization energies (B3LYP/6-31G) of planar [4n]annulenes, evaluated by a new indene-isoindene isomerization method (see Abstract graphic), reveal that all 4n pi-electron rings larger than the energetically unfavorable cyclobutadiene are only slightly destabilized by the pi-electron interactions. Cyclooctatetraene prefers the "tub" conformation because of strain effects. Generally, the antiaromatic character of the larger systems with 4n pi-electrons is revealed best by their magnetic properties rather than by their energies.     

Femtosecond dynamics of flavin cofactor in DNA photolyase: radical reduction, local solvation, and charge recombination

We report here our femtosecond studies of the photoreduction dynamics of the neutral radical flavin (FADH) cofactor in E. coli photolyase, a process converting the inactive form to the biologically active one, a fully reduced deprotonated flavin FADH(-). The observed temporal absorption evolution revealed two initial electron-transfer reactions, occurring in 11 and 42 ps with the neighboring aromatic residues of W382 and F366, respectively. The new transient absorption, observed at 550 nm previously in photolyase, was found from the excited-state neutral radical and is probably caused by strong interactions with the adenine moiety through the flavin U-shaped configuration and the highly polar/charged surrounding residues. The solvation dynamics from the locally ordered water molecules in the active site was observed to occur in approximately 2 ps. These ultrafast ordered-water motions are critical to stabilizing the photoreduction product FADH(-) instantaneously to prevent fast charge recombination. The back electron-transfer reaction was found to occur in approximately 3 ns. This slow process, consistent with ultrafast stabilization of the catalytic cofactor, favors photoreduction in photolyase.     

Piezoelectricity in quasicrystals: A group-theoretical study

Group-theoretical methods have been accepted as exact and reliable tools in studying the physical properties of crystals and quasicrystalline materials. By group representation theory, the maximum number of non-vanishing and independent second-order piezoelectric coefficients required by the seven pentagonal and two icosahedral point groups — that describe the quasicrystal symmetry groups in two and three dimensions — is determined. The schemes of non-vanishing and independent second-order piezoelectric tensor components needed by the nine point groups with five-fold rotations are identified and tabulated employing a compact notation. The results of this group-theoretical study are briefly discussed.      

The peculiar trend of cyclic perfluoroalkane electron affinities with increasing ring size

The adiabatic electron affinities (AEAs), vertical electron affinities (VEAs), and vertical detachment energies (VDEs) of cyclic perfluoroalkanes, c-C(n)F(2n) (n = 3-7), and their monotrifluoromethyl derivatives were computed using various pure and hybrid density functionals with DZP++ (polarization and diffuse function augmented double-zeta) basis sets. The theoretical AEA of c-C(4)F(8) at KMLYP/DZP++ is 0.70 eV, which exhibits satisfactory agreement with the 0.63 +/- 0.05 eV experimental value. The nonzero-point-corrected AEA of c-C(4)F(8) is predicted to be 0.41 eV at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ level of theory, which shows a slight deviation of 0.11 eV from the KMLYP estimated value of 0.52 eV for the same. With the zero-point correction from the MP2/6-311G(d) [Gallup, G. A. Chem. Phys. Lett. 2004, 399, 206] level of theory combined with the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ result, the most reliable estimate of AEA of c-C(4)F(8) is 0.60 eV. c-C(3)F(6)(-), c-C(4)F(8)(-), and c-C(5)F(10)(-) are unusual in preferring planar to near planar ring structures. The ZPE-corrected AEAs of c-C(n)F(2n) increase from n = 3 (0.24 eV) to n = 5 (0.77 eV), but then dramatically fall off to 0.40 eV for both n = 6 and n = 7. All of the other functionals predict the same trend. This is due to a change in the structural preference: C(s)() c-C(6)F(12)(-) and C(1) c-C(7)F(14)(-) are predicted to favor nonplanar rings, each with an exceptionally long C-F bond. (There also is a second, higher energy D3d minimum for C(6)F(12)(-).) The SOMOs as well as the spin density plots of the c-PFA radical anions reveal that the "extra" electron is largely localized on the unique F atoms in the larger n = 6 and n = 7 rings but is delocalized in the multiatom SOMOs of the three- to five-membered ring radical anions. The computed AEAs are much larger than the corresponding VEAs; the latter are not consistent with different functionals. The AEAs are substantially larger when a c-C(n)()F(2)(n)() fluorine is replaced by a -CF(3) group. This behavior is general; PFAs with tertiary C-F bonds have large AEAs. The VDEs for all the anions are substantial, ranging from 1.89 to 3.64 eV at the KMLYP/DZP++ level.     

