Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

I. The Superstition Hills, California, earthquakes of 24 November 1987. II. Three-dimensional velocity structure of southern California.

Part 1 of this thesis is about the 24 November, 1987, Superstition Hills earthquakes. The Superstition Hills earthquakes occurred in the western Imperial Valley in southern California. The earthquakes took place on a conjugate fault system consisting of the northwest-striking right-lateral Superstition Hills fault and a previously unknown Elmore Ranch fault, a northeast-striking left-lateral structure defined by surface rupture and a lineation of hypocenters. The earthquake sequence consisted of foreshocks, the M_s 6.2 first main shock, and aftershocks on the Elmore Ranch fault followed by the M_s 6.6 second main shock and aftershocks on the Superstition Hills fault. There was dramatic surface rupture along the Superstition Hills fault in three segments: the northern segment, the southern segment, and the Wienert fault.

In Chapter 2, M_L≥4.0 earthquakes from 1945 to 1971 that have Caltech catalog locations near the 1987 sequence are relocated. It is found that none of the relocated earthquakes occur on the southern segment of the Superstition Hills fault and many occur at the intersection of the Superstition Hills and Elmore Ranch faults. Also, some other northeast-striking faults may have been active during that time.

Chapter 3 discusses the Superstition Hills earthquake sequence using data from the Caltech-U.S.G.S. southern California seismic array. The earthquakes are relocated and their distribution correlated to the type and arrangement of the basement rocks. The larger earthquakes occur only where continental crystalline basement rocks are present. The northern segment of the Superstition Hills fault has more aftershocks than the southern segment.

An inversion of long period teleseismic data of the second mainshock of the 1987 sequence, along the Superstition Hills fault, is done in Chapter 4. Most of the long period seismic energy seen teleseismically is radiated from the southern segment of the Superstition Hills fault. The fault dip is near vertical along the northern segment of the fault and steeply southwest dipping along the southern segment of the fault.

Chapter 5 is a field study of slip and afterslip measurements made along the Superstition Hills fault following the second mainshock. Slip and afterslip measurements were started only two hours after the earthquake. In some locations, afterslip more than doubled the coseismic slip. The northern and southern segments of the Superstition Hills fault differ in the proportion of coseismic and postseismic slip to the total slip.

The northern segment of the Superstition Hills fault had more aftershocks, more historic earthquakes, released less teleseismic energy, and had a smaller proportion of afterslip to total slip than the southern segment. The boundary between the two segments lies at a step in the basement that separates a deeper metasedimentary basement to the south from a shallower crystalline basement to the north.

Part 2 of the thesis deals with the three-dimensional velocity structure of southern California. In Chapter 7, an a priori three-dimensional crustal velocity model is constructed by partitioning southern California into geologic provinces, with each province having a consistent one-dimensional velocity structure. The one-dimensional velocity structures of each region were then assembled into a three-dimensional model. The three-dimension model was calibrated by forward modeling of explosion travel times.

In Chapter 8, the three-dimensional velocity model is used to locate earthquakes. For about 1000 earthquakes relocated in the Los Angeles basin, the three-dimensional model has a variance of the the travel time residuals 47 per cent less than the catalog locations found using a standard one-dimensional velocity model. Other than the 1987 Whittier earthquake sequence, little correspondence is seen between these earthquake locations and elements of a recent structural cross section of the Los Angeles basin. The Whittier sequence involved rupture of a north dipping thrust fault bounded on at least one side by a strike-slip fault. The 1988 Pasadena earthquake was deep left-lateral event on the Raymond fault. The 1989 Montebello earthquake was a thrust event on a structure similar to that on which the Whittier earthquake occurred. The 1989 Malibu earthquake was a thrust or oblique slip event adjacent to the 1979 Malibu earthquake.

At least two of the largest recent thrust earthquakes (San Fernando and Whittier) in the Los Angeles basin have had the extent of their thrust plane ruptures limited by strike-slip faults. This suggests that the buried thrust faults underlying the Los Angeles basin are segmented by strike-slip faults.

