Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure

Relationship between air pollution and metal levels in cancerous and non-cancerous lung tissues

We aimed to check the relationships between levels of metals (Ca, Cd, Cu, Fe, Hg and Zn) in cancerous and non-cancerous lung tissues and their link to air pollution, expressed as particulate matter (PM) concentrations. The study also examines the influence on metal concentration in the lung tissue of patients' sex and the distance of their homes from the nearest emitter. We found that the general pattern of ascending concentrations in tumor tissue was as follows: Hg < Cd < Cu < Ca < Zn < Fe. In non-affected lung tissue the order of concentrations of Ca and Fe was reversed. With the exception of Cd and Cu, levels of metals were found in higher accumulations in non-cancerous tissue (e.g., Fe 326.423 and Ca 302.730 μg/g d.w) than in tumorous tissue (Fe 150.735 and Ca 15.025 μg/g d.w). Neither the PM10 (PM of a diameter of 10 μm) concentration nor sex revealed any connection with metal concentrations. The shorter the distance from the emitter, the higher the metal concentrations that tended to be observed for almost all metals, but a statistically significant (but weak) relationship was noted only for Cu in tumor tissue (rs: -0.4869)

Tropospheric distribution of sulphate aerosols mass and number concentration during INDOEX-IFP and its transport over the Indian Ocean: A GCM study

International audienceThe sulphate aerosols mass and number concentration during the Indian Ocean Experiment (INDOEX) Intensive Field Phase-1999 (INDOEX-IFP) has been simulated using an interactive chemistry GCM. The model considers an interactive scheme for feedback from chemistry to meteorology with internally resolving microphysical properties of aerosols. In particular, the interactive scheme has the ability to predict both particle mass and number concentration for the Aitken and accumulation modes as prognostic variables. On the basis of size distribution retrieved from the observations made along the cruise route during IFP-1999, the model successfully simulates the order of magnitude of aerosol number concentration. The results show the southward migration of minimum concentrations, which follows ITCZ (Inter Tropical Convergence Zone) migration. Sulphate surface concentration during INDOEX-IFP at Kaashidhoo (73.46° E, 4.96° N) gives an agreement within a factor of 2 to 3. The measured aerosol optical depth (AOD) from all aerosol species at KCO was 0.37 ± 0.11 while the model simulated sulphate AOD ranged from 0.05 to 0.11. As sulphate constitutes 29% of the observed AOD, the model predicted values of sulphate AOD are hence fairly close to the measured values. The model thus has capability to predict the vertically integrated column sulphate burden. Furthermore, the model results indicate that Indian contribution to the estimated sulphate burden over India is more than 60% with values upto 40% over the Arabian Sea. © 2012 Author(s)

DESIGN FOR MANUFACTURE OF SUPERCONDUCTING HALF WAVE CAVITIES *

Abstract 322 MHz medium velocity half wave resonators (HWR) with β = 0.29 and 0.53 have been designed at the Facility for Rare Isotope Beams (FRIB) at Michigan State University (MSU) for use in a heavy ion linac. The β = 0.29 and β = 0.53 are to provide 1.9M V and 3.7M V of accelerating voltage with a peak magnetic field of 54mT and 77mT , respectively. The cavities are designed for a peak surface electric field of 30M V /m. The cavities were optimized for manufacturing recommendations based on previous design as well as for stiffness, tunability, assembly, and cleaning. Finite element analysis simulations were performed for mechanical modal frequency analysis, liquid helium bath pressure sensitivity, Lorentz force detuning factor and mechanical force to complete the tuning range. The helium vessel, fundamental power coupler (FPC), and frequency tuner systems which interface to the cavity have been designed and prototypes fabricated

Tropospheric distribution of sulphate aerosol mass and number concentration during INDOEX-IFP and its transport over the Indian Ocean: a GCM study

International audienceAn interactive sulphate aerosol chemistry module has been incorporated in the Laboratoire de Météorologie Dynamique General Circulation Model (LMD-GCM) to simulate the sulphur chemistry during the Indian Ocean Experiment (INDOEX) Intensive Field Phase-1999 (INDOEX-IFP). The originality of this module is its ability to predict particle mass and number concentration for the Aitken and accumulation modes. The model qualitatively reproduces the spatial patterns of observations on sulphate aerosol during INDOEX. On the basis of size distribution retrieved from the observations made along the cruise route during 1998 and 1999, the model successfully simulates the order of magnitude and the general north-south gradient in aerosol number concentration. The result shows the southward migration of minimum concentrations, which follows ITCZ (Inter Tropical Convergence Zone) migration. Sulphate surface concentration during INDOEX-IFP at Kaashidhoo (73.46° E, 4.96° N) gives an agreement within a factor of 2 to 3. Predicted sulphate aerosol optical depth (AOD) matches reasonably with measured values, indicating the capability of this model to predict the vertically integrated column sulphate burden. The Indian contribution to estimated sulphate burden over India is more than 60% with values upto 40% over the Arabian Sea

A plume-in-grid approach to characterize air quality impacts of aircraft emissions at the Hartsfield-Jackson Atlanta International Airport

