<p>Structural bioinformatics deals with the analysis, classification and prediction of three-dimensional structures of biomacromolecules. It is becoming increasingly important as the number of structures is growing rapidly. This thesis describes three studies concerned with protein-function prediction and two studies about protein structure validation.</p><p>New protein structures are often compared to known structures to find out if they have a known fold, which may provide hints about their function. The functionality and performance of eleven fold-comparison servers were evaluated. None of the tested servers achieved perfect recall, so in practise a combination of servers should be used.</p><p>If fold comparison does not provide any hints about the function of a protein, structural motif searches can be employed. A survey of left-handed helices in known protein structures was carried out. The results show that left-handed helices are rare motifs, but most of them occur in active or ligand-binding sites. Their identification can therefore help to pinpoint potentially important residues.</p><p>Sometimes all available methods fail to provide hints about the function of a protein. Therefore, the potential of using docking techniques to predict which ligands are likely to bind to a particular protein has been investigated. Initial results show that it will be difficult to build a reliable automated docking protocol that will suit all proteins.</p><p>The effect of various phenomena on the precision of accessible surface area calculations was also investigated. The results suggest that it is prudent to report such values with a precision of 50 to 100 Ų.</p><p>Finally, a survey of register shifts in known protein structures was carried out. The identified potential register shifts were analysed and classified. A machine-learning approach ("rough sets") was used in an attempt to diagnose register errors in structures.</p>

<p>This thesis uses geodetic satellite data to measure present-day crustal deformation in the Zagros fold-thrust belt (SW Iran). Geodetic-type measurements are also used in down-scaled models that simulate the surface deformations seen in convergent settings like the Zagros fold-thrust belt.</p><p>Global Positioning System (GPS) measurements of three surveys between 1998 and 2001 indicate 9 ± 3 mm/yr and 5 ± 3 mm/yr shortening across the SE and NW Zagros respectively. GPS results show that in addition to the different rates and directions of shortening on either side of the NS trending Kazerun fault, local along-belt extension occurs to the east. </p><p>Differential SAR interferograms of ERS1 & 2 images between 1992 and 1999 detect 8 ± 4 mm/yr uplift rate across a newly recognized fault in SW Qeshm Island. This can be attributed to a steep imbricate thrust that may still represent the local Zagros deformation front.</p><p>The salt diapirs in the Zagros rise from a source layer that acts as a low-frictional decollement that decouples the deformation of the cover sediments from their basement in the eastern Zagros whereas the cover to the west deforms above a high-friction decollement. Physical models were prepared to simulate cover deformation in the Zagros by shortening a sand pack above adjacent high- and low-frictional decollements (represented by a ductile layer). The strain distributions differed above the two types of decollements; it was more heterogeneous above the salt where local extension in the shortening direction was dominant. A separate work also investigated systematically the role of basal friction on cover deformation in convergent settings. Accurate height measurements of the model surface by laser-scanner indicated a deformation front more distal than usual, particularly in the low-basal frictional models. The volume reduction in our shortened sand models correlated directly with their basal friction.</p>

Introduction et objectifs La microchirurgie des pathologies cordales bénignes est une chirurgie fonctionnelle dont le but est daméliorer les caractéristiques mécaniques du vibrateur laryngé. Une connaissance approfondie de la structure cordale normale, de ses altérations pathologiques et des implications bio-mécaniques de la structure tissulaire, est indispensable à la réalisation dune microchirurgie cordale de qualité. Cest grâce aux connaissances de plus en plus approfondies de la structure cordale normale et surtout de son tissu conjonctif, la lamina propria, que la microchirurgie cordale a évolué dune chirurgie de résection pure et simple à une chirurgie fonctionnelle. Cest la partie la plus superficielle de la lamina propria, lespace de Reinke, qui joue le rôle le plus important dans la production du son. Cest