Ab initio and density functional theory (DFT) studies on triflic acid with water and protonated water clusters

The structure, stability and infrared spectral signatures of triflic acid (TA) with water clusters (W_n) and protonated water clusters (TAH⁺W_n, n?=?1???6) were computed using DFT and MP2 methods. Our calculations show that a minimum of three water molecules are necessary to stabilize the dissociated zwitterionic form of TA. It can be seen from the results that there is no significant movement of protons in smaller (n?=?1 and 2) and linear (n?=?1 – 6) types of water clusters. Further, the geometries of TAW_n clusters first form a neutral pair (NP) to contact ion pair (CIP), then form a solvent separated ion pair (SSIP) in a water hexamer. These findings reveal that proton transfer may take place through NP to CIP and then CIP to SSIP. The calculated binding energies (BEs) of ion pair clusters is always higher than that of NP clusters (i.e., more stable than the NP). Existing excess proton linear chain clusters transfer a proton to adjacent water molecules via a Grotthuss mechanism, whereas the same isomers in the branched motifs do not conduct protons. Examination of geometrical parameters and infrared frequencies reveals hydronium ion (H₃O⁺ also called Eigen cation) formation in both TAW_n and protonated TAW_n clusters. The stability of Eigen water clusters is three times higher than that of other non-Eigen water clusters. Our study shows clearly that formation of ion pairs in TAW_n and TAH⁺W_n clusters greatly favors proton transfer to neighboring water molecules and also enhances the stability of these complexes.     

Differential scattering of circularly polarized light in protonated DNA in the presence of spermine

The protonation of the spermine containing calf thymus DNA (molecular mass 15 and 5 MDa) solutions has been studied by means of circular dichroism method. It has been shown that the acid-induced transition from the low-protonated B(+)-form to the double-stranded structure with presumably Hoogsteen complementation of syn-G.C-base-pairs (S-form) in case of high-molecular partially condensed DNA is accompanied by differential scattering of circularly polarized light (DSCPL). The comparative study of protonation of partially and completely condensed low-molecular DNA enabled to obtain a family of DSCPL spectra. It has been demonstrated that the B+----S-transition in partially condensed high-molecular DNA is associated with formation of large intermolecular aggregates (with dimensions about 200 divided by 400 nm) which are destructed by acid-induced DNA denaturation.     

Radial distributions of water—water distances in protein crystals

An accurate protein crystallographic structure determination requires a knowledge of the solvent contribution to the diffraction pattern. As resolutions improve, research groups are reporting coordinates of large numbers of water molecules. We examine the accuracy of these coordinates by presenting radial distributions of water—water distances from refinements at different stages and interpreting them in terms of preferred hydrogen-bonding distances and problems in solvent electron density map interpretation. Marked differences between the distributions suggest that wide variations exist in the water molecule selection and refinement criteria employed by different research groups which mask possible real differences in solvent structure.     

The role of protein-bound water molecules in microbial rhodopsins

Protein-bound internal water molecules are essential features of the structure and function of microbial rhodopsins. Besides structural stabilization, they act as proton conductors and even proton storage sites. Currently, the most understood model system exhibiting such features is bacteriorhodopsin (bR). During the last 20 years, the importance of water molecules for proton transport has been revealed through this protein. It has been shown that water molecules are as essential as amino acids for proton transport and biological function. In this review, we present an overview of the historical development of this research on bR. We furthermore summarize the recently discovered protein-bound water features associated with proton transport. Specifically, we discuss a pentameric water/amino acid arrangement close to the protonated Schiff base as central proton-binding site, a protonated water cluster as proton storage site at the proton-release site, and a transient linear water chain at the proton uptake site. We highlight how protein conformational changes reposition or reorient internal water molecules, thereby guiding proton transport. Last, we compare the water positions in bR with those in other microbial rhodopsins to elucidate how protein-bound water molecules guide the function of microbial rhodopsins. This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.     

Competitive forces in crystalline lattices - protonated isonicotinic acid in the presence of tetrachlorometallates

A crystal structure determination for bis(4-hydroxycarbonylpyridinium) chloride tetrachloroferrate(III) monohydrate shows some striking differences in the lattice compared to that of the related tetrachloroplatinate(II) compound. A variety of intermolecular contacts indicate that, while common forces may be operative in these and other related lattices, their diverse features may reflect a close balance between polar hydrogen-bonding interactions and those involving the aromatic rings.     

Identifying conserved gene clusters in the presence of homology families.

The study of conserved gene clusters is important for understanding the forces behind genome organization and evolution, as well as the function of individual genes or gene groups. In this paper, we present a new model and algorithm for identifying conserved gene clusters from pairwise genome comparison. This generalizes a recent model called "gene teams." A gene team is a set of genes that appear homologously in two or more species, possibly in a different order yet with the distance of adjacent genes in the team for each chromosome always no more than a certain threshold. We remove the constraint in the original model that each gene must have a unique occurrence in each chromosome and thus allow the analysis on complex prokaryotic or eukaryotic genomes with extensive paralogs. Our algorithm analyzes a pair of chromosomes in O(mn) time and uses O(m+n) space, where m and n are the number of genes in the respective chromosomes. We demonstrate the utility of our methods by studying two bacterial genomes, E. coli K-12 and B. subtilis. Many of the teams identified by our algorithm correlate with documented E. coli operons, while several others match predicted operons, previously suggested by computational techniques. Our implementation and data are publicly available at euler.slu.edu/ approximately goldwasser/homologyteams/.     