Earthquake and explosion travel times are inverted for the three-dimensional velocity structure of southern California in Chapter 9. The inversion reduced the variance of the travel time residuals by 47 per cent compared to the starting model, a reparameterized version of the forward model of Chapter 7. The Los Angeles basin is well resolved, with seismically slow sediments atop a crust of granitic velocities. Moho depth is between 26 and 32 km.

Stress distribution in delayed replanted teeth splinted with different orthodontic wires: a three-dimensional finite element analysis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

An in vitro study showing the three-dimensional microenvironment influence over the behavior of head and neck squamous cell carcinoma

Objectives: The Head and Neck Squamous Cell Carcinoma (HNSCC) ranks sixth worldwide. The mechanisms of growth, invasion and metastasis of this pathology are extensively studied and generally related to specific variations in signaling pathways like the PI3K-Akt; however most of these competent studies have been performed bidimensionally, which may hide important questions. This study sought to analyze the influence of the microenvironment upon the behavior of HNSCC. Study Design: The status of pAkt, NF-kappa B and Cyclin D1 proteins was accessed through immunofluorescence and western blot methods in HNSCC cell lines originating from tongue, pharynx and metastatic lymph node when submitted to a three-dimensional culture model utilizing a matrix system. A bidimensional culture model (monolayer) was used as control. Results: The HNSCC cell lines cultured three-dimensionally exhibited a growth pattern characterized by small isolated islands, different from the control group. When the three-dimensional model was applied, two of the studied cell lines showed the same expression pattern as the bidimensional model regarding nuclear or cytoplasmatic localization, as well as reduction of all protein levels; however, the cell line originated from tongue, which specially has the epidermal growth factor receptor constitutively activated, demonstrated nuclear translocation of pAkt and also an increase in the levels of Cyclin D1. Conclusions: The results suggest the influence of the microenvironment upon the behavior of HNSCC cells due to the changed expression of proteins related to tumor growth and cellular invasion. Furthermore, intrinsically genetic conditions also played important roles over the cells, despite the culture model employed.

Three-dimensional printing for perioperative planning of complex aortic arch surgery

Purpose In this study, we show the use of three-dimensional printing models for preoperative planning of surgery for patients with complex aortic arch anomalies. Description A 70-year-old man with an extensively arteriosclerotic aneurysm reaching from the ascending aorta to the descending aorta was referred to our center for complete aortic arch replacement. We visualized and reconstructed computed tomography data of the patient and fabricated a flexible three-dimensional model of the aortic arch including the aneurysm. Evaluation This model was very helpful for the preoperative decision making and planning of the frozen elephant trunk procedure owing to the exact and lifelike illustration of the native aortic arch. Conclusions Three-dimensional models are helpful in preoperative planning and postoperative evaluation of frozen elephant trunk procedures in patients with complex aortic anatomy.

A three dimensional numerical investigation of hillslope flow processes

Physically based distributed models of catchment hydrology are likely to be made available as engineering tools in the near future. Although these models are based on theoretically acceptable equations of continuity, there are still limitations in the present modelling strategy. Of interest to this thesis are the current modelling assumptions made concerning the effects of soil spatial variability, including formations producing distinct zones of preferential flow. The thesis contains a review of current physically based modelling strategies and a field based assessment of soil spatial variability. In order to investigate the effects of soil nonuniformity a fully three dimensional model of variability saturated flow in porous media is developed. The model is based on a Galerkin finite element approximation to Richards equation. Accessibility to a vector processor permits numerical solutions on grids containing several thousand node points. The model is applied to a single hillslope segment under various degrees of soil spatial variability. Such variability is introduced by generating random fields of saturated hydraulic conductivity using the turning bands method. Similar experiments are performed under conditions of preferred soil moisture movement. The results show that the influence of soil variability on subsurface flow may be less significant than suggested in the literature, due to the integrating effects of three dimensional flow. Under conditions of widespread infiltration excess runoff, the results indicate a greater significance of soil nonuniformity. The recognition of zones of preferential flow is also shown to be an important factor in accurate rainfall-runoff modelling. Using the results of various fields of soil variability, experiments are carried out to assess the validity of the commonly used concept of `effective parameters'. The results of these experiments suggest that such a concept may be valid in modelling subsurface flow. However, the effective parameter is observed to be event dependent when the dominating mechanism is infiltration excess runoff.

