Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 A˚, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced "leopard skin"-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions, can capture processes that are otherwise obscured to the amino acid-based formalism.

Direct electrochemical formation of nanostructured amorphous Co(OH)2 on gold electrodes with enhanced activity for the oxygen evolution reaction.

The oxides of cobalt have recently been shown to be highly effective electrocatalysts for the oxygen evolution reaction (OER) under alkaline conditions. In general species such as Co3O4 and CoOOH have been investigated that often require an elevated temperature step during their synthesis to create crystalline materials. In this work we investigate the rapid and direct electrochemical formation of amorphous nanostructured Co(OH)2 on gold electrodes under room temperture conditions which is a highly active precursor for the OER. During the OER some conversion to crystalline Co3O4 occurs at the surface, but the bulk of the material remains amorphous. It is found that the underlying gold electrode is crucial to the materials enhanced performance and provides higher current density than can be achieved using carbon, palladium or copper support electrodes. This catalyst exhibits excellent activity with a current density of 10 mA cm-2 at an overpotential of 360 mV with a high turnover frequency of 2.1 s-1 in 1 M NaOH. A Tafel slope of 56 mV dec-1 at low overpotentials and a slope of 122 mV dec-1 at high overpotentials is consistent with the dual barrier model for the electrocatalytic evolution of oxygen. Significantly, the catalyst maintains excellent activity for up to 24 hr of continuous operation and this approach offers a facile way to create a highly effective and stable material.

Effects of HNO3 molecular doping in graphene/Si Schottky barrier solar cells

Schottky barrier solar cells based on graphene/n-silicon heterojunction have been fabricated and characterized and the effect of graphene molecular doping by HNO3 on the solar cells performances have been analyzed. Different doping conditions and thermal annealing processes have been tested to asses and optimize the stability of the devices. The PCE of the cells increases after the treatment by HNO3 and reaches 5% in devices treated at 200 °C immediately before the exposition to the oxidant. Up to now our devices retain about 80% of efficiency over a period of two weeks, which represents a good stability result for similar devices.

Combined effect of double antireflection coating and reversible molecular doping on performance of few-layer graphene/n-silicon Schottky barrier solar cells

Few-layer graphene films were grown by chemical vapor deposition and transferred onto n-type crystalline silicon wafers to fabricate graphene/n-silicon Schottky barrier solar cells. In order to increase the power conversion efficiency of such cells the graphene films were doped with nitric acid vapor and an antireflection treatment was implemented to reduce the sunlight reflection on the top of the device. The doping process increased the work function of the graphene film and had a beneficial effect on its conductivity. The deposition of a double antireflection coating led to an external quantum efficiency up to 90% across the visible and near infrared region, the highest ever reported for this type of devices. The combined effect of graphene doping and antireflection treatment allowed to reach a power conversion efficiency of 8.5% exceeding the pristine (undoped and uncoated) device performance by a factor of 4. The optical properties of the antireflection coating were found to be not affected by the exposure to nitric acid vapor and to remain stable over time.

Sustained release and osteogenic potential of heparan sulfate-doped fibrin glue scaffolds within a rat cranial model

This paper explores the potential therapeutic role of the naturally occurring sugar heparan sulfate (HS) for the augmentation of bone repair. Scaffolds comprising fibrin glue loaded with 5 lg of embryonically derived HS were assessed, firstly as a release-reservoir, and secondly as a scaffold to stimulate bone regeneration in a critical size rat cranial defect. We show HS-loaded scaffolds have a uniform distribution of HS, which was readily released with a typical burst phase, quickly followed by a prolonged delivery lasting several days. Importantly, the released HS contributed to improved wound healing over a 3-month period as determined by microcomputed tomography (lCT) scanning, histology, histomorphometry, and PCR for osteogenic markers. In all cases, only minimal healing was observed after 1 and 3 months in the absence of HS. In contrast, marked healing was observed by 3 months following HS treatment, with nearly full closure of the defect site. PCR analysis showed significant increases in the gene expression of the osteogenic markers Runx2, alkaline phosphatase, and osteopontin in the heparin sulfate group compared with controls. These results further emphasize the important role HS plays in augmenting wound healing, and its successful delivery in a hydrogel provides a novel alternative to autologous bone graft and growth factorbased therapies.

