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.

Models of protein linear molecular motors for dynamic nanodevices

Protein molecular motors are natural nano-machines that convert the chemical energy from the hydrolysis of adenosine triphosphate into mechanical work. These efficient machines are central to many biological processes, including cellular motion, muscle contraction and cell division. The remarkable energetic efficiency of the protein molecular motors coupled with their nano-scale has prompted an increasing number of studies focusing on their integration in hybrid micro- and nanodevices, in particular using linear molecular motors. The translation of these tentative devices into technologically and economically feasible ones requires an engineering, design-orientated approach based on a structured formalism, preferably mathematical. This contribution reviews the present state of the art in the modelling of protein linear molecular motors, as relevant to the future design-orientated development of hybrid dynamic nanodevices. © 2009 The Royal Society of Chemistry.

Protein Molecular Surface Mapped at Different Geometrical Resolutions

Many areas of biochemistry and molecular biology, both fundamental and applications-orientated, require an accurate construction, representation and understanding of the protein molecular surface and its interaction with other, usually small, molecules. There are however many situations when the protein molecular surface gets in physical contact with larger objects, either biological, such as membranes, or artificial, such as nanoparticles. The contribution presents a methodology for describing and quantifying the molecular properties of proteins, by geometrical and physico-chemical mapping of the molecular surfaces, with several analytical relationships being proposed for molecular surface properties. The relevance of the molecular surface-derived properties has been demonstrated through the calculation of the statistical strength of the prediction of protein adsorption. It is expected that the extension of this methodology to other phenomena involving proteins near solid surfaces, in particular the protein interaction with nanoparticles, will result in important benefits in the understanding and design of protein-specific solid surfaces. © 2013 Nicolau et al.

Assessment of the molecular structure of an intermediate member of the triplite-zwieselite mineral series: A raman and infrared study

The mineral series triplite-zwieselite with theoretical formula (Mn2+)2(PO4)(F)-(Fe2+)2(PO4)(F) from the El Criolo granitic pegmatite, located in the Eastern Pampean Ranges of Córdoba Province, was studied using electron microprobe, thermogravimetry, and Raman and infrared spectroscopy. The analysis of the mineral provided a formula of (Fe1.00, Mn0.85, Ca0.08, Mg0.06)∑2.00(PO4)1.00(F0.80, OH0.20)∑1.00. An intense Raman band at 981 cm−1 with a shoulder at 977 cm−1 is assigned to the ν1 symmetric stretching mode. The observation of two bands for the phosphate symmetric stretching mode offers support for the concept that the phosphate units in the structure of triplite-zwieselite are not equivalent. Low-intensity Raman bands at 1012, 1036, 1071, 1087, and 1127 cm−1 are assigned to the ν3 antisymmetric stretching modes. A set of Raman bands at 572, 604, 639, and 684 cm−1 are attributed to the ν4 out-of-plane bending modes. A single intense Raman band is found at 3508 cm−1 and is assigned to the stretching vibration of hydroxyl units. Infrared bands are observed at 3018, 3125, and 3358 cm−1 and are attributed to water stretching vibrations. Supplemental materials are available for this article. Go to the publisher's online edition of Spectroscopy Letters to view the supplemental file.

The Long and Short of It: Branch Lengths and the Problem of Placing the New Zealand Short-Tailed Bat, Mystacina

The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and superfamilies. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (=Phyllostomoidea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffenbach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mystacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoidea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous-Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctilionoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.

Soluble NSF attachment protein receptor molecular mimicry by a Legionella pneumophila Dot/Icm effector

Upon infection, Legionella pneumophila uses the Dot/Icm type IV secretion system to translocate effector proteins from the Legionella-containing vacuole (LCV) into the host cell cytoplasm. The effectors target a wide array of host cellular processes that aid LCV biogenesis, including the manipulation of membrane trafficking. In this study, we used a hidden Markov model screen to identify two novel, non-eukaryotic soluble NSF attachment protein receptor (SNARE) homologs: the bacterial Legionella SNARE effector A (LseA) and viral SNARE homolog A proteins. We characterized LseA as a Dot/Icm effector of L. pneumophila, which has close homology to the Qc-SNARE subfamily. The lseA gene was present in multiple sequenced L. pneumophila strains including Corby and was well distributed among L. pneumophila clinical and environmental isolates. Employing a variety of biochemical, cell biological and microbiological techniques, we found that farnesylated LseA localized to membranes associated with the Golgi complex in mammalian cells and LseA interacted with a subset of Qa-, Qb- and R-SNAREs in host cells. Our results suggested that LseA acts as a SNARE protein and has the potential to regulate or mediate membrane fusion events in Golgi-associated pathways.