aussi lespace de Reinke qui est occupé, détruit ou remanié en cas de pathologie cordale bénigne. La microchirurgie vise à le libérer du processus pathologique. Cest en augmentant la souplesse tissulaire et la fermeture glottique en phonation que le micro-chirurgien espère améliorer les caractéristiques du son laryngé émis. Loriginalité de ce travail est de tenter, non seulement de libérer lespace vibrant de la lésion cordale, mais aussi de modifier les processus cicatriciels post-opératoires par lutilisation dun implant résorbable dacide hyaluronique estérifié. Les objectifs de ce travail sont : - de contribuer à la connaissance des résultats fonctionnels laryngés et vocaux que lon peut attendre dune microchirurgie cordale - dévaluer limpact fonctionnel, sur ces résultats, de lutilisation dun implant résorbable dacide hyaluronique estérifié, en fin dintervention chirurgicale. Caractéristiques méthodologiques Ce travail est une étude clinique, prospective et comparative. Lutilisation dun implant résorbable dacide hyaluronique estérifié en fin dintervention microchirurgicale est une technique originale développée depuis février 2003 et que nous continuons à pratiquer. Les arguments qui ont conduit à implanter de lacide hyaluronique estérifié au sein de lespace de Reinke de certaines cordes opérées, sont été exposés. Le résultat fonctionnel laryngé et vocal obtenu chez 33 patients opérés de différentes lésions cordales bénignes et traités par implantation dacide hyaluronique estérifié dans la plaie microchirurgicale en fin dintervention (groupe implanté), est comparé à celui de 50 patients également opérés de lésions cordales bénignes mais qui ne bénéficient pas dune implantation dacide hyaluronique estérifié (groupe non-implanté). Les patients ont été opérés entre février 2003 et décembre 2006. Deux études statistiques distinctes ont été pratiquées : 1) une analyse de variance comparant les données préopératoires aux données postopératoires immédiates 2) Les observations différées (en dehors de la période post-opératoire immédiate) sont analysées par une étude statistique corrélationnelle. Résultats La microchirurgie cordale des lésions bénignes savère être une chirurgie fonctionnelle efficace : elle améliore rapidement, dès le premier examen post-opératoire, la qualité vocale et le rendement phonatoire des patients opérés, et ce dans les deux groupes. Nos observations vidéo-stroboscopiques postopératoires précoces plaident en faveur de caractéristiques visco-élastiques favorables de limplant dacide hyaluronique estérifié. Si ce dernier sétait avéré trop visqueux ou trop rigide, nous aurions observé une absence dondulation muqueuse ou une détérioration de celle-ci lors du premier contrôle postopératoire. Mais une des originalités de notre travail est de réaliser un suivi clinique à long terme de lévolution vocale et laryngée de nos patients. Celle-ci est analysée par une étude statistique corrélationnelle non paramétrique. Un comportement très différent est observé: le groupe de patients implantés continue daméliorer 10 variables sur les 20 variables évaluées et quantifiées, alors que le groupe non-implanté naméliore significativement quune seule variable. Autrement dit, le groupe implanté manifeste une évolution significative et favorable au fil du temps, bien au-delà de la période post-opératoire immédiate. Le groupe contrôle, quant à lui, ne témoigne daucune évolution des paramètres vocaux et laryngés quantifiés lors de ce suivi à long terme. Lexplication de cette évolution différente pourrait être une atteinte plus sévère du groupe implanté, et donc une amélioration plus lente des paramètres vocaux et laryngés. Cela pourrait expliquer partiellement lévolution de G, R, S, I et des caractéristiques stroboscopiques droites qui étaient moins bonnes au sein du groupe implanté lors de lexamen pré-opératoire. Mais cette vision nous paraît insuffisante et réductrice : certaines variables étaient altérées de manière équivalente dans les deux groupes lors de lexamen préopératoire et névoluent favorablement quau sein du groupe implanté. Mais surtout, les deux groupes évoluent de la même manière lors du premier examen post-opératoire (analyse de variance des résultats post-opératoires immédiats, cf plus haut). Le groupe contrôle nest certes pas « normalisé » après la microchirurgie et sil ne sagissait que dune évolution retardée, elle devrait également sobserver dans le groupe contrôle. On peut donc raisonnablement envisager une action favorable de lacide hyaluronique estérifié sur le processus de cicatrisation intratissulaire : une lente amélioration de la souplesse de la couverture cordale se fait jour, grâce à une reconstitution au moins partielle dune