An integrated information management model for ecologically sustainable development

Ecologically sustainable development has become a major feature of legal systems at the international, national and local levels throughout the world. In Australia, governments have responded to environmental crises by enacting legislation imposing obligations and restrictions over privately-owned land. Whilst these obligations and restrictions may well be necessary to achieve sustainability, the approach to management of information concerning these instruments is problematic. For example, management of information concerning obligations and restrictions in Queensland is fragmented, with some instruments registered or recorded on the land title register, some on external registers, and some information only available in the legislation itself. This approach is used in most Australian jurisdictions. This fragmented approach has led to two separate but interconnected problems. First, the Torrens system is no longer meeting its goal of providing a complete and accurate picture of title. Second, this uncoordinated approach to the management of land titles, and obligations and restrictions on land use, has created a barrier to sustainable management of natural resources. This is because compliance with environmental laws is impaired in the absence of easily accessible and accurate information. These problems demonstrate a clear need for reform in this area. To determine how information concerning these obligations and restrictions may be most effectively managed, this thesis will apply a comparative methodology and consider three case studies, which each utilise different models for management of this information. These jurisdictions will be assessed according to a set of guidelines for comparison to identify which features of their systems provide for effective management of information concerning obligations and restrictions on title and use. Based on this comparison, this thesis will devise a series of recommendations for an effective system for the management of information concerning obligations and restrictions on land title and use, taking into account any potential legal issues and barriers to implementation. This series of recommendations for reform will be supplemented by suggested draft legislative provisions.

A Bayesian model predicts the response of axons to molecular gradients

Axon guidance by molecular gradients plays a crucial role in wiring up the nervous system. However, the mechanisms axons use to detect gradients are largely unknown. We first develop a Bayesian “ideal observer” analysis of gradient detection by axons, based on the hypothesis that a principal constraint on gradient detection is intrinsic receptor binding noise. Second, from this model, we derive an equation predicting how the degree of response of an axon to a gradient should vary with gradient steepness and absolute concentration. Third, we confirm this prediction quantitatively by performing the first systematic experimental analysis of how axonal response varies with both these quantities. These experiments demonstrate a degree of sensitivity much higher than previously reported for any chemotacting system. Together, these results reveal both the quantitative constraints that must be satisfied for effective axonal guidance and the computational principles that may be used by the underlying signal transduction pathways, and allow predictions for the degree of response of axons to gradients in a wide variety of in vivo and in vitro settings.

Time-dependent rates of molecular evolution

For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events.

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (<1–2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222–705 ka), Neandertals (108 ka; 70–156 ka), and modern humans (76 ka; 47–110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.

An androgen receptor mutation in the MDA-MB-453 cell line model of molecular apocrine breast cancer compromises receptor activity

Recent evidence indicates that the estrogen receptor-a-negative, androgen receptor (AR)- positive molecular apocrine subtype of breast cancer is driven by AR signaling. The MDA-MB-453 cell line is the prototypical model of this breast cancer subtype; its proliferation is stimulated by androgens such as 5a-dihydrotestosterone (DHT) but inhibited by the progestin medroxyprogesterone acetate (MPA) via AR-mediated mechanisms. We report here that the AR gene in MDAMB- 453 cells contains a G-T transversion in exon 7, resulting in a receptor variant with a glutamine to histidine substitution at amino acid 865 (Q865H) in the ligand binding domain. Compared with wild-type AR, the Q865H variant exhibited reduced sensitivity to DHT and MPA in transactivation assays in MDA-MB-453 and PC-3 cells but did not respond to non-androgenic ligands or receptor antagonists. Ligand binding, molecular modeling, mammalian two-hybrid and immunoblot assays revealed effects of the Q865H mutation on ligand dissociation, AR intramolecular interactions, and receptor stability. Microarray expression profiling demonstrated that DHT and MPA regulate distinct transcriptional programs in MDA-MB-453 cells. Gene Set Enrichment Analysis revealed that DHT- but not MPA-regulated genes were associated with estrogen-responsive transcriptomes from MCF-7 cells and the Wnt signaling pathway. These findings suggest that the divergent proliferative responses of MDA-MB-453 cells to DHT and MPA result from the different genetic programs elicited by these two ligands through the AR-Q865H variant. This work highlights the necessity to characterize additional models of molecular apocrine breast cancer to determine the precise role of AR signaling in this breast cancer subtype. Endocrine-Related Cancer (2012) 19 599–613