Diels-Alder Reaction of phosphaethene with 1,3-dienes: an ab initio study

Computations on Diels-Alder (DA) reactions of phosphaethene with 1,3-butadiene and with isoprene reveal asynchronous transition structures. The DFT (B3LYP/6-311+G) activation energies of these reactions, 12-14 kcal/mol, are much lower than that of the parent ethene-butadiene reaction, 28 kcal/mol, even though the exothermicities of all lie in the same range, from -29 to -33 kcal/mol. The transition states (TSs) for the phosphethene-butadiene or isoprene DA reactions are earlier than the TSs of the butadiene-ethene cycloaddition. Due to the weakness of the C=P pi bond compared to the C=C pi bonds, the energies required to reach the phosphaethene TSs are much less than the carbocyclic cases. The computed (1)H NMR chemical shifts and nucleus independent chemical shifts (NICS) quantify the aromatic character of the transition states. Regioselectivities of the neutral phosphaethene-isoprene DA reactions are modest, at best. However, computations on radical cation DA reactions of phosphaethene with isoprene, which proceed stepwise with open chain intermediates, can account for the high regioselectivities that have been observed in some cases.     

Bidirectional Regulation of mRNA Translation in Mammalian Cells by Using PUF Domains

The regulation of gene expression is crucial in diverse areas of biological science, engineering, and medicine. A genetically encoded system based on the RNA binding domain of the Pumilio and FBF (PUF) proteins was developed for the bidirectional regulation (i.e., either upregulation or downregulation) of the translation of a target mRNA. PUF domains serve as designable scaffolds for the recognition of specific RNA elements and the specificity can be easily altered to target any 8‐nucleotide RNA sequence. The expression of a reporter could be varied by over 17‐fold when using PUF‐based activators and repressors. The specificity of the method was established by using wild‐type and mutant PUF domains. Furthermore, this method could be used to activate the translation of target mRNA downstream of PUF binding sites in a light‐dependent manner. Such specific bidirectional control of mRNA translation could be particularly useful in the fields of synthetic biology, developmental biology, and metabolic engineering.     

Support vector regression with digital band pass filtering for the quantitative analysis of near‐infrared spectra

This paper proposes a novel calibration technique based on combining support vector regression with a digital band pass (DBP) filter for the quantitative analysis of near‐infrared spectra. The efficacy of the proposed method is investigated and validated in the determination of glucose from near‐infrared spectra of a mixture composed of urea, triacetin and glucose. In this paper, the DBP filtering was implemented as a pre‐processing technique in the frequency domain as a Gaussian band pass filter and in the time domain as a Chebyshev filter. The grid‐search optimization method was used to optimize the filter parameters. The results demonstrate that utilization of the optimized DBP filters as a pre‐processing technique improved the performance of the predictive models. Copyright © 2013 John Wiley & Sons, Ltd.     

Self-assembled reverse micelles in supercritical CO2 entrap protein in native state

Molecular dynamics simulations of random quaternary mixtures of protein-water-CO2-fluorosurfactants show the self-assembly of reverse micelles in supercritical carbon dioxide where the protein becomes entrapped inside the aqueous pool. Analyses show that the protein native state remains intact in the water pool. This is because of the bulk nature of the enclosed water that provides a suitable environment for the extracted protein. Results from ab initio calculations imply that the existing fluorosurfactants can be made more effective in stabilizing water-in-CO2 microemulsions by a partial hydrogenation in their tails. A Lewis acid-Lewis base interaction among CO2 and the surfactant tails enhances the stability of the aqueous droplets substantially. The study can help accelerate the search for surfactant process for environmentally benign applications in dense CO2.