Protein-protein docking predictions for the CAPRI experiment

We predicted structures for all seven targets in the CAPRI experiment using a new method in development at the time of the challenge. The technique includes a low-resolution rigid body Monte Carlo search followed by high-resolution refinement with side-chain conformational changes and rigid body minimization. Decoys (approximately 10(6) per target) were discriminated using a scoring function including van der Waals and solvation interactions, hydrogen bonding, residue-residue pair statistics, and rotamer probabilities. Decoys were ranked, clustered, manually inspected, and selected. The top ranked model for target 6 predicted the experimental structure to 1.5 A RMSD and included 48 of 65 correct residue-residue contacts. Target 7 was predicted at 5.3 A RMSD with 22 of 37 correct residue-residue contacts using a homology model from a known complex structure. Using a preliminary version of the protocol in round 1, target 1 was predicted within 8.8 A although few contacts were correct. For targets 2 and 3, the interface locations and a small fraction of the contacts were correctly identified.     

Functional verification of pulse frequency modulation-based image sensor for retinal prosthesis by in vitro electrophysiological experiments using frog retina

The functioning of a 16 x 16 pixel pulse frequency modulation (PFM) image sensor for retinal prosthesis is verified through in vitro electrophysiological experiments using detached frog retinas. This image sensor is a prototype for demonstrating the application to in vitro electrophysiological experiments. Each pixel of the image sensor consists of a pulse generator (PFM photosensor), a stimulus circuit, and a stimulus electrode (Al bonding pad). The image sensor is fabricated using standard 0.6 microm CMOS technology. For in vitro electrophysiological experiments, a Pt/Au stacked electrode is formed on the Al bonding pad of each pixel and the entire sensor is fixed in epoxy resin. The PFM image sensor is confirmed experimentally to provide electrical stimulus to the retinal cells in a detached frog retina.     

A CMOS Image Sensor Integrated with Plasmonic Colour Filters

Multi-pixel, 4.5?×?9???m, plasmonic colour filters, consisting of periodic subwavelength holes in an aluminium film, were directly integrated on the top surface of a complementary metal oxide semiconductor (CMOS) image sensor (CIS) using electron beam lithography and dry etch. The 100?×?100-pixel plasmonic CIS showed full colour sensitivities across the visible range determined by a photocurrent measurement. The filters were fabricated in a simple process utilising a single lithography step. This is to be compared with the traditional multi-step processing when using dye-doped polymers. The intrinsic compatibility of these plasmonic components with a standard CMOS process allows them to be manufactured in a metal layer close to the photodiodes. The incorporation of such plasmonic components may in the future enable the development of advanced CIS with low cost, low cross-talk and increased functionality.     

Overcoming Electrode‐Induced Losses in Organic Solar Cells by Tailoring a Quasi‐Ohmic Contact to Fullerenes via Solution‐Processed Alkali Hydroxide Layers

It is shown that the performance of inverted organic solar cells can be significantly improved by facilitating the formation of a quasi‐ohmic contact via solution‐processed alkali hydroxide (AOH) interlayers on top of n‐type metal oxide (aluminum zinc oxide, AZO, and zinc oxide, ZnO) layers. AOHs significantly reduce the work function of metal oxides, and are further proven to effectively passivate defect states in these metal oxides. The interfacial energetics of these electron collecting contacts with a prototypical electron acceptor (C₆₀) are investigated to reveal the presence of a large interface dipole and a new interface state between the Fermi energy and the C₆₀ highest occupied molecular orbital for AOH‐modified AZO contacts. These novel interfacial gap states are a result of ground‐state electron transfer from the metal hydroxide‐functionalized AZO contact to the adsorbed molecules, which are hypothesized to be electronically hybridized with the contact. These interface states tail all the way to the Fermi energy, providing for a highly n‐doped (metal‐like) interfacial molecular layer. Furthermore, the strong “light‐soaking” effect is no longer observed in devices with a AOH interface.     

