A unified statistical framework for sequence comparison and structure comparison

We present an approach for assessing the significance of sequence and structure comparisons by using nearly identical statistical formalisms for both sequence and structure. Doing so involves an all-vs.-all comparison of protein domains [taken here from the Structural Classification of Proteins (scop) database] and then fitting a simple distribution function to the observed scores. By using this distribution, we can attach a statistical significance to each comparison score in the form of a P value, the probability that a better score would occur by chance. As expected, we find that the scores for sequence matching follow an extreme-value distribution. The agreement, moreover, between the P values that we derive from this distribution and those reported by standard programs (e.g., blast and fasta validates our approach. Structure comparison scores also follow an extreme-value distribution when the statistics are expressed in terms of a structural alignment score (essentially the sum of reciprocated distances between aligned atoms minus gap penalties). We find that the traditional metric of structural similarity, the rms deviation in atom positions after fitting aligned atoms, follows a different distribution of scores and does not perform as well as the structural alignment score. Comparison of the sequence and structure statistics for pairs of proteins known to be related distantly shows that structural comparison is able to detect approximately twice as many distant relationships as sequence comparison at the same error rate. The comparison also indicates that there are very few pairs with significant similarity in terms of sequence but not structure whereas many pairs have significant similarity in terms of structure but not sequence.

Foldons, protein structural modules, and exons.

Foldons, which are kinetically competent, quasi-independently folding units of a protein, may be defined using energy landscape analysis. Foldons can be identified by maxima in a scan of the ratio of a contiguous segment's energetic stability gap to the energy variance of that segment's molten globule states, reflecting the requirement of minimal frustration. The predicted foldons are compared with the exons and structural modules for 16 of the 30 proteins studied. Statistical analysis indicates a strong correlation between the energetically determined foldons and Go's geometrically defined structural modules, but there are marked sequence-dependent effects. There is only a weak correlation of foldons to exons. For gammaII-crystallin, myoglobin, barnase, alpha-lactalbumin, and cytochrome c the foldons and some noncontiguous clusters of foldons compare well with intermediates observed in experiment.

A structural model of cognitive-motivational variables as explanatory factors of academic achievement in Spanish Language and Mathematics

In recent years, several explanatory models have been developed which attempt to analyse the predictive worth of various factors in relation to academic achievement, as well as the direct and indirect effects that they produce. The aim of this study was to examine a structural model incorporating various cognitive and motivational variables which influence student achievement in the two basic core skills in the Spanish curriculum: Spanish Language and Mathematics. These variables included differential aptitudes, specific self-concept, goal orientations, effort and learning strategies. The sample comprised 341 Spanish students in their first year of Compulsory Secondary Education. Various tests and questionnaires were used to assess each student, and Structural Equation Modelling (SEM) was employed to study the relationships in the initial model. The proposed model obtained a satisfactory fit for the two subjects studied, and all the relationships hypothesised were significant. The variable with the most explanatory power regarding academic achievement was mathematical and verbal aptitude. Also notable was the direct influence of specific self-concept on achievement, goal-orientation and effort, as was the mediatory effect that effort and learning strategies had between academic goals and final achievement.

Croatia and the structural funds – Doing without an Ottoman Empire bypass bridge. CEPS Commentary, 29 July 2013

In his latest commentary, Associate Senior Fellow Michael Emerson hails Croatia’s accession to the EU as a fine step forward towards the official goal of integration of the whole of the Balkans into the EU. At the same time, he warns of the folly underway of the serious attention being paid by the European Commission to the newest member state’s petition to construct a multi-million euro bridge over a 9-km stretch of Bosnian land (the ‘Neum corridor’) that inconveniently but temporarily interrupts a non-stop drive along Croatia’s Dalmatian coast.

Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii

We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of noncharged polar amino acids, particularly Gin and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15degrees-98degreesC) were used to generate IIII modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gin, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60degreesC, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes. from psychrophiles to hyperthermophiles

Structural Insights into Viral Membrane Fusion Machinery via Cryo-Electron Tomography: Influenza Virus and Human Parainfluenza Virus

Thesis (Ph.D.)--University of Washington, 2016-06

Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

The C2 domain is one of the most frequent and widely distributed calcium-binding motifs. Its structure comprises an eight-stranded beta-sandwich with two structural types as if the result of a circular permutation. Combining sequence, structural and modelling information, we have explored, at different levels of granularity, the functional characteristics of several families of C2 domains. At the coarsest level,the similarity correlates with key structural determinants of the C2 domain fold and, at the finest level, with the domain architecture of the proteins containing them, highlighting the functional diversity between the various subfamilies. The functional diversity appears as different conserved surface patches throughout this common fold. In some cases, these patches are related to substrate-binding sites whereas in others they correspond to interfaces of presumably permanent interaction between other domains within the same polypeptide chain. For those related to substrate-binding sites, the predictions overlap with biochemical data in addition to providing some novel observations. For those acting as protein-protein interfaces' our modelling analysis suggests that slight variations between families are a result of not only complementary adaptations in the interfaces involved but also different domain architecture. In the light of the sequence and structural genomic projects, the work presented here shows that modelling approaches along with careful sub-typing of protein families will be a powerful combination for a broader coverage in proteomics. (C) 2003 Elsevier Ltd. All rights reserved.

Synthesis, characterization and DFT studies of the cobalt(III) complex of a tetrapodal pentadentate N4S donor ligand

The synthesis of the pentadentate ligand 2,6-bis(3,3-dimethyl-2,4-dioxocyclohexanyl)-4-thiaheptane (N(4)Samp) is described. The synthetic pathway involves the coupling of two 1,3-(dimethylenedioxy)-2-methyl-2-(methylene-p-toluenesulfonyl)propane moieties with sodium sulfide and subsequent synthetic elaboration to prepare the final N4S donor system. The cobalt(III) complex [Co(N(4)Samp)Cl](2+) has been prepared and subsequently crystallized as the tetrachlorozincate salt. The X-ray structure analysis confirms the pentadentate nature of the ligand and shows the thioether donor occupying one apex with four equivalent amine donors effectively occupying the equatorial plane of the molecule. The sixth coordination site is occupied by a chloro ligand. The electronic absorption and C-13 NMR spectra have been studied. DFT calculations have been employed to explore structural and mechanistic comparisons between [Co(N(4)Samp)Cl](2+) and an analogous pentaamine complex.

Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices

Wurst is a protein threading program with an emphasis on high quality sequence to structure alignments (http://www.zbh.uni-hamburg.de/wurst). Submitted sequences are aligned to each of about 3000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticated structure and sequence terms. The structure terms are a log-odds probability of sequence to structure fragment compatibility, obtained from a Bayesian classification procedure. A simplex optimization was used to optimize the sequence-based terms for the goal of alignment and model quality and to balance the sequence and structural contributions against each other. Both sequence and structural terms operate with sequence profiles.

Measuring and incorporating vulnerability into conservation planning

Conservation planning is the process of locating and designing conservation areas to promote the persistence of biodiversity in situ. To do this, conservation areas must be able to mitigate at least some of the proximate threats to biodiversity. Information on threatening processes and the relative vulnerability of areas and natural features to these processes is therefore crucial for effective conservation planning. However, measuring and incorporating vulnerability into conservation planning have been problematic. We develop a conceptual framework of the role of vulnerability assessments in conservation planning and propose a definition of vulnerability that incorporates three dimensions: exposure, intensity, and impact. We review and categorize methods for assessing the vulnerability of areas and the features they contain and identify the relative strengths and weaknesses of each broad approach, Our review highlights the need for further development and evaluation of approaches to assess vulnerability and for comparisons of their relative effectiveness.

