Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Molecular dynamics (MD) simulations are performed to study the interaction of His-tagged peptide with three different metal surfaces in explicit water. The equilibrium properties are analyzed by using pair correlation functions (PCF) to give an insight into the behavior of the peptide adsorption to metal surfaces in water solvent. The intermolecular interactions between peptide residues and the metal surfaces are evaluated. By pulling the peptide away from the peptide in the presence of solvent water, peeling forces are obtained and reveal the binding strength of peptide adsorption on nickel, copper and gold. From the analysis of the dynamics properties of the peptide interaction with the metal surfaces, it is shown that the affinity of peptide to Ni surface is the strongest, while on Cu and An the affinity is a little weaker. In MD simulations including metals, the His-tagged region interacts with the substrate to an extent greater than the other regions. The work presented here reveals various interactions between His-tagged peptide and Ni/Cu/Au surfaces. The interesting affinities and dynamical properties of the peptide are also derived. The results give predictions for the structure of His-tagged peptide adsorbing on three different metal surfaces and show the different affinities between them, which assist the understanding of how peptides behave on metal surfaces and of how designers select amino sequences in molecule devices design. (c) 2007 Elsevier Ltd. All rights reserved.

Combining Plant Pathogenic Fungi and the Leaf-Mining Fly, Hydrellia pakistanae, Increases Damage to Hydrilla

Four fungal species, F71PJ Acremonium sp., F531 Cylindrocarpon sp., F542, Botrytis sp., and F964 Fusarium culmorum [Wm. G. Sm.] Sacc. were recovered from hydrilla [ Hydrilla verticillata (L. f.) Royle] shoots or from soil and water surrounding hydrilla growing in ponds and lakes in Florida and shown to be capable of killing hydrilla in a bioassay. The isolates were tested singly and in combination with the leaf-mining fly, Hydrellia pakistanae (Diptera: Ephydridae), for their capability to kill or severely damage hydrilla in a bioassay.

Structure, chemistry, and energetics of organic and inorganic adsorbates on Ga-rich GaAs and GaP(001) surfaces

The work described in this dissertation includes fundamental investigations into three surface processes, namely inorganic film growth, water-induced oxidation, and organic functionalization/passivation, on the GaP and GaAs(001) surfaces. The techniques used to carry out this work include scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations. Atomic structure, electronic structure, reaction mechanisms, and energetics related to these surface processes are discussed at atomic or molecular levels.

First, we investigate epitaxial Zn₃P₂ films grown on the Ga-rich GaAs(001)(6×6) surface. The film growth mechanism, electronic properties, and atomic structure of the Zn₃P₂/GaAs(001) system are discussed based on experimental and theoretical observations. We discover that a P-rich amorphous layer covers the crystalline Zn3P2 film during and after growth. We also propose more accurate picture of the GaP interfacial layer between Zn₃P₂ and GaAs, based on the atomic structure, chemical bonding, band diagram, and P-replacement energetics, than was previously anticipated.

Second, DFT calculations are carried out in order to understand water-induced oxidation mechanisms on the Ga-rich GaP(001)(2×4) surface. Structural and energetic information of every step in the gaseous water-induced GaP oxidation reactions are elucidated at the atomic level in great detail. We explore all reasonable ground states involved in most of the possible adsorption and decomposition pathways. We also investigate structures and energies of the transition states in the first hydrogen dissociation of a water molecule on the (2×4) surface.

Finally, adsorption structures and thermal decomposition reactions of 1-propanethiol on the Ga-rich GaP(001)(2×4) surface are investigated using high resolution STM, XPS, and DFT simulations. We elucidate adsorption locations and their associated atomic structures of a single 1-propanethiol molecule on the (2×4) surface as a function of annealing temperature. DFT calculations are carried out to optimize ground state structures and search transition states. XPS is used to investigate variations of the chemical bonding nature and coverage of the adsorbate species.

Electron diffraction and photoemission studies of clean and water-covered Si(5,5,12) and Si(112) surfaces

The structure of silicon surfaces in the orientation range (113)-(5,5,12)-(337)-(112) has been investigated using high resolution LEED and photoemission both on a spherical and on flat samples. We find that Si(5,5,12) [5.3 degrees from (113) and 0.7 degrees from (937)] is the only stable orientation between (113) and (111) and confirm the result of Baski et al. [Science 269, 1556 (1995)] that it has a 2 x 1 superstructure with a very large unit cell of 7.68 x 53.5 Angstrom(2). Adsorption measurements of water on Si(5,5,12) yield a mobile precursor kinetics with two kinds of regions saturating at 0.25 and 0.15 ML which are related to adsorption on different sites. Using these results, a modified structure model is proposed. Surfaces between (113) and (5,5,12) separate into facets of these two orientations; between (5,5,12) and (112), they separate into (5,5,12) and (111) facets. (337) facets in this range may be considered as defective (5,5,12) facets.