matrice extracellulaire par des fibroblastes dont le phénotype a été modifié par la présence dun taux élevé dacide hyaluronique au sein de la plaie microchirurgicale. Nous pourrions donc expliquer lévolution particulière de notre groupe implanté par un véritable processus régénératif au sein de lespace de Reinke. Ce processus ne peut être que lent, connaissant le caractère pauci-cellulaire de cette couche tissulaire, et donc nest pas perceptible lors du premier contrôle post-opératoire : à ce moment, les deux groupes évoluent de manière identique. Conclusions Loriginalité de notre travail réside dans lutilisation dun dérivé dacide hyaluronique afin de moduler le processus de cicatrisation post-opératoire : cest la première fois que ce type de technique est mis en oeuvre, les travaux précédemment publiés par dautres auteurs ne portant que sur des études in vitro ou sur modèles animaux. Notre travail constitue dès lors un premier pas vers une microchirurgie cordale non pas seulement fonctionnelle, mais aussi régénérative. En effet, nous nous sommes appuyés sur linfluence bénéfique que peut exercer la composition de la matrice extracellulaire sur le fonctionnement cellulaire cordal. Les résultats obtenus sont très intéressants puisquils montrent une amélioration post-opératoire, non seulement précoce mais aussi retardée, chez des patients implantés dont la souplesse cordale était, en phase pré-opératoire, sévèrement altérée. Lamélioration continue observée, au fil dune longue période de temps, chez les seuls patients implantés, est à nos yeux le résultat le plus surprenant et le plus enthousiasmant. Cette observation constitue un argument important en faveur dun processus de cicatrisation régénératif dans lespace de Reinke traité par notre technique originale dimplantation dacide hyaluronique estérifié. Notre travail nous a permis dappréhender la complexité de la structure et de la physiologie tissulaire cordale. Il soulève aussi de nombreuses questions qui dans lavenir, doivent faire lobjet de projets de recherches fondamentales : quels sont les mécanismes de lhoméostasie de la composition de la matrice extracellulaire du tissu cordal sain ? quelles sont les dérégulations à lorigine du développement des pathologies cordales bénignes ? quelle est linfluence des contraintes mécaniques sur la composition matricielle cordale ? quelle est linfluence du bagage génétique sur le développement des lésions bénignes ? quels sont les processus de cicatrisation du tissu cordal humain ? De la même manière que par le passé, ce sont les connaissances approfondies de la structure laminaire cordale qui ont modifié le geste microchirurgical, ce sont les réponses à ces questions qui permetteront certainement à la microchirurgie cordale dévoluer vers une chirurgie de plus en plus régénérative.

Structural bioinformatics deals with the analysis, classification and prediction of three-dimensional structures of biomacromolecules. It is becoming increasingly important as the number of structures is growing rapidly. This thesis describes three studies concerned with protein-function prediction and two studies about protein structure validation. New protein structures are often compared to known structures to find out if they have a known fold, which may provide hints about their function. The functionality and performance of eleven fold-comparison servers were evaluated. None of the tested servers achieved perfect recall, so in practise a combination of servers should be used. If fold comparison does not provide any hints about the function of a protein, structural motif searches can be employed. A survey of left-handed helices in known protein structures was carried out. The results show that left-handed helices are rare motifs, but most of them occur in active or ligand-binding sites. Their identification can therefore help to pinpoint potentially important residues. Sometimes all available methods fail to provide hints about the function of a protein. Therefore, the potential of using docking techniques to predict which ligands are likely to bind to a particular protein has been investigated. Initial results show that it will be difficult to build a reliable automated docking protocol that will suit all proteins. The effect of various phenomena on the precision of accessible surface area calculations was also investigated. The results suggest that it is prudent to report such values with a precision of 50 to 100 Å2. Finally, a survey of register shifts in known protein structures was carried out. The identified potential register shifts were analysed and classified. A machine-learning approach ("rough sets") was used in an attempt to diagnose register errors in structures.

