Order independent structural alignment of circularly permuted proteins

Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because current detection methods can miss many occurances, mistaking random repeats as circular permutation. Here we develop a method for detecting circularly permuted proteins from structural comparison. Sequence order independent alignment of protein structures can be regarded as a special case of the maximum-weight independent set problem, which is known to be computationally hard. We develop an efficient approximation algorithm by repeatedly solving relaxations of an appropriate intermediate integer programming formulation, we show that the approximation ratio is much better then the theoretical worst case ratio of $r = 1/4$. Circularly permuted proteins reported in literature can be identified rapidly with our method, while they escape the detection by publicly available servers for structural alignment.Comment: 5 pages, 3 figures, Accepted by IEEE-EMBS 2004 Conference Proceeding

Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites

<p>Abstract</p> <p>Background</p> <p>Protein surfaces comprise only a fraction of the total residues but are the most conserved functional features of proteins. Surfaces performing identical functions are found in proteins absent of any sequence or fold similarity. While biochemical activity can be attributed to a few key residues, the broader surrounding environment plays an equally important role.</p> <p>Results</p> <p>We describe a methodology that attempts to optimize two components, global shape and local physicochemical texture, for evaluating the similarity between a pair of surfaces. Surface shape similarity is assessed using a three-dimensional object recognition algorithm and physicochemical texture similarity is assessed through a spatial alignment of conserved residues between the surfaces. The comparisons are used in tandem to efficiently search the Global Protein Surface Survey (GPSS), a library of annotated surfaces derived from structures in the PDB, for studying evolutionary relationships and uncovering novel similarities between proteins.</p> <p>Conclusion</p> <p>We provide an assessment of our method using library retrieval experiments for identifying functionally homologous surfaces binding different ligands, functionally diverse surfaces binding the same ligand, and binding surfaces of ubiquitous and conformationally flexible ligands. Results using surface similarity to predict function for proteins of unknown function are reported. Additionally, an automated analysis of the ATP binding surface landscape is presented to provide insight into the correlation between surface similarity and function for structures in the PDB and for the subset of protein kinases.</p

Predicting HLA Class I Non-Permissive Amino Acid Residues Substitutions

Prediction of peptide binding to human leukocyte antigen (HLA) molecules is essential to a wide range of clinical entities from vaccine design to stem cell transplant compatibility. Here we present a new structure-based methodology that applies robust computational tools to model peptide-HLA (p-HLA) binding interactions. The method leverages the structural conservation observed in p-HLA complexes to significantly reduce the search space and calculate the system’s binding free energy. This approach is benchmarked against existing p-HLA complexes and the prediction performance is measured against a library of experimentally validated peptides. The effect on binding activity across a large set of high-affinity peptides is used to investigate amino acid mismatches reported as high-risk factors in hematopoietic stem cell transplantation.</p

Variation in Stemmatal Morphology of Larvae of Liodessus noviaffinis Miller (Dytiscidae: Hydroporinae: Bidessini)

Second and third instars tentatively identified as Liodessus noviaffinis Miller have six dorsolateral stemmata near the origin of each antenna. However, each stemma lacks a corneal (cuticular) lens on the surface exterior to its internal sensory pigmented components

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

WRF-CMAQ two-way coupled system with aerosol feedback: software development and preliminary results

Air quality models such as the EPA Community Multiscale Air Quality (CMAQ) require meteorological data as part of the input to drive the chemistry and transport simulation. The Meteorology-Chemistry Interface Processor (MCIP) is used to convert meteorological data into CMAQ-ready input. Key shortcoming of such one-way coupling include: excessive temporal interpolation of coarsely saved meteorological input and lack of feedback of atmospheric pollutant loading on simulated dynamics. We have developed a two-way coupled system to address these issues. A single source code principle was used to construct this two-way coupling system so that CMAQ can be consistently executed as a stand-alone model or part of the coupled system without any code changes; this approach eliminates maintenance of separate code versions for the coupled and uncoupled systems. The design also provides the flexibility to permit users: (1) to adjust the call frequency of WRF and CMAQ to balance the accuracy of the simulation versus computational intensity of the system, and (2) to execute the two-way coupling system with feedbacks to study the effect of gases and aerosols on short wave radiation and subsequent simulated dynamics. Details on the development and implementation of this two-way coupled system are provided. When the coupled system is executed without radiative feedback, computational time is virtually identical when using the Community Atmospheric Model (CAM) radiation option and a slightly increased (~8.5 %) when using the Rapid Radiative Transfer Model for GCMs (RRTMG) radiation option in the coupled system compared to the offline WRF-CMAQ system. Once the feedback mechanism is turned on, the execution time increases only slightly with CAM but increases about 60 % with RRTMG due to the use of a more detailed Mie calculation in this implementation of feedback mechanism. This two-way model with radiative feedback shows noticeably reduced bias in simulated surface shortwave radiation and 2 m temperatures as well improved correlation of simulated ambient ozone and PM&lt;sub&gt;2.5&lt;/sub&gt; relative to observed values for a test case with significant tropospheric aerosol loading from California wildfires

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

Modeling the impact of sea-spray on particle concentrations in a coastal city

Abstract 18 An atmospheric chemistry-transport model is used to assess the impacts of sea-spray chemistry 19 on the particle composition in and downwind of a coastal city -Vancouver, British Columbia. 20 Reactions in/on sea-spray affect the entire particle ensemble and particularly the size distribution 21 of particle nitrate. 2

Modeling the impact of sea-spray on particle concentrations in a coastal city

An atmospheric chemistry-transport model is used to assess the impacts of sea-spray chemistry on the particle composition in and downwind of a coastal city--Vancouver, British Columbia. Reactions in/on sea-spray affect the entire particle ensemble and particularly the size distribution of particle nitrate. Urban air quality, and particularly airborne particles, is a major concern in terms of human health impacts. Sea-spray is known to be a major component of the particle ensemble at coastal sites yet relatively few air quality models include the interaction of gases with sea-spray and the fate of the particles produced. Sea-spray is not an inert addition to the particle ensemble because heterogeneous chemistry in/on sea-spray droplets changes the droplets composition and the particle size distribution, which impacts deposition and the ion balance in different particle size fractions. It is shown that the ISOPART model is capable of simulating gas and particle concentrations in the coastal metropolis of Vancouver and the surrounding valley. It is also demonstrated that to accurately simulate ambient concentrations of particles and reactive/soluble gases in a coastal valley it is absolutely critical to include heterogeneous chemistry in/on sea-spray. Partitioning of total particle-NO{sub 3}{sup -} between sea-spray and NH{sub 4}NO{sub 3} is highly sensitive to the amount of sea-spray present, and hence the initial vertical profile, sea-spray source functions [48] and the wind speed. When a fixed wind speed is used to initialize the sea-spray vertical profiles, as expected, the sea-spray concentration decays with distance inland, but the particle-NO{sub 3}{sup -} concentration decays more slowly because it is also a function of the uptake rate for HNO{sub 3}. The simulation results imply model analyses of air quality in coastal cities conducted without inclusion of sea-spray interactions may yield highly misleading results in terms of emission sensitivities of the PM size distribution. The sensitivity of the model results to the initial sea spray profile further suggests there would be great benefit in better definition of the vertical profile of size resolved sea-spray for use in such model studies

High throughput mutagenesis for identification of residues regulating human prostacyclin (hIP) receptor

The human prostacyclin receptor (hIP receptor) is a seven-transmembrane G protein-coupled receptor (GPCR) that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR) mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structurefunction relationship of GPCRs. © 2014 Bill et al