Summer monsoon intensity controls C-4/C-3 plant abundance during the last 35 ka in the Chinese Loess Plateau: Carbon isotope evidence from bulk organic matter and individual leaf waxes

IEECAS SKLLQG

Flower color chimera and abnormal leaf mutants induced by C-12(6+) heavy ions in Salvia splendens Ker-Gawl.

The effect of C-12(6+) heavy ions bombardment on mutagenesis in Salvia splendens Ker-Gawl. was studied. Dose-response studies indicated that there was a peak of malformation frequency of S. splendens at 200 Gy. Abnormal leaf mutants of the bileaf, trileaf and tetraleaf conglutination were selected. Meanwhile, a bicolor flower chimera with dark red and fresh red flower was isolated in M1 generation of S. splendens. Random amplified polymorphic DNA (RAPD) analysis demonstrated that DNA variations existed among the wild-type, fresh and dark red flower shoots of the chimera. The dark red flower shoots of the chimera were conserved and cultivated at a large-scale through micropropagation. MS supplemented with 2.0 mg/L BA and 0.3 mg/L NAA was the optimal medium in which the maximum proliferation ratio (5.2-fold) and rooting rate (88%) were achieved after 6 weeks. Our findings provide an important method to improve the ornamental quality of S. splendens.

Morphological Adaptations to Drought and Reproductive Strategy of the Moss Syntrichia caninervis in the Gurbantunggut Desert, China

The biological soil crusts (BSCs) in the Gurbantunggut Desert, the largest fixed and semi-fixed desert in China, feature moss-dominated BSCs, which play an indispensable role in sand fixation. Syntrichia caninervis Mitt. (S. caninervis) serves as one of the most common species in BSCs in the desert. In this study we examined the morphological structure of S. caninervis from leafy gametophyte to protonema using light and scanning electron microscopy (SEM). We also examined the relationships between the morphological structure of S. caninervis and environmental factors. We found that: (1) this moss species is commonly tufted on the sand surface, and its leaves are folded upwards and twisted around the stem under dry conditions; (2) the cells on both upper and lower leaf surfaces have C-shaped dark papillae, which may reflect sunlight to reduce the damage from high temperature; (3) the leaf costa is excurrent, forming an awn with forked teeth; and (4) the protonema cells are small and thickset with thick cell walls and the cytoplasm is highly concentrated with a small vacuole. In addition, we also found that the protonema cells always form pouches on the tip of the mother cells during the process of cell polarization. Our results suggest that S. caninervis has, through its life cycle, several morphological and structural characteristics to adapt to dry environmental conditions. These morphological features of S. caninervis may also be found in other deserts in the world due to the world-wide distribution of the species.

General rules for predicting where a catalytic reaction should occur on metal surfaces: A density functional theory study of C-H and C-O bond breaking/making on flat, stepped, and kinked metal surfaces

To predict where a catalytic reaction should occur is a fundamental issue scientifically. Technologically, it is also important because it can facilitate the catalyst's design. However, to date, the understanding of this issue is rather limited. In this work, two types of reactions, CH4 CH3 + H and CO C + 0 on two transition metal surfaces, were chosen as model systems aiming to address in general where a catalytic reaction should occur. The dissociations of CH4 - CH3 + H and CO --> C + O and their reverse reactions on flat, stepped, and kinked Rh and Pd surfaces were studied in detail. We find the following: First, for the CH4 Ch(3) + H reaction, the dissociation barrier is reduced by similar to0.3 eV on steps and kinks as compared to that on flat surfaces. On the other hand, there is essentially no difference in barrier for the association reaction of CH3 + H on the flat surfaces and the defects. Second, for the CO C + 0 reaction, the dissociation barrier decreases dramatically (more than 0.8 eV on Rh and Pd) on steps and kinks as compared to that on flat surfaces. In contrast to the CH3 + H reaction, the C + 0 association reaction also preferentially occurs on steps and kinks. We also present a detailed analysis of the reaction barriers in which each barrier is decomposed quantitatively into a local electronic effect and a geometrical effect. Our DFT calculations show that surface defects such as steps and kinks can largely facilitate bond breaking, while whether the surface defects could promote bond formation depends on the individual reaction as well as the particular metal. The physical origin of these trends is identified and discussed. On the basis of our results, we arrive at some simple rules with respect to where a reaction should occur: (i) defects such as steps are always favored for dissociation reactions as compared to flat surfaces; and (ii) the reaction site of the association reactions is largely related to the magnitude of the bonding competition effect, which is determined by the reactant and metal valency. Reactions with high valency reactants are more likely to occur on defects (more structure-sensitive), as compared to reactions with low valency reactants. Moreover, the reactions on late transition metals are more likely to proceed on defects than those on the early transition metals.