COMPUTER assisted technologies to enhance CONCURRENce in building DESIGN

Modern organisms are adapted to a wide variety of habitats and lifestyles. The processes of evolution have led to complex, interdependent, well-designed mechanisms of todays world and this research challenge is to transpose these innovative solutions to resolve problems in the context of architectural design practice, e.g., to relate design by nature with design by human. In a design by human environment, design synthesis can be performed with the use of rapid prototyping techniques that will enable to transform almost instantaneously any 2D design representation into a physical three-dimensional model, through a rapid prototyping printer machine. Rapid prototyping processes add layers of material one on top of another until a complete model is built and an analogy can be established with design by nature where the natural lay down of earth layers shapes the earth surface, a natural process occurring repeatedly over long periods of time. Concurrence in design will particularly benefit from rapid prototyping techniques, as the prime purpose of physical prototyping is to promptly assist iterative design, enabling design participants to work with a three-dimensional hardcopy and use it for the validation of their design-ideas. Concurrent design is a systematic approach aiming to facilitate the simultaneous involvment and commitment of all participants in the building design process, enabling both an effective reduction of time and costs at the design phase and a quality improvement of the design product. This paper presents the results of an exploratory survey investigating both how computer-aided design systems help designers to fully define the shape of their design-ideas and the extent of the application of rapid prototyping technologies coupled with Internet facilities by design practice. The findings suggest that design practitioners recognize that these technologies can greatly enhance concurrence in design, though acknowledging a lack of knowledge in relation to the issue of rapid prototyping.

O modelo tridimensional físico e seu papel na educação patrimonial

Este artigo versa sobre uma pesquisa integrante do Núcleo de Apoio à Pesquisa em Estudos de Linguagem em Arquitetura e Cidade (N.ELAC), que desenvolve pesquisas em Linguagem e Representação. Entre as diversas formas de representação em arquitetura, a presente pesquisa traz o modelo tridimensional físico como ferramenta que proporciona maior facilidade de leitura do projeto, sendo mais concreta que os desenhos técnicos. Objetiva-se, assim, destacar a importância do modelo físico como meio de aproximação da população ao patrimônio arquitetônico. Como estudo de caso, foi escolhido o Edifício E1, obra de Ernest Mange e Hélio Duarte. Localizado no campus da USP em São Carlos, é considerado patrimônio da cidade, entretanto, encontra-se praticamente enclausurado no interior do campus, dificultando maior contato da comunidade com o edifício. O projeto do edifício utilizou apenas o desenho como representação, não incluindo nenhum tipo de modelo tridimensional (físico ou digital). A partir de um levantamento das representações gráficas utilizadas pelos projetistas, foi possível fazer uma comparação entre o nível de compreensão do projeto apenas com as peças gráficas dos arquitetos e a partir do modelo físico, produzido pela pesquisadora. Foi realizado um pré-teste em escola pública municipal, despertando o interesse desses alunos pelo edifício em questão.

