Molecular dynamics simulations of human butyrylcholinesterase

Herein, we present results from molecular dynamics (MD) simulations of the human butyrylcholinesterase (BuChE) enzyme in aqueous solution. Two configurations of the unbound form of BuChE differing in the presence or absence of a sodium ion inside the protein gorge were simulated for 10 and 5 ns, respectively. Besides complementing the structural information provided by X-ray data, the MD simulations give insight into the structure of the native BuChE enzyme. For example, it is shown that: the nucleophilic Ser(198) residue and the various binding subsites in the BuChE catalytic cavity are readily accessible from the exterior of the protein; the presence of the sodium ion dynamically explores two different binding sites in the gorge leading to the active site and stabilizes the productive conformation of the Glu(325)/His(438)/Ser(198) catalytic triad; several long-lived water bridges are fully integrated into the architecture of the active site; the positions of the residues at the rim of the gorge region display large deviations with respect to the crystal structure; and two side doors, constituted by residues situated at the tip of the acyl- and Omega-loops, respectively, open wide enough to allow the passage of water molecules. In conclusion, we compare our theoretical results with those from previous work on mouse acetylcholinesterase and discuss their implications for substrate binding and catalysis in BuChE.     

Host acceptance behaviour of Colorado potato beetle larvae influenced by potato glandular trichomes

ABSTRACT. In no-choice tests, larvae of the Colorado potato beetle, Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae), avoided contact with, and were less frequently observed feeding on, excised foliage of the resistant wild potato Solanum berthaultii Hawkes than on leaves of the cultivated potato, S.tuberosum L. For older larvae, reduced feeding was a consequence of less frequent contact with S.berthaultii leaves. However, first instars appeared unable to penetrate the adhesive barrier presented by glandular trichomes of S. berthaultii , and those that remained on the leaflets fed less often than did first instars on S. tuberosum. Removal of the trichome barrier by wiping leaflets with tissue paper did not attenuate the apparent repellent effect of S. berthaulti foliage, but led to increased incidence of feeding by first instars. Inhibition of larval feeding may therefore rely on a mechanical barrier provided by the glandular trichomes of S.berthaultii.     

Freeze-fracturing and deep-etching with the volatile cryoprotectant ethanol reveals true membrane surfaces of kidney structures

Summary With the conventional freeze-fracture technique applied to biological specimens, cell membranes split along an interior plane and two membrane faces are produced. True membrane surfaces remain hidden and can only be uncovered by deep-etching. To date, deep-etching could not be satisfactorily performed in the presence of cryoprotective agents since conventional cryoprotectants do not sublime due to their low vapour pressure. This lack of suitable volatile cryoprotectants has limited deep-etching so far to very small objects which can be cryofixed without cryoprotectants. As a consequence, our freeze-fracture knowledge of cell surfaces is still poor.The present study shows that ethanol is a suitable volatile cryoprotectant for the freeze-fracture technique, and provides a novel approach to the routine deep-etching of freeze-fracture specimens without the need for special equipment. With ethanol deep-etching, true outer cell-surfaces are demonstrated within the kidneys of rat and Psammomys.     

Does the common topknot Zeugopterus punctatus (Teleosteii: Pleuronectiformes: Scophthalmidae) use a novel Venturi-effect attachment mechanism? A testable hypothesis

Common topknots (Zeugopterus punctatus) attach to vertical rock surfaces and overhangs. It has been speculated that attachment is by a suction cup, with the median (anal, dorsal) fins providing a peripheral seal. Here the authors propose that the attachment is actually based on a Venturi effect. The rear portions of the median fins continually move in a fan-like fashion (at c. 4 cycles per second). This movement produces a tailward fluid flow that ventilates the shallow underbody space between the fish and its rocky substratum. The anterior portions of the median fins seal the space laterally, but the space is open anterior (beneath the raised head) and posterior to the sea. The mid-underbody space likely has a lower cross-sectional area than does the front intake or rear exit, so flow should be faster (and pressure lower) within it than outside, thus providing pressure gradient suction. Topknots attach to rough and heavily biofouled surfaces, presumably because the high numbers of fin rays and their associated membranes plus fine muscle control allow effective sealing. The attachment ability is shared by all members of the flatfish tribe Phrynorhombini; it can be related to anatomical peculiarities and constitutes a probable synapomorphy for this clade.     

Characterization of Methicillin-resistant Staphylococcus aureus isolated from public surfaces on a university campus, student homes and local community

Aim: Isolation and characterization of methicillin‐resistant Staphylococcus aureus (MRSA) from frequently touched nonhospital environmental surfaces at a large university, student homes and community sites. Methods and Results: Twenty‐four isolates from 21 (4·1%, n = 509) surfaces were MRSA positive and included 14 (58%, n = 24) SCCmec type IV, two (8%, n = 24) type I, and eight (33%, n = 24) were not type I‐IV (NT). Six different multilocus sequencing types were identified by PCR and sequencing. PCR assays identified one (4·2%, n = 24) Panton‐Valentine leukocidin (PVL) positive, 22 (92%, n = 24) arginine catabolic mobile element (ACME) positive and 23 (96%, n = 24) multidrug‐resistant (kanamycin, macrolide, tetracycline) MRSA isolates. Eleven (46%, n = 24) USA300 isolates were determined by pulsed‐field gel electrophoresis. Conclusion: The MRSA‐positive environmental surfaces were identified in student homes (11·8%, n = 85), the community (2·3%, n = 130) and the university (2·7%, n = 294). USA300 strains were isolated from the university, student homes and community samples. This is the first report of the animal clone ST97 on urban environmental surfaces. Significance and Impact of the Study: The study highlights the distribution of USA300 on frequently touched surfaces. Whether contact with these MRSA contaminated environmental surfaces are associated with increased risk of transmission of MRSA to people needs further research.     