This thesis uses geodetic satellite data to measure present-day crustal deformation in the Zagros fold-thrust belt (SW Iran). Geodetic-type measurements are also used in down-scaled models that simulate the surface deformations seen in convergent settings like the Zagros fold-thrust belt. Global Positioning System (GPS) measurements of three surveys between 1998 and 2001 indicate 9 ± 3 mm/yr and 5 ± 3 mm/yr shortening across the SE and NW Zagros respectively. GPS results show that in addition to the different rates and directions of shortening on either side of the NS trending Kazerun fault, local along-belt extension occurs to the east. Differential SAR interferograms of ERS1 &amp; 2 images between 1992 and 1999 detect 8 ± 4 mm/yr uplift rate across a newly recognized fault in SW Qeshm Island. This can be attributed to a steep imbricate thrust that may still represent the local Zagros deformation front. The salt diapirs in the Zagros rise from a source layer that acts as a low-frictional decollement that decouples the deformation of the cover sediments from their basement in the eastern Zagros whereas the cover to the west deforms above a high-friction decollement. Physical models were prepared to simulate cover deformation in the Zagros by shortening a sand pack above adjacent high- and low-frictional decollements (represented by a ductile layer). The strain distributions differed above the two types of decollements; it was more heterogeneous above the salt where local extension in the shortening direction was dominant. A separate work also investigated systematically the role of basal friction on cover deformation in convergent settings. Accurate height measurements of the model surface by laser-scanner indicated a deformation front more distal than usual, particularly in the low-basal frictional models. The volume reduction in our shortened sand models correlated directly with their basal friction.

Proteins performing catalytic roles predominantly occur in a few protein folds. Functional diversity within a common structural scaffold has been attributed to conformational features that enable exploration of reaction space. In this study, we examined specific aspects of functional diversity in the Double Stranded β-helix(cupin) fold. The cupin domain is a hyper-stable protein fold that can support a variety of functions. Variation in function using a conserved active site in the cupin fold is achieved by changes in the residues that line the active site cavity as well as by the choice of a metal cofactor. Although this appears to be a likely basis for functional diversification, a few exceptions exist. It is thus interesting to examine how enzymes with the same structure, metal cofactor and ligand coordination catalyze a diverse range of reactions. This thesis describes two bi-cupins, BacB (also known as bacilysin synthase, YwfC) and Quercetinase (YxaG). BacB is a part of the protein machinery involved in the synthesis of a di-peptide antibiotic bacilysin. The case of the bicupin protein BacB illustrates the problem of functional annotation of proteins with the cupin fold. None of the predicted functions for this enzyme could be experimentally validated in vitro. The crystal structure, determined by Single-wavelength Anomalous Dispersion (SAD) based on the bound metal-ion at the active site provided a basis to evaluate the catalytic role of this protein. Eventually, the function of this protein could be determined based on characterizing the gene product of bacA, the gene preceding bacB in the B. subtilis bac operon. The crystal structure determination of BacB also led to an analysis of multiple crystal forms, with implications for the role of molecular symmetry in forming protein crystals. The stability of the cupin domain was examined using B. subtilis quercetinase as a model system. The availability of the crystal structure and a robust activity assay enabled us to examine the role of fragment complementation in the stability of the cupin scaffold and its implications for the function of this enzyme. This thesis also has a section on the use of structural homology for function annotation for cupin proteins. The results presented here thus provide a frame-work to understand the structural basis for functional diversity in the cupin family. This thesis is organized as follows: Chapter 1: This chapter provides an introduction to the Double Stranded β-Helix-Helix (DSBH or cupin) fold. Proteins with a cupin scaffold are remarkably diverse - spanning both enzymatic and non-enzymatic functions. This chapter presents a compilation of previous reports encompassing eighteen different functional classes. These functions include seed storage, transcription factors and a host of various enzymatic activities. Cupin proteins can be monocupins, bicupins or multi-domain cupins based on the number of DSBH domains in a single polypeptide chain. Very few multi-domain cupin proteins have been identified and this is generally not considered to be a significant sub-group. The inference that cupin proteins with more than one domain are products of gene duplication events is also examined in detail. The latter