Long term recovery of median nerve repair using laser‐activated chitosan adhesive films

Sutures remain the standard peripheral nerve repair technique, whether applied directly or indirectly to nerve tissue. Unfortunately, significant postoperative complications can result, such as inflammation, neuroma formation and foreign body reactions. Photochemical‐tissue‐bonding (PTB) using rose Bengal (RB) integrated into a chitosan bioadhesive is an alternative nerve repair device that removes the need for sutures. Rats were arranged into three groups: RB‐chitosan adhesives‐repair, end‐to‐end epineural suture‐repair (surgical standard) and sham laser‐irradiated control. Groups were compared through histological assessment, electrophysiological recordings and grip motor strength. RB‐chitosan adhesive repaired nerves displayed comparable results when compared to the standard suture‐repair based on histological and electrophysiological findings. Functionally, RB‐chitosan adhesive was associated with a quicker and more pronounced recovery of grip force when compared to the suture‐repair. (© 2013 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

Water-mediated contacts in the trp-repressor operator complex recognition process

Water-mediated contacts are known as an important recognition tool in trp-repressor operator systems. One of these contacts involves two conserved base pairs (G(6).C(-6) and A(5). T(-5)) and three amino acids (Lys 72, Ile 79, and Ala 80). To investigate the nature of these contacts, we analyzed the X-ray structure (PDB code: 1TRO) of the trp-repressor operator complex by means of molecular dynamics simulations. This X-ray structure contains two dimers that exhibit structural differences. From these two different starting structures, two 10 ns molecular dynamics simulations have been performed. Both of our simulations show an increase of water molecules in the major groove at one side of the dimer, while the other side remains unchanged compared to the X-ray structure. Though the maximum residence time of the concerned water molecules decreases with an increase of solvent at the interface, these water molecules continue to play an important role in mediating DNA-protein contacts. This is shown by new stable amino acids-DNA distances and a long water residence time compared to free DNA simulation. To maintain stability of the new contacts, the preferential water binding site on O6(G6) is extended. This extension agrees with mutation experiment data on A5 and G6, which shows different relative affinity due to mutation on these bases [A. Joachimiak, T. E. Haran, P. B. Sigler, EMBO Journal 1994, Vol. 13, No. (2) pp. 367-372]. Due to the rearrangements in the system, the phosphate of the base G6 is able to interconvert to the B(II) substate, which is not observed on the other half side of the complex. The decrease of the number of hydrogen bonds between protein and DNA backbone could be the initial step of the dissociation process of the complex, or in other words an intermediate complex conformation of the association process. Thus, we surmise that these features show the importance of water-mediated contacts in the trp-repressor operator recognition process.     

“Top‐Down” Li Deposition Pathway Enabled by an Asymmetric Design for Li Composite Electrode

Designing Li composite electrodes with host frameworks for accommodating Li metal has been considered to be an effective approach to suppress Li dendrites. Herein, an asymmetric design of a Mo net/Li metal film (MLF) composite electrode is developed by an inverted thermal infusion method. The asymmetric MLF electrode has a dense oxide passivated layer on the top side, a porous Mo net matrix on the back side, and active Li layer in between. The back side has a larger specific area and higher electric field than the top side, which contacts with the separator upon cycling, triggering the preferred Li deposition and stripping of the porous back side of the electrode far from the separator. The surface passivation layer on the top side of the electrode as an artificial solid electrolyte interphase ensures the stable contact with the electrolyte and separator. Meanwhile, the porous structure of the supporting Mo net provides enough space for accommodating the volume change during Li deposition and stripping. This asymmetry design enables a unique “top down” growth pathway for Li deposition in the MLF electrode, suppressing the dendrite growth effectively. The design strategy provides a new direction for high‐energy dendrite‐free Li metal anodes.     

Synthesis, characterization and biocidal activity of some transition metal(II) complexes with isatin salicylaldehyde acyldihydrazones

Cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes with two new unsymmetrical ligands, isatin salicylaldehyde oxalic acid dihydrazide (isodh) and isatin salicylaldehyde malonic acid dihydrazide (ismdh) were synthesized and characterized by elemental analyses, electrical conductance, magnetic moments, electronic, NMR, ESR and IR spectral studies. The isodh acts as a dibasic tetra dentate ligand bonding through two >C=N-, a deprotonated phenolate and deprotonated indole enolate groups to the metal. The ismdh ligand shows monobasic tetra dentate behaviour in bonding with metal ion through two >C=N-, indole >C=O and a deprotonated phenolate group. The electronic spectral data suggest 4-coordinate square planar geometry for Co(II), Ni(II) and Cu(II) complexes of isodh, whereas, 6-coordinate octahedral structure for the ismdh complexes. The ESR studies also indicate a square planar and distorted octahedral environment around Cu(II) for isodh and ismdh complexes, respectively. Most of the metal complexes show better antifungal activity than the standard and a significant antibacterial activity against various fungi and bacteria.     

