Measures of residue density in protein structures

A hierarchy of residue density assessments and packing properties in protein structures are contrasted, including a regular density, a variety of charge densities, a hydrophobic density, a polar density, and an aromatic density. These densities are investigated by alternative distance measures and also at the interface of multiunit structures. Amino acids are divided into nine structural categories according to three secondary structure states and three solvent accessibility levels. To take account of amino acid abundance differences across protein structures, we normalize the observed density by the expected density defining a density index. Solvent accessibility levels exert the predominant influence in determinations of the regular residue density. Explicitly, the regular density values vary approximately linearly with respect to solvent accessibility levels, the linearity parameters depending on the amino acid. The charge index reveals pronounced inequalities between lysine and arginine in their interactions with acidic residues. The aromatic density calculations in all structural categories parallel the regular density calculations, indicating that the aromatic residues are distributed as a random sample of all residues. Moreover, aromatic residues are found to be over-represented in the neighborhood of all amino acids. This result might be attributed to nucleation sites and protein stability being substantially associated with aromatic residues.

The polo-box-dependent induction of ectopic septal structures by a mammalian polo kinase, Plk, in Saccharomyces cerevisiae

Members of the polo subfamily of protein kinases play pivotal roles in cell-cycle control and proliferation. In addition to a high degree of sequence similarity in the kinase domain, polo kinases contain a strikingly conserved motif termed “polo-box” in the noncatalytic C-terminal domain. We have previously shown that the mammalian polo-like kinase Plk is a functional homolog of Saccharomyces cerevisiae Cdc5. Here, we show that, in a polo-box- and kinase activity-dependent manner, ectopic expression of Plk in budding yeast can induce a class of cells with abnormally elongated buds. In addition to localization at spindle poles and cytokinetic neck filaments, Plk induces and localizes to ectopic septin ring structures within the elongated buds. In contrast, mutations in the polo-box abolish both localization to, and induction of, septal structures. Consistent with the polo-box-dependent subcellular localization, the C-terminal domain of Plk, but not its polo-box mutant, is sufficient for subcellular localization. Our data suggest that Plk may contribute a signal to initiate or promote cytokinetic event(s) and that an intact polo-box is required for regulation of these cellular processes.

Defensive extrusive ectosymbionts of Euplotidium (Ciliophora) that contain microtubule-like structures are bacteria related to Verrucomicrobia

Epixenosomes, ectosymbionts on hypotrich ciliates (genus Euplotidium) defend their host against the ciliate predator Litonotus lamella. Although here only Euplotidium itoi and Euplotidium arenarium from tide pools along a rocky shore near Leghorn (Ligurian sea) were studied in detail, these epibionts are certainly present on specimens of E. itoi and on other Euplotidium species in similar north coastal habitats. The complex life history of epixenosomes has two main stages. In stage I, cells with typical prokaryotic structure divide by binary fission. Stage II cells show complex organization with different cytoplasmic compartments where an extrusive apparatus within a proteinaceous matrix, although not membrane-bounded, differs from the remaining cytoplasm. The ejection process is involved in defense; extrusive apparatus is surrounded by a basket consisting of bundles of tubules. These tubules, 22 ± 3 nm in diameter, delimited by a wall made up of globular structures, are sensitive to inhibitor of tubulin polymerization (nocodazole/4°C temperature) and react positively with different antitubulin antibodies, two of which are monoclonal. The prokaryotic vs. eukaryotic nature of epixenosomes was resolved by comparative sequence analysis of amplified small subunit rRNA genes and in situ hybridization with fluorescently labeled rRNA-targeted polynucleotide probes. These unique ectosymbionts are phylogenetically related to Verrucomicrobia. Epixenosomes represent marine symbionts in this recently discovered division of the Bacteria.

Characterizations of diverse residue clusters in protein three-dimensional structures.

