Structural model of cytochrome b559 in photosystem II based on a mutant with genetically fused subunits

Photosystem II is a reaction center protein complex located in photosynthetic membranes of plants, algae, and cyanobacteria. Using light energy, photosystem II catalyzes the oxidation of water and the reduction of plastoquinone, resulting in the release of molecular oxygen. A key component of photosystem II is cytochrome b559, a membrane-embedded heme protein with an unknown function. The cytochrome is unusual in that a heme links two separate polypeptide subunits, α and β, either as a heterodimer (αβ) or as two homodimers (α2 and β2). To determine the structural organization of cytochrome b559 in the membrane, we used site-directed mutagenesis to fuse the coding regions of the two respective genes in the cyanobacterium Synechocystis sp. PCC 6803. In this construction, the C terminus of the α subunit (9 kDa) is attached to the N terminus of the β subunit (5 kDa) to form a 14-kDa αβ fusion protein that is predicted to have two membrane-spanning α-helices with antiparallel orientations. Cells containing the αβ fusion protein grow photoautotrophically and assemble functional photosystem II complexes. Optical spectroscopy shows that the αβ fusion protein binds heme and is incorporated into photosystem II. These data support a structural model of cytochrome b559 in which one heme is coordinated to an α2 homodimer and a second heme is coordinated to a β2 homodimer. In this model, each photosystem II complex contains two cytochrome b559 hemes, with the α2 heme located near the stromal side of the membrane and the β2 heme located near the lumenal side.

A structural model for a homeotic protein-extradenticle-DNA complex accounts for the choice of HOX protein in the heterodimer.

The genes of the homeotic complex (HOX) encode DNA binding homeodomain proteins that control developmental fates by differentially regulating the transcription of downstream target genes. Despite their unique in vivo functions, disparate HOX proteins often bind to very similar DNA sequences in vitro. Thus, a critical question is how HOX proteins select the correct sets of target genes in vivo. The homeodomain proteins encoded by the Drosophila extradenticle gene and its mammalian homologues, the pbx genes, contribute to HOX specificity by cooperatively binding to DNA with HOX proteins. For example, the HOX protein labial cooperatively binds with extradenticle protein to a 20-bp oligonucleotide that is sufficient to direct a labial-like expression pattern in Drosophila embryos. Here we have analyzed the protein-DNA interactions that are important for forming the labial-extradenticle-DNA complex. The data suggest a model in which labial and extradenticle, separated by only 4 bp, bind this DNA as a heterodimer in a head-to-tail orientation. We have confirmed several aspects of this model by characterizing extradenticle-HOX binding to mutant oligonucleotides. Most importantly, mutations in base pairs predicted to contact the HOX N-terminal arm resulted in a change in HOX preference in the heterodimer, from labial to Ultrabithorax. These results demonstrate that extradenticle prefers to bind cooperatively with different HOX proteins depending on subtle differences in the heterodimer binding site.

Comparison of the defensive elicitation activity of cerato-populin and cerato-platanin: a structural model