First-principle study of interfacial properties between γ-TiAl and TiC,VN

The adhesion, wettability, atomic bonding and electronic structure of γ-TiAl(110)/TiC(100) and γ-TiAl(110)/VN(100) interfaces were performed and investigated using first-principle calculations. Surface energy of γ-TiAl, TiC and VN with low crystal indices was calculated and compared, respectively. The three Al-terminated γ-TiAl(110)/ceramic(100) interface models were investigated to illustrate the interfacial bonding nature. The structure of Al atom placed on the top of the metalloid C and N atoms at the interface is the preferred interfacial structure with the larger work of adhesion. The electronic structure results show that the structure with metalloid site exists with the stronger polar covalent bonding between the interfacial Al and metalloid atom. The interfacial structure with metal site exhibits a mixture of the metallic features with some degree of covalent features. The simulation results are in agreement with the experimental results, in which the γ-TiAl/TiC interface exhibits the better wettability and stronger bonding than the γ-TiAl/VN interface.     

A model for the sickle hemoglobin fiber using both mutation sites

The standard molecular model of the fiber of the sickle hemoglobin (HbS: beta6 Glu-->Val) has been revised to allow both beta6 mutation sites to participate in intermolecular contacts, rather than only one beta6 site as previously thought, for four molecules per 14-molecule fiber cross section. This structure accurately predicts the copolymerization of hybridized mixtures of HbS with HbA or HbC (beta6 Glu-->Lys), which could not be reconciled with prior models in which only half the beta6 sites were required for assembly. This model suggests new contacts within the fiber and raises the question of whether these cross-linked double strands could possess added stability important in such processes as nucleation.     

Regeneration of adhesive tail pad scales in the New Zealand gecko (Hoplodactylus maculatus) (Reptilia;Squamata;Lacertilia) can serve as an experimental model to analyze setal formation in lizards generally

During the regeneration of the tail in the arboreal New Zealand gecko (Hoplodactylus maculatus) a new set of tail scales,modified into pads bearing setae 5-20 μm long,is also regenerated.Stages of the formation of these specialized scales from epidermal pegs that invaginate the dermis of the regenerating tail are described on the basis of light and electron microscopic images.Within the pegs a differentiating clear layer interfaces with the spinulae and setae of the Oberh(a)utchen according to a process similar to that described for the digital pads.A layer of clear cytoplasm surrounds the growing tiny setae and eventually comifies around them and their spatular ends,later leaving the new setae free-standing on the epidermal surface.The fresh adhesive pads help the gecko to maintain the prehensile function of its regenerated tail as together with the axial skeleton (made of a cylinder of elastic cartilage) the pads allow the regenerated tail to curl aroundtwigs and small branches just like the original tail.The regeneration of caudal adhesive pads represents an ideal system to study the cellular processes that determine setal formation under normal or experimental manipulation as the progressive phases of the formation of the setae can be sequentially analyzed.     

Neuroligins mediate excitatory and inhibitory synapse formation: involvement of PSD-95 and neurexin-1beta in neuroligin-induced synaptic specificity

The balance between excitatory and inhibitory synapses is a tightly regulated process that requires differential recruitment of proteins that dictate the specificity of newly formed contacts. However, factors that control this process remain unidentified. Here we show that members of the neuroligin (NLG) family, including NLG1, NLG2, and NLG3, drive the formation of both excitatory and inhibitory presynaptic contacts. The enrichment of endogenous NLG1 at excitatory contacts and NLG2 at inhibitory synapses supports an important in vivo role for these proteins in the development of both types of contacts. Immunocytochemical and electrophysiological analysis showed that the effects on excitatory and inhibitory synapses can be blocked by treatment with a fusion protein containing the extracellular domain of neurexin-1beta. We also found that overexpression of PSD-95, a postsynaptic binding partner of NLGs, resulted in a shift in the distribution of NLG2 from inhibitory to excitatory synapses. These findings reveal a critical role for NLGs and their synaptic partners in controlling the number of inhibitory and excitatory synapses. Furthermore, relative levels of PSD-95 alter the ratio of excitatory to inhibitory synaptic contacts by sequestering members of the NLG family to excitatory synapses.     

