Nuestros resultados previos han mostrado que una sola exposición a un estímulo estresante de elevada intensidad como la inmovilización (IMO) causa una reducción de la respuesta del eje hipotalámico-pituitario-adrenal (HPA) al mismo, pero no a un nuevo, estímulo estresante y este efecto se incrementa con el tiempo transcurrido (días o semanas) entre las dos exposiciones. La menor respuesta al mismo estímulo sugiere que una exposición previa a la IMO es capaz de inducir un cierto nivel de adaptación frente al mismo estímulo. Por lo tanto, la adaptación observada en respuesta al estrés crónico podría ser consecuencia del tiempo transcurrido entre la primera y la última exposición al estrés y no de la repetición del estímulo. Los objetivos del presente trabajo han sido: (a) comparar los efectos a largo plazo de una sola exposición al nado o a la IMO con los efectos de la exposición repetida; (b) estudiar el papel de los glucocorticoides o el miedo generados durante la primera exposición a la IMO en la inducción de los efectos a largo plazo de una sola exposición al estrés. Se utilizaron ratas macho adultas como animales de experimentación y se analizaron los niveles plasmáticos de ACTH, corticosterona y glucosa.No observamos adaptación del eje HPA, pero sí de la glucosa y otras variables, al nado crónico. Una sola exposición al nado no causó efectos a largo plazo en la respuesta del eje HPA al mismo estímulo, en contraposición con lo observado con la IMO. Por ello, decidimos comparar los efectos de una exposición única o repetida a la IMO en animales intactos y en animales adrenalectomizados suplementados con corticosterona en el agua de bebida (ADX+B). En los intactos, los efectos de la exposición repetida a la IMO sobre el eje HPA fueron muy similares a los de una sola exposición, pero en los ADX+B, una sola exposición a la IMO no modificó la respuesta de la ACTH al mismo estímulo, lo que sugiere que los glucocorticoides no serían necesarios para la adaptación a la IMO crónica, pero estarían implicados en la inducción o en la expresión de los efectos a largo plazo. Para profundizar en el papel de los glucocorticoides en la inducción de los efectos a largo plazo se manipuló su efecto biológico durante la primera exposición a la IMO inhibiendo su síntesis con metirapona, bloqueando sus receptores con el RU38486 o potenciando su liberación con la administración de ACTH. Los resultados sugieren que los glucocorticoides podrían estar implicados, aunque sólo parcialmente, en la inducción de los efectos a largo plazo sobre el eje HPA. La manipulación de los niveles de miedo/ansiedad con el fármaco ansiogénico FG7142 antes de la exposición al nado o el ansiolítico diazepam antes de la exposición a la IMO no modificó los efectos a largo plazo del estrés per se, lo que sugiere que el miedo/ansiedad no es un factor importante en la inducción de los efectos a largo plazo. Aunque una sola exposición previa a la IMO protegió parcialmente de la anorexia asociada a una nueva exposición al mismo estímulo, ninguna manipulación experimental fue capaz de modificar el efecto del estrés previo, indicando que los mecanismos neuroquímicos implicados en la inducción de los efectos a largo plazo de la IMO sobre la ingesta y el eje HPA son distintos. La futura caracterización de la respuesta conductual a la IMO podría ser de gran valor para determinar si la exposición a la IMO es un modelo experimental del síndrome de estrés postraumático en humanos. / We have previously observed that a single exposure of rats to severe stressors such as immobilization in wooden boards (IMO) results in a desensitization of the hypothalamic-pituitary-adrenal (HPA) response to the same, but not a novel, stressor and this process enhances with time (days/weeks) elapsed between the two exposures to the stressor. The lower HPA response to the same stressor suggests that some degree of adaptation developed after a single exposure to IMO and therefore is unclear whether adaptation to chronic repeated IMO may be explained by the time elapsed between the first and the final exposure rather than by repetition of the stressful situation. Thus the purposes of the present work were: (a) to compare the long-term effects of single exposure to forced swimming (FS) or IMO with repeated exposure; (b) to study the role of glucocorticoids or fear generated during the first exposure to IMO on the induction of long-term effects of an acute exposure to the same stressor. Two-month-old male Sprague-Dawley rats maintained under controlled conditions were used. Plasma levels of ACTH, corticosterone and glucose levels were measured. We found no significant adaptation of the HPA axis to chronic FS, but did of glucose and other variables. A single exposure to FS did not cause long-term