Measurements of cysteine reactivity during protein unfolding suggest the presence of competing pathways

Evidence that proteins may unfold utilizing complex competing pathways comes from a new pulse-labeling protocol in which the change in reactivity of a single cysteine residue in a protein during unfolding is measured, making use of its easily monitored reaction with the Ellman reagent, dithionitrobenzoic acid. The kinetics of unfolding of two single cysteine-containing mutant forms of the small protein barstar, C82A, which contains only Cys40, and C40A, which contains only Cys82, have been studied. The data suggest that unfolding occurs via two parallel pathways, each forming competing intermediates. In one of these early intermediates, Cys40 and Cys82 are already as reactive as they are in the fully unfolded protein, while in the other intermediate, the Cys thiol groups are unreactive. One more long-lived intermediate also needs to be included on the pathway defined by the early intermediate with unreactive Cys thiol groups to account for the difference in the rates of fluorescence change and of change in Cys40 reactivity. The demonstration of multiple intermediates and pathways for unfolding indicates that protein unfolding reactions can be as complex as protein folding reactions.     

A theoretical treatment of the turnover of protein-bound phosphate in the presence of both protein kinase and phosphatase activities

Preparations of membrane fragments from brain have previously been shown to contain tightly bound protein kinase and phophatase enzymes which, together, are responsible for the turnover of protein-bound phosphate in the membrane.An equation has now been derived which describes the time-course of the phophorylation of the membrane-bound proteins in terms of the activities of the kinase and phosphatase enzymes and the initial state of phosphorylation of the membrane proteins. The use of this equation makes it possible to define the effects of substances or treatments which alter the overall rate of protein phosphorylation and to show whether kinase activity, phosphotase activity, or initial state of protein phosphorylation is being changed.Treatment of membrane fragmetns with NaI is found to decrease both protein kinase and phosphatase activities. Na⁺ decreases overall protein phosphorylation solely by decreasing phosphotase activity and cyclic AMP stimulates protein phosphorylation by an action on kinase activity alone.It has been deduced that if there is more than one type of site for protein phosphorylation in cerebral membrane fragments these should react with the kinase at equal rates and with the phosphatase at equal rates.It is hoped that the treatment given in this paper may prove generally applicable to situatiions where the rate of enzymic reaction is controlled by the concentration of substrate.     

X-ray crystallographic studies of substrate binding to aristolochene synthase suggest a metal ion binding sequence for catalysis

The universal sesquiterpene precursor, farnesyl diphosphate (FPP), is cyclized in an Mg(2+)-dependent reaction catalyzed by the tetrameric aristolochene synthase from Aspergillus terreus to form the bicyclic hydrocarbon aristolochene and a pyrophosphate anion (PP(i)) coproduct. The 2.1-A resolution crystal structure determined from crystals soaked with FPP reveals the binding of intact FPP to monomers A-C, and the binding of PP(i) and Mg(2+)(B) to monomer D. The 1.89-A resolution structure of the complex with 2-fluorofarnesyl diphosphate (2F-FPP) reveals 2F-FPP binding to all subunits of the tetramer, with Mg(2+)(B)accompanying the binding of this analogue only in monomer D. All monomers adopt open activesite conformations in these complexes, but slight structural changes in monomers C and D of each complex reflect the very initial stages of a conformational transition to the closed state. Finally, the 2.4-A resolution structure of the complex with 12,13-difluorofarnesyl diphosphate (DF-FPP) reveals the binding of intact DF-FPP to monomers A-C in the open conformation and the binding of PP(i), Mg(2+)(B), and Mg(2+)(C) to monomer D in a predominantly closed conformation. Taken together, these structures provide 12 independent "snapshots" of substrate or product complexes that suggest a possible sequence for metal ion binding and conformational changes required for catalysis.     

A critical role of protein-bound water in the catalytic cycle of cytochrome P-450 camphor.

The rates of NADH oxidation during the hydroxylation of camphor by cytochrome P-450cam were followed in the presence of co-solvents used to increase the osmotic pressure surrounding the protein-bound water. As a result, the measured Vmax decreases independently of the perturbant tested. Roughly 28 molecules of water, involved during the catalytic cycle, are deduced from the variation of Vmax as a function of osmotic pressure. These molecules, in part, could be those present in the cytochrome P-450cam-putidaredoxin interface.     