Identification of the sources of primary organic aerosols at urban schools : a molecular marker approach

Children are particularly susceptible to air pollution and schools are examples of urban microenvironments that can account for a large portion of children’s exposure to airborne particles. Thus this paper aimed to determine the sources of primary airborne particles that children are exposed to at school by analyzing selected organic molecular markers at 11 urban schools in Brisbane, Australia. Positive matrix factorization analysis identified four sources at the schools: vehicle emissions, biomass burning, meat cooking and plant wax emissions accounting for 45%, 29%, 16% and 7%, of the organic carbon respectively. Biomass burning peaked in winter due to prescribed burning of bushland around Brisbane. Overall, the results indicated that both local (traffic) and regional (biomass burning) sources of primary organic aerosols influence the levels of ambient particles that children are exposed at the schools. These results have implications for potential control strategies for mitigating exposure at schools.

Accounting for management costs in sensitivity analyses of matrix population models

Traditional sensitivity and elasticity analyses of matrix population models have been used to inform management decisions, but they ignore the economic costs of manipulating vital rates. For example, the growth rate of a population is often most sensitive to changes in adult survival rate, but this does not mean that increasing that rate is the best option for managing the population because it may be much more expensive than other options. To explore how managers should optimize their manipulation of vital rates, we incorporated the cost of changing those rates into matrix population models. We derived analytic expressions for locations in parameter space where managers should shift between management of fecundity and survival, for the balance between fecundity and survival management at those boundaries, and for the allocation of management resources to sustain that optimal balance. For simple matrices, the optimal budget allocation can often be expressed as simple functions of vital rates and the relative costs of changing them. We applied our method to management of the Helmeted Honeyeater (Lichenostomus melanops cassidix; an endangered Australian bird) and the koala (Phascolarctos cinereus) as examples. Our method showed that cost-efficient management of the Helmeted Honeyeater should focus on increasing fecundity via nest protection, whereas optimal koala management should focus on manipulating both fecundity and survival simultaneously. These findings are contrary to the cost-negligent recommendations of elasticity analysis, which would suggest focusing on managing survival in both cases. A further investigation of Helmeted Honeyeater management options, based on an individual-based model incorporating density dependence, spatial structure, and environmental stochasticity, confirmed that fecundity management was the most cost-effective strategy. Our results demonstrate that decisions that ignore economic factors will reduce management efficiency. ©2006 Society for Conservation Biology.

Biomechanical analyses of the performance of Paralympians: From foundation to elite level

Biomechanical analysis of sport performance provides an objective method of determining performance of a particular sporting technique. In particular, it aims to add to the understanding of the mechanisms influencing performance, characterization of athletes, and provide insights into injury predisposition. Whilst the performance in sport of able-bodied athletes is well recognised in the literature, less information and understanding is known on the complexity, constraints and demands placed on the body of an individual with a disability. This paper provides a dialogue that outlines scientific issues of performance analysis of multi-level athletes with a disability, including Paralympians. Four integrated themes are explored the first of which focuses on how biomechanics can contribute to the understanding of sport performance in athletes with a disability and how it may be used as an evidence-based tool. This latter point questions the potential for a possible cultural shift led by emergence of user-friendly instruments. The second theme briefly discusses the role of reliability of sport performance and addresses the debate of two-dimensional and three-dimensional analysis. The third theme address key biomechanical parameters and provides guidance to clinicians, and coaches on the approaches adopted using biomechanical/sport performance analysis for an athlete with a disability starting out, to the emerging and elite Paralympian. For completeness of this discourse, the final theme is based on the controversial issues on the role of assisted devices and the inclusion of Paralympians into able-bodied sport is also presented. All combined, this dialogue highlights the intricate relationship between biomechanics and training of individuals with a disability. Furthermore, it illustrates the complexity of modern training of athletes which can only lead to a better appreciation of the performances to be delivered in the London 2012 Paralympic Games