We present new methods for identifying and analyzing statistically significant residue clusters that occur in three-dimensional (3D) protein structures. Residue clusters of different kinds occur in many contexts. They often feature the active site (e.g., in substrate binding), the interface between polypeptide units of protein complexes, regions of protein-protein and protein-nucleic acid interactions, or regions of metal ion coordination. The methods are illustrated with 3D clusters centering on four themes. (i) Acidic or histidine-acidic clusters associated with metal ions. (ii) Cysteine clusters including coordination of metals such as zinc or iron-sulfur structures, cysteine knots prominent in growth factors, multiple sets of buried disulfide pairings that putatively nucleate the hydrophobic core, or cysteine clusters of mostly exposed disulfide bridges. (iii) Iron-sulfur proteins and charge clusters. (iv) 3D environments of multiple histidine residues. Study of diverse 3D residue clusters offers a new perspective on protein structure and function. The algorithms can aid in rapid identification of distinctive sites, suggest correlations among protein structures, and serve as a tool in the analysis of new structures.

Clusters of charged residues in protein three-dimensional structures.

Statistically significant charge clusters (basic, acidic, or of mixed charge) in tertiary protein structures are identified by new methods from a large representative collection of protein structures. About 10% of protein structures show at least one charge cluster, mostly of mixed type involving about equally anionic and cationic residues. Positive charge clusters are very rare. Negative (or histidine-acidic) charge clusters often coordinate calcium, or magnesium or zinc ions [e.g., thermolysin (PDB code: 3tln), mannose-binding protein (2msb), aminopeptidase (1amp)]. Mixed-charge clusters are prominent at interchain contacts where they stabilize quaternary protein formation [e.g., glutathione S-transferase (2gst), catalase (8act), and fructose-1,6-bisphosphate aldolase (1fba)]. They are also involved in protein-protein interaction and in substrate binding. For example, the mixed-charge cluster of aspartate carbamoyl-transferase (8atc) envelops the aspartate carbonyl substrate in a flexible manner (alternating tense and relaxed states) where charge associations can vary from weak to strong. Other proteins with charge clusters include the P450 cytochrome family (BM-3, Terp, Cam), several flavocytochromes, neuraminidase, hemagglutinin, the photosynthetic reaction center, and annexin. In each case in Table 2 we discuss the possible role of the charge clusters with respect to protein structure and function.

Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae.

The diphtheria tox repressor (DtxR) of Corynebacterium diphtheriae plays a critical role in the regulation of diphtheria toxin expression and the control of other iron-sensitive genes. The crystal structures of apo-DtxR and of the metal ion-activated form of the repressor have been solved and used to identify motifs involved in DNA and metal ion binding. Residues involved in binding of the activated repressor to the diphtheria tox operator, glutamine 43, arginine 47, and arginine 50, were located and confirmed by site-directed mutagenesis. Previous biochemical and genetic data can be explained in terms of these structures. Conformational differences between apo- and Ni-DtxR are discussed with regard to the mechanism of action of this repressor.

Resistência à fadiga de tubo API 5L X65 cladeado e soldado circunferencialmente com eletrodos de Inconel® 625