Plants can defend themselves from potential pathogenic microorganisms relying on a complex interplay of signaling pathways: activation of the MAPK cascade, transcription of defense related genes, production of reactive oxygen species, nitric oxide and synthesis of other defensive compounds such as phytoalexins. These events are triggered by the recognition of pathogen’s effectors (effector-triggered immunity) or PAMPs (PAMP-triggered immunity). The Cerato Platanin Family (CPF) members are Cys-rich proteins secreted and localized on fungal cell walls, involved in several aspects of fungal development and pathogen-host interactions. Although more than hundred genes of the CPF have been identified and analyzed, the structural and functional characterization of the expressed proteins has been restricted only to few members of the family. Interestingly, those proteins have been shown to bind chitin with diverse affinity and after foliar treatment they elicit defensive mechanisms in host and non-host plants. This property turns cerato platanins into interesting candidates, worth to be studied to develop new fungal elicitors with applications in sustainable agriculture. This study focus on cerato-platanin (CP), core member of the family and on the orthologous cerato-populin (Pop1). The latter shows an identity of 62% and an overall homology of 73% with respect to CP. Both proteins are able to induce MAPKs phosphorylation, production of reactive oxygen species and nitric oxide, overexpression of defense’s related genes, programmed cell death and synthesis of phytoalexins. CP, however, when compared to Pop1, induces a faster response and, in some cases, a stronger activity on plane leaves. Aim of the present research is to verify if the dissimilarities observed in the defense elicitation activity of these proteins can be associated to their structural and dynamic features. Taking advantage of the available CP NMR structure, Pop1’s 3D one was obtained by homology modeling. Experimental residual dipolar couplings and 1H, 15N, 13C resonance assignments were used to validate the model. Previous works on CPF members, addressed the highly conserved random coil regions (loops b1-b2 and b2-b3) as sufficient and necessary to induce necrosis in plants’ leaves: that region was investigated in both Pop1 and CP. In the two proteins the loops differ, in their primary sequence, for few mutations and an insertion with a consequent diversification of the proteins’ electrostatic surface. A set of 2D and 3D NMR experiments was performed to characterize both the spatial arrangement and the dynamic features of the loops. NOE data revealed a more extended network of interactions between the loops in Pop1 than in CP. In addition, in Pop1 we identified a salt bridge Lys25/Asp52 and a strong hydrophobic interaction between Phe26/Trp53. These structural features were expected not only to affect the loops’ spatial arrangement, but also to reduce the degree of their conformational freedom. Relaxation data and the order parameter S2 indeed highlighted reduced flexibility, in particular for loop b1-b2 of Pop1. In vitro NMR experiments, where Pop1 and CP were titrated with oligosaccharides, supported the hypothesis that the loops structural and dynamic differences may be responsible for the different chitin-binding properties of the two proteins: CP selectively binds tetramers of chitin in a shallow groove on one side of the barrel defined by loops b1-b2, b2-b3 and b4-b5, Pop1, instead, interacts in a non-specific fashion with oligosaccharides. Because the region involved in chitin-binding is also responsible for the defense elicitation activity, possibly being recognized by plant's receptors, it is reasonable to expect that those structural and dynamic modifications may also justify the different extent of defense elicitation. To test that hypothesis, the initial steps of a protocol aimed to the identify a receptor for CP, in silico, are presented.

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.

A structural model of Social Security's disability determination process /

"August 1997."

Biogenesis of caveolae: a structural model for caveolin-induced domain formation

Caveolae are striking morphological features of the plasma membrane of mammalian cells. Caveolins, the major proteins of caveolae, play a crucial role in the formation of these invaginations of the plasma membrane; however, the precise mechanisms involved are only just starting to be unravelled. Recent studies suggest that caveolae are stable structures first generated in the Golgi complex. Their formation and exit from the Golgi complex is associated with caveolin oligomerisation, acquisition of detergent insolubility, and association with cholesterol. Modelling of caveolin-membrane interactions together with in vitro studies of caveolin peptides are providing new insights into how caveolin-lipid interactions could generate the unique architecture of the caveolar domain.

The structural effects of divalent cations and insulin on phospholipid model membranes /