O uso da maquete física como ferramenta de leitura do patrimônio cultural

O presente artigo vincula-se às pesquisas do Núcleo de Apoio à Pesquisa em Estudos de Linguagem em Arquitetura e Cidade (N.ELAC), que atua na área de Linguagem e Representação. Diante das diversas formas de representação em arquitetura (desenho, maquete, modelos digitais), nesta pesquisa o modelo tridimensional físico é trazido como ferramenta que proporciona maior facilidade de leitura do projeto e tratado como meio de aproximação da comunidade ao patrimônio arquitetônico, envolvendo, sobretudo, a arquitetura moderna paulista. Como estudo de caso, escolheu-se o Edifício E1, obra de Ernest Mange e Hélio Duarte. Localizado no campus da USP em São Carlos, é considerado patrimônio da cidade, entretanto, encontra-se praticamente enclausurado no interior do campus, dificultando maior contato da comunidade com o edifício. Durante sua execução, foi utilizado apenas o desenho como ferramenta de representação de projeto, não incluindo nenhum tipo de modelo tridimensional (físico ou digital). A partir do levantamento das representações gráficas utilizadas, foi possível fazer uma comparação entre o nível de compreensão do projeto apenas com as peças gráficas dos arquitetos e a partir do modelo físico, produzido pela pesquisadora. Realizou-se um pré-teste em escola pública municipal, que indicou um aumento no interesse desses alunos pelo edifício em questão.

O uso de modelos nos processos projetuais contemporâneos

Durante o processo de projeto, o arquiteto transpõe suas ideias para o campo real, do concreto. Os diversos modos de expressão e representação têm como função mediar essa interação, diminuindo a distância entre esses dois campos. Vive-se hoje, um momento de intensa transformação das estratégias projetuais, propiciada pelos novos meios digitais. Assim, esta pesquisa, centra-se na comparação entre diversos momentos do uso de modelos nos processos projetivos contemporâneos, através de uma investigação em escritórios de arquitetura paulistanos que utilizam o modelo físico como parte de seus processos de projeto. Busca-se entender qual o papel dessa ferramenta de representação e suas potencialidades nos dias atuais. Como estudo de caso, faz-se uma análise comparativa entre o uso das maquetes digital e física, destacando dois estudos: a maquete do Conjunto Ponte dos Remédios, do arquiteto Marcos Acayaba e as maquetes de estudos elaboradas pelo escritório Andrade Morettin Arquitetos, para o concurso para o Instituto Moreira Salles/SP. Entre os objetivos desse trabalho também se encontra uma análise da contribuição dos modelos físicos no Ensino de Arquitetura.

O uso do modelo físico e digital nos processos de projeto da arquitetura contemporânea

Durante o processo de projeto, o arquiteto transpõe suas ideias para o campo real, do concreto. Os diversos modos de expressão e representação têm como função mediar essa interação, diminuindo a distância entre esses dois campos. Vive-se hoje, um momento de intensa transformação das estratégias projetuais, propiciadas pelos novos meios digitais. Esta pesquisa tem como objetivo o estudo do uso das representações tridimensionais, especificamente dos modelos físicos e digitais. Pretende-se flagrar os momentos contributivos dos modelos no processo projetivo e as características intrínsecas a eles. A discussão busca não apenas destacar a importância dessa ferramenta, como também, traçar uma breve comparação entre a tecnologia digital e a feitura manual. Para este trabalho foram selecionados alguns arquitetos significativos do cenário da arquitetura paulista em cujos projetos comparecem o uso de modelos. Como estudos de caso tem-se a Residência do arquiteto Marcos Acayaba e o projeto vencedor do Concurso para o Instituto Moreira Salles/ SP, do escritório Andrade Morettin Arquitetos. Soma-se a estes objetivos, a apresentação do uso de modelos físicos e digitais em uma experiência didática projetiva.

Seasonal and interannual variability of primary and export production in the South China Sea: a three-dimensional physical-biogeochemical model study