As recentes descobertas de petróleo e gás na camada do Pré-sal representam um enorme potencial exploratório no Brasil, entretanto, os desafios tecnológicos para a exploração desses recursos minerais são imensos e, consequentemente, têm motivado o desenvolvimento de estudos voltados a métodos e materiais eficientes para suas produções. Os tubos condutores de petróleo e gás são denominados de elevadores catenários ou do inglês \"risers\", e são elementos que necessariamente são soldados e possuem fundamental importância nessa cadeia produtiva, pois transportam petróleo e gás natural do fundo do mar à plataforma, estando sujeitos a carregamentos dinâmicos (fadiga) durante sua operação. Adicionalmente, um dos problemas centrais à produção de óleo e gás das reservas do Pré-Sal está diretamente associado a meios altamente corrosivos, tais como H2S e CO2. Uma forma mais barata de proteção dos tubos é a aplicação de uma camada de um material metálico resistente à corrosão na parte interna desses tubos (clad). Assim, a união entre esses tubos para formação dos \"risers\" deve ser realizada pelo emprego de soldas circunferenciais de ligas igualmente resistentes à corrosão. Nesse contexto, como os elementos soldados são considerados possuir defeitos do tipo trinca, para a garantia de sua integridade estrutural quando submetidos a carregamentos cíclicos, é necessário o conhecimento das taxas de propagação de trinca por fadiga da solda circunferencial. Assim, neste trabalho, foram realizados ensaios de propagação de trinca por fadiga na região da solda circunferencial de Inconel® 625 realizada em tubo de aço API 5L X65 cladeado, utilizando corpos de prova do tipo SEN(B) (Single Edge Notch Bending) com relações entre espessura e largura (B/W) iguais a 0,5, 1 e 2. O propósito central deste trabalho foi de obter a curva da taxa de propagação de trinca por fadiga (da/dN) versus a variação do fator de intensidade de tensão (ΔK) para o metal de solda por meio de ensaios normatizados, utilizando diferentes técnicas de acompanhamento e medição da trinca. A monitoração de crescimento da trinca foi feita por três técnicas: variação da flexibilidade elástica (VFE), queda de potencial elétrico (QPE) e análise de imagem (Ai). Os resultados mostraram que as diferentes relações B/W utilizadas no estudo não alteraram significantemente as taxas de propagação de trinca por fadiga, respeitado que a propagação aconteceu em condições de escoamento em pequena escala na frente da trinca. Os resultados de propagação de trinca por fadiga permitiram a obtenção das regiões I e II da curva da/dN versus ΔK para o metal de solda. O valor de ΔKlim obtido para o mesmo foi em torno de 11,8 MPa.m1/2 e os valores encontrados das constantes experimentais C e m da equação de Paris-Erdogan foram respectivamente iguais a 1,55 x10-10 [(mm/ciclo)/(MPa.m1/2)m] e 4,15. A propagação de trinca no metal de solda deu-se por deformação plástica, com a formação de estrias de fadiga.

Control of Redundant Joint Structures Using Image Information During the Tracking of Non-Smooth Trajectories

Visual information is increasingly being used in a great number of applications in order to perform the guidance of joint structures. This paper proposes an image-based controller which allows the joint structure guidance when its number of degrees of freedom is greater than the required for the developed task. In this case, the controller solves the redundancy combining two different tasks: the primary task allows the correct guidance using image information, and the secondary task determines the most adequate joint structure posture solving the possible joint redundancy regarding the performed task in the image space. The method proposed to guide the joint structure also employs a smoothing Kalman filter not only to determine the moment when abrupt changes occur in the tracked trajectory, but also to estimate and compensate these changes using the proposed filter. Furthermore, a direct visual control approach is proposed which integrates the visual information provided by this smoothing Kalman filter. This last aspect permits the correct tracking when noisy measurements are obtained. All the contributions are integrated in an application which requires the tracking of the faces of Asperger children.

Construction of Structures I in Moodle: a new teaching methodology in the Degree of Building Engineer

The subject of Construction of Structures I studies, from a constructive point of view and taking into account current legislation, reinforced concrete structures used in buildings, through the acquisition of knowledge and construction criteria required in the profession of a Technical Architect. The contents acquired in this course are essential for further professional development of technicians and are closely related to many of the subjects taught in the same or other courses of the Degree in Technical Architecture at the University of Alicante. The aim of this paper is to present, analyze and discuss the development of a new methodology proposed in the mentioned subject, as it supposed an important change in the traditional way of teaching Construction and Structures I. In order to incorporate new teaching tools in 2013-2014, the course has been implemented by using a Moodle software tool to promote blended learning with online exercises. Our Moodle community allows collaborative work within an open-source platform where teachers and students share a new and personalized learning environment. Students are easily used to the interface and the platform, value the constant connection with teachers or other fellows and completely agree with the possibility of making questions or share documents 24 hours a day. The proposed methodology consists of lectures and practical classes. In the lectures, the basics of each topic are discussed; class attendance, daily study and conducting scheduled exercises are indispensable. Practical classes allow to consolidate the knowledge gained in theory classes by solving professional exercises and actual construction problems related to structures, that shall be compulsorily delivered online. So, after the correction of the teacher and the subsequent feedback of students, practical exercises ensure lifelong learning of the student, who can download any kind of material at any time (constructive details, practical exercises and even corrected exams). Regarding the general evaluation system, goals achievement is assessed on an ongoing basis (65% of the final mark) along the course through written and graphic evidences in person and online, as well as a individual development of a workbook. In all cases, the acquisition of skills, the ability to synthesize, the capacity of logical and critical thinking are assessed. The other 35 % of the mark is evaluated by a complementary graphic exam. Participation in the computing platform is essential and the student is required to do and present, at least 90% of the practices proposed. Those who do not comply with the practices in each specific date could not be assessed continuously and may only choose the final exam. In conclusion, the subject of Construction of Structures I is essential in the development of the regulated profession of Technical Architect as they are considered, among other professional profiles, as specialists in construction of building structures. The use of a new communication platform and online teaching allows the acquisition of knowledge and constructive approaches in a continuous way, with a more direct and personal monitoring by the teacher that has been highly appreciated by almost 100% of the students. Ultimately, it is important to say that the use of Moodle in this subject is a very interesting tool, which was really well welcome by students in one of the densest and important subjects of the Degree of Technical Architecture.