It is well accepted that structural studies with model membranes are of considerable value in understanding the structure of biological membranes. Many studies with models of pure phospholipids have been done; but the effects of divalent cations and protein on these models would make these studies more applicable to intact membrane. The present study, performed with above view, is a structural analysis of divalent io~cardio1ipin complexes using the technique of x-ray diffraction. Cardiolipin, precipitated from dilute solution by divalent ionscalcium, magnesium and barium, contains little water and the structure formed is similar to the structure of pure cardiolipin with low water content. The calcium-cardiolipin complex forms a pure hexagonal type II phase that exists from 40 to 400 C. The molar ratio of calcium and cardiolipin in the complex is 1 : 1. Cardiolipin, precipitated with magnesium and barium forms two co-existing phases, lamellar and hexagonal, the relative quantity of the two phases being dependent on temperature. The hexagonal phase type II consisting of water filled channels formed by adding calcium to cardiolipin may have a remarkable permeability property in intact membrane. Pure cardiolipin and insulin at pH 3.0 and 4.0 precipitate but form no organised structure. Lecithin/cardiolipin and insulin precipitated at pH 3.0 give a pure lamellar phase. As the lecithin/cardiolipin molar ratio changes from 93/7 to SO/50, (a) the repeat distance of the lamellar changes from 72.8 X to 68.2 A; (b) the amount of protein bound increases in such a way that cardiolipin/insulin molar ratio in the complex reaches a maximum constant value at lecithin/cardiolipin molar ratio 70/30. A structural model based on these data shows that the molecular arrangement of lipid and protein is a lipid bilayer coated with protein molecules. The lipid-protein interaction is chiefly electrostatic and little, if any, hydrophobic bonding occurs in this particular system. So, the proposed model is essentially the same as Davson-Daniellifs model of biological membrane.

Constructing a Structural Macroeconomic Model Using Multiple Techniques

This project constructs a structural model of the United States Economy. This task is tackled in two separate ways: first econometric methods and then using a neural network, both with a structure that mimics the structure of the U.S. economy. The structural model tracks the performance of U.S. GDP rather well in a dynamic simulation, with an average error of just over 1 percent. The neural network performed well, but suffered from some theoretical, as well as some implementation issues.

Functional-structural plant modelling using a combination of architectural analysis, L-systems and a canonical model of function

This paper presents a new method for producing a functional-structural plant model that simulates response to different growth conditions, yet does not require detailed knowledge of underlying physiology. The example used to present this method is the modelling of the mountain birch tree. This new functional-structural modelling approach is based on linking an L-system representation of the dynamic structure of the plant with a canonical mathematical model of plant function. Growth indicated by the canonical model is allocated to the structural model according to probabilistic growth rules, such as rules for the placement and length of new shoots, which were derived from an analysis of architectural data. The main advantage of the approach is that it is relatively simple compared to the prevalent process-based functional-structural plant models and does not require a detailed understanding of underlying physiological processes, yet it is able to capture important aspects of plant function and adaptability, unlike simple empirical models. This approach, combining canonical modelling, architectural analysis and L-systems, thus fills the important role of providing an intermediate level of abstraction between the two extremes of deeply mechanistic process-based modelling and purely empirical modelling. We also investigated the relative importance of various aspects of this integrated modelling approach by analysing the sensitivity of the standard birch model to a number of variations in its parameters, functions and algorithms. The results show that using light as the sole factor determining the structural location of new growth gives satisfactory results. Including the influence of additional regulating factors made little difference to global characteristics of the emergent architecture. Changing the form of the probability functions and using alternative methods for choosing the sites of new growth also had little effect. (c) 2004 Elsevier B.V. All rights reserved.

Travel context : development of a model to measure destination brand performance across different travel situations