Evaluation of Hydrodynamic Drag on Experimental Fouling-release Surfaces,using Rotating Disks

Fouling by biofilms significantly increases frictional drag on ships' hulls. A device, the friction disk machine, designed to measure torque on rotating disks, was used to examine differences among experimental fouling-release coatings in the drag penalty due to accumulated biofilms. Penalties were measured as the percentage change in the frictional resistance coefficient C_f. Drag penalties due to microfouling ranged from 9% to 29%, comparable to previously reported values. An antifouling control coating showed a smaller drag penalty than the fouling-release coatings. There were also significant differences among the fouling-release coatings in drag due to biofilm formation. These results indicate that the friction disk machine may serve as a valuable tool for investigating the effects of experimental coatings, both antifouling and fouling-release, on microfouling and associated drag penalties.     

Bacterial Biofilm in Seawater: Cell Surface Properties of Early-attached Marine Bacteria

The development of antifouling strategies in seawater requires knowledge of the physico-chemical properties of the cell surfaces of early adherent bacteria. The hydrophilic, electrostatic and the Lewis acid-base cell surface properties of eleven marine bacteria were characterized. Although these bacteria adhered to a hydrophilic support immersed for 3 and 6?h, they presented various physico-chemical properties. Eleven strains possessed a hydrophilic surface and five a hydrophobic surface. Although the majority of the bacteria presented an electron-donating character, some could not generate Lewis acid-base interactions with the support. On the other hand, all strains possessed an isoelectric point ranging from 2.2 to 3.4 and were negatively charged at the pH of seawater. Hydrophilicity was a preponderant property among these bacteria, but other properties should not be ignored. The development of new antifouling paints must take account all the possible interaction levels used by the bacteria to adhere to an immersed surface.     

The surface properties of some silicone and fluorosilicone coating materials immersed in seawater

Changes in the surface properties of some silicone elastomers (General Electric RTV11, RTV160 and RTV655) and fluorosilicones (‐(Si(CH₃)((CH₂)₃‐O(CH₂)₂(CF₂)_XCF₃)‐O)_n‐, x = 5,7,9) on prolonged immersion in water (distilled water, artificial seawater, filtered and unfiltered seawater) have been investigated using measurements of advancing and receding contact angles, of surface roughness and of water uptake. Considerable increases in hydrophilicity and surface rugosity are attributed mainly to surface structural rearrangements accompanying absorption of water; these effects are greater for the fluorosilicones and the rugosity of RTV160 also increased considerably. Observations of early marine settlement (up to 16 weeks in flowing seawater), visualised by scanning electron microscopy, showed patchy attachment mainly of bacteria and microalgae while mature biofilms were formed on the poly(methylmethacrylate) controls. Although settlement was least on RTV11 and greatest on the fluorosilicones, the range of variation was small relative to the differences in the long‐term fouling resistance of the materials. The design requirements for fouling resistance of a smooth, soft, uniform surface are supported.     

Atomistic Simulation of Mineral Surfaces

Abstract

Atomistic simulation techniques are now able to model the structure of mineral surfaces at the atomic level. In this paper we begin to address the question of whether surface reactivity can be studied reliably by modelling the surface reactivity of calcite, fluorite and forsterite under aqueous conditions. We first used energy minimisation techniques to investigate the interaction between the minerals calcite and fluorite with water and methanoic acid. The relative adsorption energies suggest that methanoic acid preferentially adsorbs onto fluorite surfaces, while water adsorbs preferentially onto calcite as inferred from experiments on mineral separation. Molecular Dynamics simulations were also used to model the effect of temperature on the adsorption of water on the calcite {1014} and fluorite {111} surfaces. Furthermore we used these techniques to model point defect formation at surfaces. We are also interested in modelling the competition between associative and dissociative adsorption on mineral surfaces. Simulations of adsorption of water on the low-index forsterite surfaces have predicted the adsorption energies and equilibrium morphology. The calculated equilibrium morphology adequately reproduces the experimental morphology of forsterite suggesting that the relative stabilities of the surfaces, both unhydrated and hydroxylated, are calculated correctly.     

Exhaustive comparison and classification of ligand‐binding surfaces in proteins

Many proteins function by interacting with other small molecules (ligands). Identification of ligand‐binding sites (LBS) in proteins can therefore help to infer their molecular functions. A comprehensive comparison among local structures of LBSs was previously performed, in order to understand their relationships and to classify their structural motifs. However, similar exhaustive comparison among local surfaces of LBSs (patches) has never been performed, due to computational complexity. To enhance our understanding of LBSs, it is worth performing such comparisons among patches and classifying them based on similarities of their surface configurations and electrostatic potentials. In this study, we first developed a rapid method to compare two patches. We then clustered patches corresponding to the same PDB chemical component identifier for a ligand, and selected a representative patch from each cluster. We subsequently exhaustively as compared the representative patches and clustered them using similarity score, PatSim. Finally, the resultant PatSim scores were compared with similarities of atomic structures of the LBSs and those of the ligand‐binding protein sequences and functions. Consequently, we classified the patches into ～2000 well‐characterized clusters. We found that about 63% of these clusters are used in identical protein folds, although about 25% of the clusters are conserved in distantly related proteins and even in proteins with cross‐fold similarity. Furthermore, we showed that patches with higher PatSim score have potential to be involved in similar biological processes.