In situ damage detection in frame structures through coupled response measurements

Due to the existence of global modes and local modes of the neighbouring members, damage detection on a structure is more challenging than damage on isolated beams. Detection of an artificial circumferential crack on a joint in a frame-like welded structure is studied in this paper using coupled response measurements. Similarity to real engineering structures is maintained in the fabrication of the test frame. Both the chords and the branch members have hollow sections and the branch members have smaller sizes. The crack is created by a hacksaw on a joint where a branch meets the chord. The methodology is first demonstrated on a single hollow section beam. The test results are then presented for the damaged and undamaged frame. The existence of the damage is clearly observable from the experimental results. It is suggested that this approach offers the-potential to detect damage in welded structures such as cranes, mining equipment, steel-frame bridges, naval and offshore structures. (C) 2003 Elsevier Ltd. All rights reserved.

Towards identifying the new structures formed on the γ-radiolysis of Ultem

Ultem irradiated up to 10.0 MGy has been analysed using C-13, H-1 and D-2 proton-carbon and proton-proton correlation NMR spectroscopy to shed light on the formation of new structures. Chemical shifts and correlation data were used to determine the structure or partial structures of several new components. The spectra indicated the presence of new groups and structures involving the isopropylidene group, the imide ring, and hydrogen-abstraction reactions. Possible pathways for formation of the new structures are proposed and the G-values for their formation have been estimated. (C) 2003 Elsevier Science Ltd. All rights reserved.

Potent cyclic antagonists of the complement C5a receptor on human polymorphonulcear leukocytes. Relationships between structures and activity

Human C5a is a plasma protein with potent chemoattractant and pro-inflammatory properties, and its overexpression correlates with severity of inflammatory diseases. C5a binds to its G protein-coupled receptor (C5aR) on polymorphonuclear leukocytes (PMNLs) through a high-affinity helical bundle and a low-affinity C terminus, the latter being solely responsible for receptor activation. Potent and selective C5a antagonists are predicted to be effective anti-inflammatory drugs, but no pharmacophore for small molecule antagonists has yet been developed, and it would significantly aid drug design. We have hypothesized that a turn conformation is important for activity of the C terminus of C5a and herein report small cyclic peptides that are stable turn mimics with potent antagonism at C5aR on human PMNLs. A comparison of solution structures for the C terminus of C5a, small acyclic peptide ligands, and cyclic antagonists supports the importance of a turn for receptor binding. Competition between a cyclic antagonist and either C5a or an acyclic agonist for C5aR on PMNLs supports a common or overlapping binding site on the C5aR. Structure-activity relationships for 60 cyclic analogs were evaluated by competitive radioligand binding with C5a (affinity) and myeloperoxidase release (antagonist potency) from human PMNLs, with 20 compounds having high antagonist potencies (IC50, 20 nM(-1) muM). Computer modeling comparisons reveal that potent antagonists share a common cyclic backbone shape, with affinity-determining side chains of defined volume projecting from the cyclic scaffold. These results define a new pharmacophore for C5a antagonist development and advance our understanding of ligand recognition and receptor activation of this G protein-coupled receptor.