Purpose: There is a lack of theory relating to destination brand performance measurement in the destination branding literature, which emerged in the late 1990s (see for example Dosen, Vransevic, & Prebezac, 1998). Additionally, there is a lack of research about the importance of travel context in consumers’ destination decision making (Hu & Ritchie, 1993). This study develops a structural model to measure destination brand performance across different travel situations. The theory of planned behaviour (TpB) was utilised as a framework to underpin the consumer-based brand equity (CBBE) hierarchy to develop a model of destination brand performance. Research approach: A proposed model of destination brand performance was developed through a review of the literature. The first study was used to identify destination image attributes (the core construct) using an analysis of the literature, a document analysis, and personal interviews using the Repertory Test qualitative technique. Underpinned by Personal Construct Theory (PCT), the Repertory Test enables the elicitation of attributes consumers use to evaluate destinations when considering travel. Data was examined in the first study to i) identify any attribute differences in travel contexts and ii) create a scale for use in a questionnaire. A second study was conducted to test the proposed model using a questionnaire with eight groups of participants to assess four destinations across two travel contexts. The model was tested utilising structural equation modelling. Findings: The first study resulted in a list of 29 destination image attributes for use in a scale index. Attributes were assessed across travel contexts and few differences were identified. The second study assessed the congruence of destination brand identity (the destination marketing organisation’s desired image) and destination brand image (the actual perceptions held by consumers) using importance-performance analyses. Finally, the proposed model of destination brand performance was tested. Overall the data supported the model of destination brand performance across travel contexts and destinations. Additionally, this was compared to consumers’ decision sets, further supporting the model. Value: This research provides a contribution to the destination marketing literature through the development of a measurement of destination brand performance underpinned by TpB. Practically; it will provide destination marketing organisations with a tool to track destination brand performance, relative to key competing places, over time. This is important given the development of a destination brand is a long term endeavour.

Extending and validating the is-impact model in Saudi Arabia : accounting for computer network quality

Organizations from every industry sector seek to enhance their business performance and competitiveness through the deployment of contemporary information systems (IS), such as Enterprise Systems (ERP). Investments in ERP are complex and costly, attracting scrutiny and pressure to justify their cost. Thus, IS researchers highlight the need for systematic evaluation of information system success, or impact, which has resulted in the introduction of varied models for evaluating information systems. One of these systematic measurement approaches is the IS-Impact Model introduced by a team of researchers at Queensland University of technology (QUT) (Gable, Sedera, & Chan, 2008). The IS-Impact Model is conceptualized as a formative, multidimensional index that consists of four dimensions. Gable et al. (2008) define IS-Impact as "a measure at a point in time, of the stream of net benefits from the IS, to date and anticipated, as perceived by all key-user-groups" (p.381). The IT Evaluation Research Program (ITE-Program) at QUT has grown the IS-Impact Research Track with the central goal of conducting further studies to enhance and extend the IS-Impact Model. The overall goal of the IS-Impact research track at QUT is "to develop the most widely employed model for benchmarking information systems in organizations for the joint benefit of both research and practice" (Gable, 2009). In order to achieve that, the IS-Impact research track advocates programmatic research having the principles of tenacity, holism, and generalizability through extension research strategies. This study was conducted within the IS-Impact Research Track, to further generalize the IS-Impact Model by extending it to the Saudi Arabian context. According to Hofsted (2012), the national culture of Saudi Arabia is significantly different from the Australian national culture making the Saudi Arabian culture an interesting context for testing the external validity of the IS-Impact Model. The study re-visits the IS-Impact Model from the ground up. Rather than assume the existing instrument is valid in the new context, or simply assess its validity through quantitative data collection, the study takes a qualitative, inductive approach to re-assessing the necessity and completeness of existing dimensions and measures. This is done in two phases: Exploratory Phase and Confirmatory Phase. The exploratory phase addresses the first research question of the study "Is the IS-Impact Model complete and able to capture the impact of information systems in Saudi Arabian Organization?". The content analysis, used to analyze the Identification Survey data, indicated that 2 of the 37 measures of the IS-Impact Model are not applicable for the Saudi Arabian Context. Moreover, no new measures or dimensions were identified, evidencing the completeness and content validity of the IS-Impact Model. In addition, the Identification Survey data suggested several concepts related to IS-Impact, the most prominent of which was "Computer Network Quality" (CNQ). The literature supported the existence of a theoretical link between IS-Impact and CNQ (CNQ is viewed as an antecedent of IS-Impact). With the primary goal of validating the IS-Impact model within its extended nomological network, CNQ was introduced to the research model. The Confirmatory Phase addresses the second research question of the study "Is the Extended IS-Impact Model Valid as a Hierarchical Multidimensional Formative Measurement Model?". The objective of the Confirmatory Phase was to test the validity of IS-Impact Model and CNQ Model. To achieve that, IS-Impact, CNQ, and IS-Satisfaction were operationalized in a survey instrument, and then the research model was assessed by employing the Partial Least Squares (PLS) approach. The CNQ model was validated as a formative model. Similarly, the IS-Impact Model was validated as a hierarchical multidimensional formative construct. However, the analysis indicated that one of the IS-Impact Model indicators was insignificant and can be removed from the model. Thus, the resulting Extended IS-Impact Model consists of 4 dimensions and 34 measures. Finally, the structural model was also assessed against two aspects: explanatory and predictive power. The analysis revealed that the path coefficient between CNQ and IS-Impact is significant with t-value= (4.826) and relatively strong with â = (0.426) with CNQ explaining 18% of the variance in IS-Impact. These results supported the hypothesis that CNQ is antecedent of IS-Impact. The study demonstrates that the quality of Computer Network affects the quality of the Enterprise System (ERP) and consequently the impacts of the system. Therefore, practitioners should pay attention to the Computer Network quality. Similarly, the path coefficient between IS-Impact and IS-Satisfaction was significant t-value = (17.79) and strong â = (0.744), with IS-Impact alone explaining 55% of the variance in Satisfaction, consistent with results of the original IS-Impact study (Gable et al., 2008). The research contributions include: (a) supporting the completeness and validity of IS-Impact Model as a Hierarchical Multi-dimensional Formative Measurement Model in the Saudi Arabian context, (b) operationalizing Computer Network Quality as conceptualized in the ITU-T Recommendation E.800 (ITU-T, 1993), (c) validating CNQ as a formative measurement model and as an antecedent of IS Impact, and (d) conceptualizing and validating IS-Satisfaction as a reflective measurement model and as an immediate consequence of IS Impact. The CNQ model provides a framework to perceptually measure Computer Network Quality from multiple perspectives. The CNQ model features an easy-to-understand, easy-to-use, and economical survey instrument.