Friction ridges in cockroach climbing pads: anisotropy of shear stress measured on transparent,microstructured substrates

The contact of adhesive structures to rough surfaces has been difficult to investigate as rough surfaces are usually irregular and opaque. Here we use transparent, microstructured surfaces to investigate the performance of tarsal euplantulae in cockroaches (Nauphoeta cinerea). These pads are mainly used for generating pushing forces away from the body. Despite this biological function, shear stress (force per unit area) measurements in immobilized pads showed no significant difference between pushing and pulling on smooth surfaces and on 1-μm high microstructured substrates, where pads made full contact. In contrast, on 4-μm high microstructured substrates, where pads made contact only to the top of the microstructures, shear stress was maximal during a push. This specific direction dependence is explained by the interlocking of the microstructures with nanometre-sized “friction ridges” on the euplantulae. Scanning electron microscopy and atomic force microscopy revealed that these ridges are anisotropic, with steep slopes facing distally and shallow slopes proximally. The absence of a significant direction dependence on smooth and 1-μm high microstructured surfaces suggests the effect of interlocking is masked by the stronger influence of adhesion on friction, which acts equally in both directions. Our findings show that cockroach euplantulae generate friction using both interlocking and adhesion.     

Tactile hairs and leg reflexes in wandering spiders: physiological and anatomical correlates of reflex activity in the leg ganglia

Intracellular recordings and Lucifer-yellow fillings were used in a wandering spider,Cupiennius salei Keys., to identify central neuronal correlates of local reflex activity in muscle c2, which inserts on the leg coxa. Here we describe related neuronal elements in the hindleg neuromere of the fused, subesophageal-ganglion complex:

Factors influencing the potential mobility and bioavailability of metals in dried lake sediments

Abstract

Samples taken from polluted creek sediments were dried at temperatures between 20°C and 100°C (either in air or under a nitrogen atmosphere) and selective chemical extraction procedures were then used to examine the effect of drying temperature and oxidation on the bonding mode distribution patterns of Zn, Pb, Cd and Cu. Exposure to air during the drying stage tended to increase the fraction of total metal which was less firmly bound (i.e. ion exchangeable, weakly sorbed). Less metal was present in these categories when higher drying temperatures were used, and temperature changes had a larger effect when the samples were dried under nitrogen. The drying process appears to promote metal migration to phases having a stronger bonding power. In most of the samples studied, heating caused Pb to migrate to the carbonate phase while accumulation in the organic/sulfide phases was the dominant process for Cu and Cd. In the case of Zn, migration to the carbonate phase was favoured in some studies (e.g. using air-dried samples), in other sediments the migration end-point was the organic/sulfide phases. During storage of dried samples at room temperature for prolonged periods (e.g. months) the amount of less firmly bound metal tended to increase, and nullified the distribution changes induced by drying. The effect was most pronounced in the case of Cd. The study highlights that significant errors in metal distribution pattern analyses can arise from sample preparation procedures and it has provided information on the possible mobilisation of metal when dredged sediment is land-dumped, i.e. allowed to dry in air.     

Microsystem for transfection of exogenous molecules with spatio-temporal control into adherent cells

Several non-viral techniques involving the use of liposomes, particle bombardment and electroporation have been used for efficient transfection of plasmids and other molecules into cells. Current approaches target whole or bulk regions of tissue, lacking the desired spatial control over the transfection process. In this study, we present a novel approach using microsystems to achieve spatial and temporal control over the transfection process in adherent cells. A 6x6 MEA (microelectrode array) with 100 microm microelectrode dimension was developed on a silicon substrate using standard microfabrication procedures and passivated with a biocompatible layer. Using finite element models, electric field intensities were simulated and locations of optimal electroporation zones in the cell culture on the microelectrode surface were predicted. The MEA was subsequently tested using 3T3 fibroblasts cultured on the MEA surface for 96 h and stimulation voltages in the range of 2-5 V in the presence of propidium iodide (PI), a cell impermeant dye. Maximum electric field intensities in the z-direction were estimated to be in the range of 320-820 V/cm for applied differential voltages in the range of 2-5 V. Cells directly on the top and on the edges of the stimulating microelectrodes in the MEA were preferentially transfected with PI as predicted by the simulations. The results of these experiments demonstrate that spatial and temporal control of desired regions of transfection in vitro can be achieved using MEAs and electroporation.     

Structural constraints on the covariance matrix derived from multiple aligned protein sequences

Residue contact predictions were calculated based on the mutual information observed between pairs of positions in large multiple protein sequence alignments. Where previously only the statistical properties of these data have been considered important, we introduce new measures to impose constraints that make the contact map more consistent with a three dimensional structure. These included global (bulk) properties and local secondary structure properties. The latter allowed the contact constraints to be employed at the level of filtering pairs of secondary structure contacts which led to a more efficient (lower-level) implementation in the PLATO structure prediction server. Where previously the measure of success with this method had been whether the correct fold was predicted in the top 10 ranked models, with the current implementation, our summary statistic is the number of correct folds included in the top 10 models--which is on average over 50 percent.     