Fatigue in rubber vulcanisates

A study has been made of the effect of single extensions and continuous fatigue on the structures of various natural rubber networks. The change in network structure of a conventional vulcanisate on a single extension manifests itself as permanent set. The change in network structure has been assessed by the use of the chemical probes, propan-2-thiol/piperidine, hexane-thiol/piperidine and triphenyl phosphine, which determine the polysulphide and disulphide crosslink densities and main chain modification respectively. The permanent set induced on a single extension of a conventional sulphur vulcanisate has been shown to result from the destruction and reformation of polysulphide crosslinks. The magnitude of the effect was dependent upon the degree of extension and showed a maximum at extensions corresponding to the onset of stress-induced crystallisation. The incorporation of a reinforcing filler, HAF-carbon black, magnified the effect. Vulcanisates that possessed only mono and disulphide crosslinks did not show any significant permanent set. The continuous changes in network structure during fatigue have also been determined, and the effects of carbon black and antioxidants on these changes and the fatigue life have been assessed. During fatigue the overall crosslink density increased slightly, which resulted from the destruction of polysulphide crosslinks. and their replacement by principally disulphide crosslinks. Antioxidants reduced the rate of destruction of polysulphide crosslinks and increased the fatigue life of the rubber network. The fatigue life of the network also depended upon the concentration of free chain ends. These chain ends were incorporated into the network by masticating rubber under nitrogen in the presence of bis (diisopropyl)thiophosphoryl disulphide, which improved the fatigue resistance by up to 9%.

System identification of linear vibrating structures

Methods of dynamic modelling and analysis of structures, for example the finite element method, are well developed. However, it is generally agreed that accurate modelling of complex structures is difficult and for critical applications it is necessary to validate or update the theoretical models using data measured from actual structures. The techniques of identifying the parameters of linear dynamic models using Vibration test data have attracted considerable interest recently. However, no method has received a general acceptance due to a number of difficulties. These difficulties are mainly due to (i) Incomplete number of Vibration modes that can be excited and measured, (ii) Incomplete number of coordinates that can be measured, (iii) Inaccuracy in the experimental data (iv) Inaccuracy in the model structure. This thesis reports on a new approach to update the parameters of a finite element model as well as a lumped parameter model with a diagonal mass matrix. The structure and its theoretical model are equally perturbed by adding mass or stiffness and the incomplete number of eigen-data is measured. The parameters are then identified by an iterative updating of the initial estimates, by sensitivity analysis, using eigenvalues or both eigenvalues and eigenvectors of the structure before and after perturbation. It is shown that with a suitable choice of the perturbing coordinates exact parameters can be identified if the data and the model structure are exact. The theoretical basis of the technique is presented. To cope with measurement errors and possible inaccuracies in the model structure, a well known Bayesian approach is used to minimize the least squares difference between the updated and the initial parameters. The eigen-data of the structure with added mass or stiffness is also determined using the frequency response data of the unmodified structure by a structural modification technique. Thus, mass or stiffness do not have to be added physically. The mass-stiffness addition technique is demonstrated by simulation examples and Laboratory experiments on beams and an H-frame.

Elastic-plastic analysis of complete building structures

In this Thesis, details of a proposed method for the elastic-plastic failure load analysis of complete building structures are given. In order to handle the problem, a computer programme in Atlas Autocode is produced. The structures consist of a number of parallel shear walls and intermediate frames connected by floor slabs. The results of an experimental investigation are given to verify the theoretical results and to demonstrate various factors that may influence the behaviour of these structures. Large full scale practical structures are also analysed by the proposed method and suggestions are made for achieving design economy as well as for extending research in various aspects of this field. The existing programme for elastic-plastic analysis of large frames is modified to allow for the effect of composite action of structural members, i.e. reinforced concrete floor slabs and the supporting steel beams. This modified programme is used to analyse some framed type structures with composite action as well as those which incorporate plates and shear walls. The results obtained are studied to ascertain the influence of composite action and other factors on the load carrying capacity of both bare frames and complete building structures. The theoretical failure load presented in this thesis does not predict the overall failure load of the structure nor does it predict the partial failure load of the shear walls and slabs but it merely predicts the partial failure load of a single frame and assumes that the loss of stiffess of such a frame renders the overall structure unusable. For most structures the analysis proposed in this thesis is likely to break down prematurely due to the failure of the slab and shear wall system and this factor must be taken into account in any future work on such structures. The experimental work reported in this thesis is acknowledged to be unsatisfactory as a verification of the limited theory proposed. In particular perspex was not found to be a suitable material for testing at high loads, micro-concrete may be more suitable.