Raman and infrared spectroscopic studies of phurcalite from Red Canyon, Utah, USA – Implications for the molecular structure

Raman and infrared spectra of the uranyl mineral phurcalite, Ca2(UO2)3O2(PO4)2⋅7H2O, from Red Canyon, Utah, USA, were studied and tentatively interpreted. Observed bands were assigned to the stretching and bending vibrations of (UO2)2+ and (PO4)3− units and to the stretching and bending vibrations and libration modes of water molecules. Approximate lengths of U–O in (UO2)2+ and O–H⋯O hydrogen bond lengths were inferred from observed stretching vibrations. The presence of structurally nonequivalent U6+ and P5+ was inferred from the number of corresponding stretching bands of (UO2)2+ and (PO4)3− units observed in the Raman and infrared spectra..

Choose wisely: Network, ontology and annotation resources for the analysis of Staphylococcus aureus omics data

Staphylococcus aureus (S. aureus) is a prominent human and livestock pathogen investigated widely using omic technologies. Critically, due to availability, low visibility or scattered resources, robust network and statistical contextualisation of the resulting data is generally under-represented. Here, we present novel meta-analyses of freely-accessible molecular network and gene ontology annotation information resources for S. aureus omics data interpretation. Furthermore, through the application of the gene ontology annotation resources we demonstrate their value and ability (or lack-there-of) to summarise and statistically interpret the emergent properties of gene expression and protein abundance changes using publically available data. This analysis provides simple metrics for network selection and demonstrates the availability and impact that gene ontology annotation selection can have on the contextualisation of bacterial omics data.

A vibrational spectroscopic study of the borate mineral ezcurrite Na4B10O17·7H2O – Implications for the molecular structure

We have studied the boron containing mineral ezcurrite Na4B10O17·7H2O using electron microscopy and vibrational spectroscopy. Both tetrahedral and trigonal boron units are observed. The nominal resolution of the Raman spectrometer is of the order of 2 cm−1 and as such is sufficient enough to identify separate bands for the stretching bands of the two boron isotopes. The Raman band at 1037 cm−1 is assigned to BO stretching vibration. Raman bands at 1129, 1163, 1193 cm−1 are attributed to BO stretching vibration of the tetrahedral units. The Raman band at 947 cm−1 is attributed to the antisymmetric stretching modes of tetrahedral boron. The sharp Raman peak at 1037 cm−1 is from the 11-B component such a mode, then it should have a smaller 10-B satellite near (1.03) × (1037) = 1048 cm−1, and indeed a small peak at 1048 is observed. The broad Raman bands at 3186, 3329, 3431, 3509, 3547 and 3576 cm−1 are assigned to water stretching vibrations. Broad infrared bands at 3170, 3322, 3419, 3450, 3493, 3542, 3577 and 3597 cm−1 are also assigned to water stretching vibrations. Infrared bands at 1330, 1352, 1389, 1407, 1421 and 1457 cm−1 are assigned to the antisymmetric stretching vibrations of trigonal boron. The observation of so many bands suggests that there is considerable variation in the structure of ezcurrite. Infrared bands at 1634, 1646 and 1681 cm−1 are assigned to water bending modes. The number of water bending modes is in harmony with the number of water stretching vibrations.

Vibrational spectroscopic characterization of the arsenate mineral barahonaite: Implications for the molecular structure

The mineral barahonaite is in all probability a member of the smolianinovite group. The mineral is an arsenate mineral formed as a secondary mineral in the oxidized zone of sulphide deposits. We have studied the barahonaite mineral using a combination of Raman and infrared spectroscopy. The mineral is characterized by a series of Raman bands at 863 cm−1 with low wavenumber shoulders at 802 and 828 cm−1. These bands are assigned to the arsenate and hydrogen arsenate stretching vibrations. The infrared spectrum shows a broad spectral profile. Two Raman bands at 506 and 529 cm−1 are assigned to the triply degenerate arsenate bending vibration (F 2, ν4), and the Raman bands at 325, 360, and 399 cm−1 are attributed to the arsenate ν2 bending vibration. Raman and infrared bands in the 2500–3800 cm−1 spectral range are assigned to water and hydroxyl stretching vibrations. The application of Raman spectroscopy to study the structure of barahonaite is better than infrared spectroscopy, probably because of the much higher spatial resolution.