A theoretical study on the halogen bonding interactions of C6F5I with a series of group 10 metal monohalides

The halogen bonding interactions between C₆F₅I and a series of transition metal monohalides trans-[M(X)(2-C₅NF₄)-(PR₃)₂] (M = Ni, Pd, Pt; X = F, Cl, Br; R = Me, Cy) have been studied with quantum chemical calculations. Optimized geometries of the halogen bonding complexes indicate that angles C₁-I···X are basically linear (178–180°) and angles I···X-M mainly range from 90 to 150°. The strength of these metal-influenced halogen bonds alters with different metal centers, metal-bound halogen atoms and the substitutes on phosphine ligands. Electrostatic potential and natural bond orbital analysis show that both of the electrostatic and orbital interactions make a contribution to the formation of halogen bonds, while the electrostatic term plays a dominant role. AIM analysis suggests that, for trans-[M(F)(2-C₅NF₄)-(PR₃)₂] (M = Ni, Pd, Pt) monomers, the formed halogen bonding complexes are stabilized by local concentration of the charge of intermediate character, while for the metal monomers containing chlorine and bromine, a typical closed-shell interaction exist. These results prove that the structures and geometries of these halogen bonding complexes can be tuned by changing the halogen atoms and metal centers, which may provide useful information for the design and synthesis of new functional materials.

Assessing methods for identifying pair-wise atomic contacts across binding interfaces

An essential step in understanding the molecular basis of protein-protein interactions is the accurate identification of inter-protein contacts. We evaluate a number of common methods used in analyzing protein-protein interfaces: a Voronoi polyhedra-based approach, changes in solvent accessible surface area (DeltaSASA) and various radial cutoffs (closest atom, Cbeta, and centroid). First, we compared the Voronoi polyhedra-based analysis to the DeltaSASA and show that using Voronoi polyhedra finds knob-in-hole contacts. To assess the accuracy between the Voronoi polyhedra-based approach and the various radial cutoff methods, two sets of data were used: a small set of 75 experimental mutants and a larger one of 592 structures of protein-protein interfaces. In an assessment using the small set, the Voronoi polyhedra-based methods, a solvent accessible surface area method, and the closest atom radial method identified 100% of the direct contacts defined by mutagenesis data, but only the Voronoi polyhedra-based method found no false positives. The other radial methods were not able to find all of the direct contacts even using a cutoff of 9A. With the larger set of structures, we compared the overall number contacts using the Voronoi polyhedra-based method as a standard. All the radial methods using a 6-A cutoff identified more interactions, but these putative contacts included many false positives as well as missed many false negatives. While radial cutoffs are quicker to calculate as well as to implement, this result highlights why radial cutoff methods do not have the proper resolution to detail the non-homogeneous packing within protein interfaces, and suggests an inappropriate bias in pair-wise contact potentials. Of the radial cutoff methods, using the closest atom approach exhibits the best approximation to the more intensive Voronoi calculation. Our version of the Voronoi polyhedra-based method QContacts is available at .     

Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions

ATP is an important substrate of numerous biochemical reactions in living cells. Molecular recognition of this ligand by proteins is very important for understanding enzymatic mechanisms. Considerable insight into the problem may be gained via molecular docking simulations. At the same time, standard docking protocols are often insufficient to predict correct conformations for protein-ATP complexes. Thus, in most cases the native-like solutions can be found among the docking poses, but current scoring functions have only limited ability to discriminate them from false positives. To improve the selection of correct docking solutions obtained with the GOLD software, we developed a new ranking criterion specific for ATP-protein binding. The method is based on detailed analysis of the intermolecular interactions in 40 high-resolution 3D structures of ATP-protein complexes (the training set). We found that the most important factors governing this recognition are hydrogen-bonding, stacking between adenine and aromatic protein residues, and hydrophobic contacts between adenine and protein residues. To address the latter, we applied the formalism of 3D molecular hydrophobicity potential. The results obtained were used to construct an ATP-oriented scoring criterion as a linear combination of the terms describing these intermolecular interactions. The criterion was then validated using the test set of 10 additional ATP-protein complexes. As compared with the standard scoring functions, the new ranking criterion significantly improved the selection of correct docking solutions in both sets and allowed considerable enrichment at the top of the list containing docking poses with correct solutions.