This study examined the impacts of aircraft emissions during the landing and takeoff cycle on PM2.5 concentrations during the months of June 2002 and July 2002 at the Hartsfield-Jackson Atlanta International Airport. Primary and secondary pollutants were modeled using the Advanced Modeling System for Transport, Emissions, Reactions, and Deposition of Atmospheric Matter (AMSTERDAM). AMSTERDAM is a modified version of the Community Multiscale Air Quality (CMAQ) model that incorporates a plume-in-grid process to simulate emissions sources of interest at a finer scale than can be achieved using CMAQ's model grid. Three fundamental issues were investigated: the effects of aircraft on PM2.5 concentrations throughout northern Georgia, the differences resulting from use of AMSTERDAM's plume-in-grid process rather than a traditional CMAQ simulation, and the concentrations observed in aircraft plumes at sub-grid scales. Comparison of model results with an air quality monitor located in the vicinity of the airport found that normalized mean bias ranges from -77.5% to 6.2% and normalized mean error ranges from 40.4% to 77.5%, varying by species. Aircraft influence average PM2.5 concentrations by up to 0.232 μg m-3 near the airport and by 0.001-0.007 μg m-3 throughout the Atlanta metro area. The plume-in-grid process increases concentrations of secondary PM pollutants by 0.005-0.020 μg m-3 (compared to the traditional grid-based treatment) but reduces the concentration of non-reactive primary PM pollutants by up to 0.010 μg m-3, with changes concentrated near the airport. Examination of sub-grid scale results indicates that puffs within 20 km of the airport often have average PM2.5 concentrations one order of magnitude higher than aircraft contribution to the grid cells containing those puffs, and within 1-4 km of emitters, puffs may have PM2.5 concentrations 3 orders of magnitude greater than the aircraft contribution to their grid cells. 21% of all aircraft-related puffs from the Atlanta airport have at least 0.1 μg m-3 PM2.5 concentrations. Median daily puff concentrations vary between 0.017 and 0.134 μg m-3, while maximum daily puff concentrations vary between 6.1 and 42.1 μg m-3 during the 2-month period. In contrast, median daily grid concentrations vary between 0.015 and 0.091 μg m-3, while maximum daily grid concentrations vary between 0.751 and 2.55 μg m-3. Future researchers may consider using AMSTERDAM to understand the impacts of aircraft emissions at other airports, for proposed future airports, for airport expansion projects under various future scenarios, and for other national-scale studies specifically when the maximum impacts at fine scales are of interest

A 41,500 year-old decorated ivory pendant from Stajnia Cave (Poland)

Evidence of mobiliary art and body augmentation are associated with the cultural innovations introduced by Homo sapiens at the beginning of the Upper Paleolithic. Here, we report the discovery of the oldest known human-modified punctate ornament, a decorated ivory pendant from the Paleolithic layers at Stajnia Cave in Poland. We describe the features of this unique piece, as well as the stratigraphic context and the details of its chronometric dating. The Stajnia Cave plate is a personal 'jewellery' object that was created 41,500 calendar years ago (directly radiocarbon dated). It is the oldest known of its kind in Eurasia and it establishes a new starting date for a tradition directly connected to the spread of modern Homo sapiens in Europe

FLORA: a novel method to predict protein function from structure in diverse superfamilies

Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure embellishments to a common structural core. The majority of prediction algorithms employ local templates built on known or predicted functional residues. Here, we present a novel method (FLORA) that automatically generates structural motifs associated with different functional sub-families (FSGs) within functionally diverse domain superfamilies. Templates are created purely on the basis of their specificity for a given FSG, and the method makes no prior prediction of functional sites, nor assumes specific physico-chemical properties of residues. FLORA is able to accurately discriminate between homologous domains with different functions and substantially outperforms (a 2–3 fold increase in coverage at low error rates) popular structure comparison methods and a leading function prediction method. We benchmark FLORA on a large data set of enzyme superfamilies from all three major protein classes (α, β, αβ) and demonstrate the functional relevance of the motifs it identifies. We also provide novel predictions of enzymatic activity for a large number of structures solved by the Protein Structure Initiative. Overall, we show that FLORA is able to effectively detect functionally similar protein domain structures by purely using patterns of structural conservation of all residues

3V: cavity, channel and cleft volume calculator and extractor

As larger macromolecular structures become available, there is a growing need to understand their ‘internal’ volumes—such as deep clefts, channels and cavities—as these often play critical roles in their function. The 3V web server can automatically extract and comprehensively analyze all the internal volumes from input RNA and protein structures. It rapidly finds internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces, one with as large as possible a probe radius and the other with a solvent radius (typically 1.5 Å for water). The outputs are volumetric representations, both as images and downloadable files, which can be used for further analysis

Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites

A new binding site comparison algorithm using optimal superposition of the continuous pharmacophoric property distributions is reported. The method demonstrates high sensitivity in discovering both, distantly homologous and convergent binding sites. Good quality of superposition is also observed on multiple examples. Using the new approach, a measure of site similarity is derived and applied to clustering of ligand binding pockets in PDB