Structural properties of a family of hydrogen-bonded co-crystals formed between gemfibrozil and hydroxy derivatives of t-butylamine, determined directly from powder X-ray diffraction data

We report the formation and structural properties of co-crystals containing gemfibrozil and hydroxy derivatives of t-butylamine H2NC(CH3)3-n(CH2OH)n, with n=0, 1, 2 and 3. In each case, a 1:1 co-crystal is formed, with transfer of a proton from the carboxylic acid group of gemfibrozil to the amino group of the t-butylamine derivative. All of the co-crystal materials prepared are polycrystalline powders, and do not contain single crystals of suitable size and/or quality for single crystal X-ray diffraction studies. Structure determination of these materials has been carried out directly from powder X-ray diffraction data, using the direct-space Genetic Algorithm technique for structure solution followed by Rietveld refinement. The structural chemistry of this series of co-crystal materials reveals well-defined structural trends within the first three members of the family (n=0, 1, 2), but significantly contrasting structural properties for the member with n=3. © 2007 Elsevier Inc. All rights reserved.

Affect networks:a structural analysis of the relationship between work ties and job-related affect

The relationship between organizational networks and employees' affect was examined in 2 organizations. In Study 1, social network analysis of work ties and job-related affect for 259 employees showed that affect converged within work interaction groups. Similarity of affect between employees depended on the presence of work ties and structural equivalence. Affect was also related to the size and density of employees' work networks. Study 2 used a 10-week diary study of 31 employees to examine a merger of 2 organizational divisions and found that negative changes in employees' affect were related to having fewer cross-divisional ties and to experiencing greater reductions in network density. The findings suggest that affect permeates through and is shaped by organizational networks.

Structural funds and the knowledge-based economy:a regional case-study (1999-2009)

The research presented in this thesis investigates the nature of the relationship between the development of the Knowledge-Based Economy (KBE) and Structural Funds (SF) in European regions. A particular focus is placed on the West Midlands (UK) and Silesia (Poland). The time-frame taken into account in this research is the years 1999 to 2009. This is methodologically addressed by firstly establishing a new way of calculating the General Index of the KBE for all of the EU regions; secondly, applying a number of statistical methods to measure the influence of the Funds on the changes in the regional KBE over time; and finally, by conducting a series of semi-structured stakeholder interviews in the two key case study regions: the West Midlands and Silesia. The three main findings of the thesis are: first, over the examined time-frame, the values of the KBE General Index increased in over 66% of the EU regions; furthermore, the number of the “new” EU regions in which the KBE increased over time is far higher than in the “old” EU. Second, any impact of Structural Funds on the regional KBE occurs only in the minority of the European regions and any form of functional dependency between the two can be observed only in 30% of the regions. Third, although the pattern of development of the regional KBE and the correlation coefficients differ in the cases of Silesia and the West Midlands, the analysis of variance carried out yields identical results for both regions. Furthermore, the qualitative analysis’ results show similarities in the approach towards the Structural Funds in the two key case-study regions.

Influence of the sputtering flow regime on the structural properties and magnetic behavior of Fe-Ga thin films (Ga ∼ 30 at.%)

In this paper we analyze the structure of Fe-Ga layers with a Ga content of ∼30 at.% deposited by the sputtering technique under two different regimes. We also studied the correlation between the structure and magnetic behavior of the samples. Keeping the Ar pressure fixed, we modified the flow regime from ballistic to diffusive by increasing the distance between the target and the substrate. X-ray diffraction measurements have shown a lower structural quality when growing in the diffusive flow. We investigated the impact of the growth regime by means of x-ray absorption fine structure (XAFS) measurements and obtained signs of its influence on the local atomic order. Full multiple scattering and finite difference calculations based on XAFS measurements point to a more relevant presence of a disordered A2 phase and of orthorhombic Ga clusters on the Fe-Ga alloy deposited under a diffusive regime; however, in the ballistic sample, a higher presence of D0_3/B2 phases is evidenced. Structural characteristics, from local to long range, seem to determine the magnetic behavior of the layers. Whereas a clear in-plane magnetic anisotropy is observed in the film deposited under ballistic flow, the diffusive sample is magnetically isotropic. Therefore, our experimental results provide evidence of a correlation between flow regime and structural properties and its impact on the magnetic behavior of a rather unexplored compositional region of Fe-Ga compounds.

Finite element model calibration of an instrumented RC building based on seismic excitation including non-structural components and soil-structure- interaction

Peer reviewed