The poor penetration of topical burn agent through burn eschar on a porcine burn model [Letter to the Editor]

We read with great interest the article entitled “Enhancing drugs absorption through third-degree burn wound eschar” by Manafi et al. [1]. The authors addressed the concern of poor penetration of topically applied anti-microbials through burn eschar and detailed the improvement of this penetration by penetration enhancers. Here, we would like to report the poor penetration of a topical agent into the viable deep dermal layer under burn eschar on a porcine burn model [2]. In burn treatment, a common practice is the topical application of either anti-microbial products or wound enhancing agents. While the activity of anti-microbial products is designed to fight against microbes on the wound surface but with the least toxicity to viable tissue, wound enhancing agents need to reach the viable tissue layer under the burn eschar. Many studies have reported the accelerated healing of superficial burn wounds and skin graft donor sites by the topical application of exogeneous growth factors [3]. It is well known that the efficacy of the penetration of a topical agent on intact skin mostly depends on the molecular size of the product [4] and [5]. While burn injury destroys this epidermal physiological barrier, the coagulated burn tissue layer on the burn wound surface makes it difficult for topical agents to reach viable tissue....

Gas-phase reactions of aryl radicals with 2-butyne : an experimental and theoretical investigation employing the N-methyl-pyridinium-4-yl radical cation

Aromatic radicals form in a variety of reacting gas-phase systems, where their molecular weight growth reactions with unsaturated hydrocarbons are of considerable importance. We have investigated the ion-molecule reaction of the aromatic distonic N-methyl-pyridinium-4-yl (NMP) radical cation with 2-butyne (CH3C CCH3) using ion trap mass spectrometry. Comparison is made to high-level ab initio energy surfaces for the reaction of NMP and for the neutral phenyl radical system. The NMP radical cation reacts rapidly with 2-butyne at ambient temperature, due to the apparent absence of any barrier. The activated vinyl radical adduct predominantly dissociates via loss of a H atom, with lesser amounts of CH3 loss. High-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry allows us to identify small quantities of the collisionally deactivated reaction adduct. Statistical reaction rate theory calculations (master equation/RRKM theory) on the NMP + 2-butyne system support our experimental findings, and indicate a mechanism that predominantly involves an allylic resonance-stabilized radical formed via H atom shuttling between the aromatic ring and the C-4 side-chain, followed by cyclization and/or low-energy H atom beta-scission reactions. A similar mechanism is demonstrated for the neutral phenyl radical (Ph center dot)+2-butyne reaction, forming products that include 3-methylindene. The collisionally deactivated reaction adduct is predicted to be quenched in the form of a resonance-stabilized methylphenylallyl radical. Experiments using a 2,5-dichloro substituted methyl-pyridiniumyl radical cation revealed that in this case CH3 loss from the 2-butyne adduct is favoured over H atom loss, verifying the key role of ortho H atoms, and the shuttling mechanism, in the reactions of aromatic radicals with alkynes. As well as being useful phenyl radical analogues, pyridiniumyl radical cations may form in the ionosphere of Titan, where they could undergo rapid molecular weight growth reactions to yield polycyclic aromatic nitrogen hydrocarbons (PANHs).

Molecular sliding filament model for muscular contraction based on multiscale investigation

A multiscale approach that bridges the biophysics of the actin molecules at nanoscale and the biomechanics of actin filament at microscale level is developed and used to evaluate the mechanical performances of actin filament bundles. In order to investigate the contractile properties of skeletal muscle which is induced by the protein motor of myosin, a molecular model is proposed in the prediction of the dynamic behaviors of skeletal muscle based on classic sliding filament model. Randomly distributed myosin motors are applied on a 2.2 μm long sarcomere, whose principal components include actin and myosin filaments. It can be found that, the more myosin motors on the sarcomere, the faster the sarcomere contracts. The result demonstrates that the sarcomere shortening speed cannot increase infinitely by the modulation of myosin, thus providing insight into the self-protective properties of skeletal muscles. This molecular filament sliding model provides a theoretical way to evaluate the properties of skeletal muscles, and contributes to the understandings of the molecular mechanisms in the physiological phenomenon of muscular contraction.