part of this chapter aims to provide an introduction to the two model proteins B. subtilis BacB and Quercetinase. Chapter 2: This chapter describes studies on a bi-cupin protein BacB involved in bacilysin synthesis. Bacilysin is a non-ribosomally synthesized dipeptide antibiotic that is active against a wide range of bacteria and some fungi. Synthesis of bacilysin (L-alanine-[2,3-epoxycyclohexano-4]-L-alanine) is achieved by proteins in the bac operon, also referred to as the bacABCDE (ywfBCDEF) gene cluster in B. subtilis. The production of this antibiotic is regulated via a stringent response and branches off the pathway for aromatic amino-acid biosynthesis at prephenate. Extensive genetic analysis from several strains of B. subtilis suggests that the bacABC gene cluster encodes all the proteins that synthesize the epoxyhexanone ring of L-anticapsin. This data, however, could not be reconciled with the putative functional assignments for these proteins whereby BacA, a prephenate hydratase along with a potential isomerase/guanylyl transferase, BacB and an oxidoreductase, BacC, could synthesize L-anticapsin. Here, based on the characterization of the reaction products of BacA and BacB as well as the crystal structure of BacB, we demonstrate that B. subtilis BacB catalyzes the synthesis of 2-oxo-3-(4-oxocyclohexa-2,5-dienyl)propanoic acid, a precursor to L-anticapsin. The mass and NMR spectra of the reaction product of BacA suggest that BacA is a decarboxylase that acts on prephenate. BacB is an oxidase. This protein is a bi-cupin, with two putative active sites each containing a bound metal ion. Additional electron density at the active site of the C-terminal domain of BacB could be interpreted as a bound phenylpyruvicacid (PPY). A significant decrease in the catalytic activity of a point variant of BacB with a mutation at the N-terminal domain suggests that the N-terminal cupin domain is involved in catalysis. Chapter 3 is based on the crystal packing analysis of three different crystal forms of B. subtilis BacB. BacB is an oxidase that catalyzes the production of the di-peptide antibiotic bacilysin. This protein is a bi-cupin with two double stranded β-helix domains fused in a compact arrangement. BacB crystallizes in three crystal forms, belonging to the triclinic, monoclinic and tetragonal space groups. These different crystal forms could be obtained in similar crystallization conditions. We also note that a slight disturbance to the crystallization droplet results in nucleation events, eventually resulting in a different crystal form. All three crystal forms of BacB diffract to high resolution, thus enabling the structure determination and analysis of the packing arrangements of BacB in different space groups. Metal ions at the lattice interface dominate the different packing arrangements. The crystal packing reveals that a dimer of BacB serves as the template on which higher order symmetrical arrangements are formed. BacB, however, is a monomer in solution. The different crystal forms of BacB thus provide experimental evidence to the hypothesis that molecular symmetry could aid crystallization. Chapter 4 provides a conformational analysis of the cupin fold using B. subtilis quercetinase as a model system to understand the conformational determinants of functional diversity. Controlled proteolysis experiments revealed that this enzyme is active, thermo-stable and maintains its quaternary arrangement even after substantial (ca 33 %) cleavage of the protein. The results presented in this chapter thus show that the cupin scaffold offers a balance between protein stability and function by locating the active site and substrate recognition features in the most stable region of the protein. Chapter 5 is based on the phylogenetic analysis of cupin domains. The members of cupin superfamily exhibit large variations in their sequences, functions, organization of domains, quaternary association and the nature of bound metal ion despite having a conserved β-barrel structural scaffold. Here, an attempt was made to understand structure-function relationships among the members of this diverse superfamily and identify the principles governing functional diversity. The cupin superfamily also contains proteins for which structures are available through world-wide structural genomics initiatives but characterized as “hypothetical”. We have explored the feasibility of obtaining clues to functions of such proteins by means of comparative analysis with cupins of known structure and function. This phylogenetic strategy was applied to BacB leading to clustering with oxidoreductases. BacB was experimentally demonstrated to be an oxidase. Chapter 6 is a summary of the work reported in this thesis and the conclusions that can be drawn based on these studies. The appendix section of this thesis comprises additional experimental details, methodology and aspects of the techniques used in this study. Appendix I contains a description of a methodology for Molecular Replacement (MR) calculations in obtaining phase information for protein crystallography. Appendix II provides additional details of experimental protocols.