To investigate the seasonal and interannual variations in biological productivity in the South China Sea (SCS), a Pacific basin-wide physical - biogeochemical model has been developed and used to estimate the biological productivity and export flux in the SCS. The Pacific circulation model, based on the Regional Ocean Model Systems (ROMS), is forced with daily air-sea fluxes derived from the NCEP (National Centers for Environmental Prediction) reanalysis between 1990 and 2004. The biogeochemical processes are simulated with a carbon, Si(OH)(4), and nitrogen ecosystem (CoSiNE) model consisting of silicate, nitrate, ammonium, two phytoplankton groups (small phytoplankton and large phytoplankton), two zooplankton grazers (small micrograzers and large mesozooplankton), and two detritus pools. The ROMS-CoSiNE model favourably reproduces many of the observed features, such as ChI a, nutrients, and primary production (PP) in the SCS. The modelled depth-integrated PP over the euphotic zone (0-125 m) varies seasonally, with the highest value of 386 mg C m (-2) d (-1) during winter and the lowest value of 156 mg C m (-2) d (-1) during early summer. The annual mean value is 196 mg C m (-2) d (-1). The model-integrated annual mean new production (uptake of nitrate), in carbon units, is 64.4 mg C m (-2) d (-1) which yields an f-ratio of 0.33 for the entire SCS. The modelled export ratio (e-ratio: the ratio of export to PP) is 0.24 for the basin-wide SCS. The year-to-year variation of biological productivity in the SCS is weaker than the seasonal variation. The large phytoplankton group tends to dominate over the smaller phytoplankton group, and likely plays an important role in determining the interannual variability of primary and new production.

A three-dimensional coupled physical-biological model study in the spring of 1993 in the Bohai Sea of China

A three-dimensional (3-D) coupled physical and biological model was used to investigate the physical processes and their influence on the ecosystem dynamics of the Bohai Sea of China. The physical processes include M-2 tide, time - varying wind forcing and river discharge. Wind records from I to 31 May in 1993 were selected to force the model. The biological model is based on a simple, nitrate and phosphate limited, lower trophic food web system. The simulated results showed that variation of residual currents forced by M, tide, river discharge and time-varying wind had great impact on the distribution of phytoplankton biomass in the Laizhou Bay. High phytoplankton biomass appeared in the upwelling region. Numerical experiments based on the barotropic model and baroclinic model with no wind and water discharge were also conducted. Differences in the results by the baroclinic model and the barotropic model were significant: more patches appeared in the baroclinic model comparing with the barotropic model. And in the baroclinic model, the subsurface maximum phytoplankton biomass patches formed in the stratified water.

The Displacement and Strain Field of Three-Dimensional Rheologic Model of Earthquake Preparation

Based on the three-dimensional elastic inclusion model proposed by Dobrovolskii, we developed a rheological inclusion model to study earthquake preparation processes. By using the Corresponding Principle in the theory of rheologic mechanics, we derived the analytic expressions of viscoelastic displacement U(r, t) , V(r, t) and W(r, t), normal strains epsilon(xx) (r, t), epsilon(yy) (r, t) and epsilon(zz) (r, t) and the bulk strain theta (r, t) at an arbitrary point (x, y, z) in three directions of X axis, Y axis and Z axis produced by a three-dimensional inclusion in the semi-infinite rheologic medium defined by the standard linear rheologic model. Subsequent to the spatial-temporal variation of bulk strain being computed on the ground produced by such a spherical rheologic inclusion, interesting results are obtained, suggesting that the bulk strain produced by a hard inclusion change with time according to three stages (alpha, beta, gamma) with different characteristics, similar to that of geodetic deformation observations, but different with the results of a soft inclusion. These theoretical results can be used to explain the characteristics of spatial-temporal evolution, patterns, quadrant-distribution of earthquake precursors, the changeability, spontaneity and complexity of short-term and imminent-term precursors. It offers a theoretical base to build physical models for earthquake precursors and to predict the earthquakes.

Three-Dimensional Network Model And Its Parameter Calibration

A material model, whose framework is parallel spring-bundles oriented in 3-D space, is proposed. Based on a discussion of the discrete schemes and optimum discretization of the solid angles, a 3-D network cell consisted of one-dimensional components is developed with its geometrical and physical parameters calibrated. It is proved that the 3-D network model is able to exactly simulate materials with arbitrary Poisson ratio from 0 to 1/2, breaking through the limit that the previous models in the literature are only suitable for materials with Poisson ratio from 0 to 1/3. A simplified model is also proposed to realize high computation accuracy within low computation cost. Examples demonstrate that the 3-D network model has particular superiority in the simulation of short-fiber reinforced composites.