Hydrogen-bonding alterations of the protonated Schiff base and water molecule in the chloride pump of Natronobacterium pharaonis

Halorhodopsin is a light-driven chloride ion pump. Chloride ion is bound in the Schiff base region of the retinal chromophore, and unidirectional chloride transport is probably enforced by the specific hydrogen-bonding interaction with the protonated Schiff base and internal water molecules. In this article, we study hydrogen-bonding alterations of the Schiff base and water molecules in halorhodopsin of Natronobacterium pharaonis (pHR) by assigning their N-D and O-D stretching vibrations in D(2)O, respectively. Highly accurate low-temperature Fourier transform infrared spectroscopy revealed that hydrogen bonds of the Schiff base and water molecules are weak in the unphotolyzed state, whereas they are strengthened upon retinal photoisomerization. Halide dependence of the stretching vibrations enabled us to conclude that the Schiff base forms a direct hydrogen bond with Cl(-) only in the K intermediate. Hydrogen bond of the Schiff base is further strengthened in the L(1) intermediate, whereas the halide dependence revealed that the acceptor is not Cl(-), but presumably a water molecule. Thus, it is concluded that the hydrogen-bonding interaction between the Schiff base and Cl(-) is not a driving force of the motion of Cl(-). Rather, the removal of its hydrogen bonds with the Schiff base and water(s) makes the environment around Cl(-) less polar in the L(1) intermediate, which presumably drives the motion of Cl(-) from its binding site to the cytoplasmic domain.     

Exploring the effect of confinement on water clusters in carbon nanotubes

Using armchair-type single-walled carbon nanotubes (SWCNTs) of different sizes as model compounds for lignite, the effect of water molecule confinement on the water-holding capacity of lignite pores was investigated. Results indicated that the water-holding capacity of pores with diameters of <10 nm was eight times larger than that of pores with diameters of 100 nm. The configuration of the cluster of water molecules in each SWCNT and the binding energy between each SWCNT and the water molecules within it were calculated by means of density functional theory using a hybrid functional: M06-2X/6-311+G**, 6-31G*. The results prove that the configurations of the water molecules in the SWCNTs are very different to their configuration in the unconfined state. In vacuum, the cluster of three water molecules adopted a trimer configuration, while they presented a linear configuration in the 6.78 Å SWCNT. Similarly, in vacuum, the cluster of five water molecules formed a five-membered ring, while they favored a linear configuration in the 6.78 Å SWCNT, a zigzag configuration in the 8.14 Å SWCNT, and a trimer?+?1?+?1 configuration (i.e., a trimer plus two isolated water molecules) in the 9.49 Å, 10.85 Å, and 13.75 Å SWCNTs. There was found to be a degree of competition between the coupling energy of the water molecules with the SWCNT and the hydrogen bonding among the water molecules. When the diameter of the SWCNT was >1 nm, the hydrogen bonding among the water molecules dominated, while the coupling energy of the water molecules with the SWCNT amounted to only 30–40% of the total interaction energy of the water molecules.

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Graphical Abstract Computed equilibrium structures of five water molecules confined in SWCNTs with diameters of 6.78 Å, 8.14 Å, 9.49 Å, 10.85 Å, and 13.75 Å, and in vacuum

     

The phenetic distances of the living Druze from other human populations suggest a major genetic drift from the Western Eurasian ancestral category

The objectives were to determine the expression frequency and sexual dimorphism of 16 non-metric crown traits on the sample of permanent dentitions of the living Druze population (a Near Eastern genetic isolate) in Jordan, and to assess the biological affinity of this sample to 21 regional groups, and to the living general Jordanian population, based on these traits. Druze schoolchildren (46 males, 40 females; mean age = 16.0, sd = 0.5 years) were studied in 2011. The traits were classified using the Arizona State University dental anthropology system, counted with the individual count method, and dichotomized according to the criteria of Scott and Turner for the purpose of group comparisons. Fisher's exact test for dichotomized scores was used to assess sexual dimorphism in these traits. Smith's mean measure of divergence was used to measure all pairwise distance values among the groups. Sexual dimorphism was found in five traits (i.e., UI2 interruption grooves, 3-cusped UM2, UM1 Carabelli's tubercle/cusp, 4-cusp LM1, and LM2 Y-groove pattern). This study revealed that the dental pattern of living Druze, which is similar to that of the general Jordanian population, is sufficiently distinct from the Western Eurasian pattern and all other known dental patterns to form a distinct dental pattern for the regional group or subcategory to which these two populations belong. Moreover, the relatively large distance values of the living Druze and Jordanians from the other world groups considered, including the Western Eurasian groups, suggest a similar major genetic difference of these two populations from the Western Eurasian ancestry.     

Ozone produced by corona discharge in the presence of water

Significant levels of ozone have been detected in a reaction flask that was designed for studies using negative air ions generated from corona discharge. While diluting the gas in the vessel at the rate of 1.5 liters/min., more than 1.0 ppm O₃ was measured in the vessel when grounded water was present. Ozone levels were much less (15 ppb) in ambient air near the ion generator. Even in the absence of water, O₃ levels were only 7 ppb in the reaction flask. Without the corona discharge apparatus, levels of ozone in the gas phase (with water present) averaged 6 ppb. These results demonstrate that when negative air ions are generated from corona discharge in the presence of water, significant levels of ozone are produced. Therefore, O₃ could be directly responsible for many of the oxidizing effects that have been reportedly due to negative air ions.