No description available.

The thesis investigates alternative visions of democracy through a design project that allows different public groups and individuals to more actively participate in the political realm. The site for the proposed project is the UN Headquarters in New York City, chosen for its juxtaposition of old and new world orders. The project manifests its vision through an architectural representation intended as a platform of multiplicities. Using tools from the backdrop of everyday life: security needs and communication, it attempts to break the static nature of the UN by making it more interactive--like the borderless, virtual world of the Internet we increasingly inhabit today-- and through its new architectural framework to create a self-perpetuating system for social justice.

The thesis investigates alternative visions of democracy through a design project that allows different public groups and individuals to more actively participate in the political realm. The site for the proposed project is the UN Headquarters in New York City, chosen for its juxtaposition of old and new world orders. The project manifests its vision through an architectural representation intended as a platform of multiplicities. Using tools from the backdrop of everyday life: security needs and communication, it attempts to break the static nature of the UN by making it more interactive--like the borderless, virtual world of the Internet we increasingly inhabit today-- and through its new architectural framework to create a self-perpetuating system for social justice.

Structural analysis of surface and subsurface data from the Middle Magdalena Valley basin and Eastern Cordillera fold-thrust belt to construct a kinematic model for its Cenozoic structural and stratigraphic evolution. The La Salina west-vergent thrust system marks the boundary between the Paleogene foreland basin of the Middle Magdalena basin and the Eastern Cordillera fold-thrust belt. New low-temperature thermochonological and sandstone petrographic analyses provide constraints on ages of thrust deformation and sediment dispersal. Apatite fission track (AFT) and U-Th/He thermochronological results show the timing of three structural events along the La Salina fault system: (1) late Eocene-early Oligocene (~43–35 Ma) initial hanging wall exhumation; (2) continued middle Miocene (~15 Ma) exhumation; and (3) continued but more rapid late Miocene (~12–3 Ma) hanging wall exhumation. Vitrinite reflectance results provide estimates of maximum burial depths for the hanging wall of the La Salina fault ranging from 4 to 6 km., this depth of burial estimates constrain the basin geometry during its late Eocene to late Miocene evolution. The eastern hanging wall of the La Salina fault displays a broad anticline-syncline pair affecting Cretaceous to Eocene strata with no significant faulting, whereas the western footwall contains a complex series of tight, thrust-related folds in Eocene-Quaternary strata. For foreland basin province, a proposed triangle zone accommodates a small amount of east-west shortening (< 1000 m) along the frontal thrust system by east-vergent backthrusting within a broader passive-roof duplex. East-west shortening in the Cenozoic stratigraphic section was also accommodated by detachment folding, which produced localized areas of steep dips. In the proposed kinematic restoration, the most recent phase of deformation represents out-of-sequence reactivation of the La Salina fault that is consistent with irregular crosscutting relationships of some footwall structures. Earliest exhumation by ~45–30 Ma in the Eastern Cordillera fold-thrust belt province matches (1) an increased proportion of sedimentary lithic fragments; and (2) a high degree of compositional maturity (Q88F4Lf8). Exhumation since ~15 Ma in the foreland province coincides with (1) the highest accumulation rates observed for the upper Miocene Real Group; and (2) a decrease in compositional maturity (Q55F8Lf36). / text