Susceptibility of the critical structural components of railway bridges to the changes in train speed

Modern trains with different axle configurations, speeds and loads are used in railway networks. As a result, one of the most important questions of the mangers involved in bridge managements systems (BMS) is how these changes affect the structural behavior of the critical components of the railway bridges. Although researchers have conducted, many investigations on the dynamic effects of the moving loads on bridges, the influence of the changes in the speed of the train on the demand by capacity ratios of the different critical components of the bridge have not yet been properly studied. This study is important, because different components with different capacities and roles for carrying loads in the structure may be affected differently. To investigate the above phenomenon in this research, a structural model of a simply supported bridge is developed. It will be verified that the dynamic behavior of this bridge is similar to a group of railway bridges in Australia. Demand by capacity ratios of the critical components of the bridge, when it is subjected to a train load with different speeds will be calculated. The results show that the effect of increase or decrease of speed should not be underestimated. The outcome is very significant as it is contrary to what is currently expected, i.e. by reducing the speed of the train, the demand by capacity ratio of components may increase and make the bridge unsafe for carrying live load.

Cohabitation, marriage, and divorce in a model of match quality

The objective of this research is to further our understanding of how and why individuals enter and leave coresidential relationships. We develop and estimate an economic model of nonmarital cohabitation, marriage, and divorce that is consistent with current data on the formation and dissolution of relationships. Jovanovic's (Journal of Political Economy 87 (1979), 972-90) theoretical matching model is extended to help explain household formation and dissolution behavior. Implications of the model reveal what factors influence the decision to start a relationship, what form this relationship will take, and the relative stability of the various types of unions. The structural parameters of the model are estimated using longitudinal data from a sample of female high school seniors from the United States. New numerical methods are developed to reduce computational costs associated with estimation. The empirical results have interesting interpretations given the structural model. They show that a significant cause of cohabitation is the need to learn about potential partners and to hedge against future bad shocks. The estimated parameters are used to conduct several comparative dynamic experiments. For example, we show that policy experiments changing the cost of divorce have little effect on relationship choices.