effects on the responsiveness of the HPA axis to the same stressor in contrast to that observed after IMO. We then studied the effects of single versus repeated exposure to IMO on the HPA response to the same stressor in both sham-operated and adrenalectomized rats maintained with corticosterone in their drinking saline (ADX+B). In sham rats, daily exposure to IMO had similar effects on the HPA axis that a previous single session. In contrast, in ADX+B rats, a reduction of the ACTH response to the stressor was observed in repeated but not single IMO rats. The present result suggest that the glucocorticoids are not mandatory for the development or adaptation of the HPA axis to chronic IMO, but they may be involved in the induction or expression of long-term effects of IMO on the HPA responsiveness to the same stressor. In order to better study the role of glucocorticoids in the induction of long-term effects to IMO, three different experimental approaches were used during the first exposure to IMO: (i) inhibition of corticosterone synthesis with metyrapone; (ii) blockade of glucocorticoid receptors with RU38486; and (iii) potentiation of glucocorticoids release with the concomitant administration of exogenous ACTH. Taken together, the data suggest that glucocorticoids play only a partial role in the induction of long-term effects of IMO on the HPA. To study the contribution of fear/anxiety generated during the first exposure to stress we study the effect of the administration of the anxiogenic drug FG7142 in rats exposed to a moderate stressor (FS) or that of the anxiolytic diazepam in rats exposed to IMO. No effect of drugs was observed, suggesting that fear/anxiety is not one of the factors involved in the induction of the long-term effects of stress on the responsiveness of the HPA axis. Although a previous exposure to IMO was able to induce a partial protection on the effects on subsequent IMO-induced anorexia, neither the manipulation of glucocorticoid levels or function nor the administration of anxiety-related drugs were able to modify this protective effect. These results indicate that neurochemical mechanisms inducing long-term effects of food intake are different from those inducing changes in the HPA axis. The characterization of the behavioural response to IMO may be of value to determine whether or not exposure to IMO is an animal model for post-traumatic stress disorder.

Cada any milers d'hectàrees forestals es destrueixen a causa dels incendis forestals. Investigar quins són els mecanismes que controlen la ignició i la propagació dels incendis forestals és necessari per planificar estratègies eficients de lluita contra els incendis forestals i per establir plans de gestió de les àrees forestals. Durant aquests darrers seixanta anys des del món de la recerca s'han formulat models per descriure el comportament dels focs forestals de superfície, principalment, i en un menor grau els focs de capçades. No obstant, aquests models tenen un punt feble significatiu: cap d'ells ha estat desenvolupat per ser utilitzat com a eina predictiva del comportament del foc després d'actuacions d'atac indirecte amb retardants a llarg termini (o retardants). A més, la majoria de treballs desenvolupats fins ara amb retardants a llarg termini han tingut l'objectiu d'avaluar diferents productes per al seu ús públic per comparació amb un de referència.L'objectiu del present estudi ha estat millorar el coneixement sobre l'efecte dels retardants a llarg termini en el comportament dels incendis forestals. L'efecte dels retardants sobre la intensitat del front de flames ha estat quantificat per a diferents condicions (sense pendent/sense vent, sota la influència del vent, sota la influència del pendent), així com l'efecte dels retardants sobre la calor de combustió del combustible forestal i l'emissivitat de la flama. Avaluar com varien aquests dos últims paràmetres per la presència de retardant al combustible és un primer pas per incloure en els models de propagació l'efecte de les operacions d'atac indirecte amb retardants.Per a les condicions experimentals provades en aquest estudi, hem trobat que la intensitat del front de flames es redueix en un factor de 0.8 per la presència de retardant. També s'ha observat que la quantitat de calor alliberada durant la combustió amb flama es redueix en un factor de 0.18 per la presència de retardants i que l'emissivitat de la flama no es veu afectada per la presència de retardants. Aquests resultats indiquen que la presència de retardant redueix la intensitat del front de flames fonamentalment perquè es redueix la quantitat de calor efectivament alliberada per unitat de massa de combustible, més que perquè les propietats radiatives de la flama es canviïn. / Every year, thousands of hectares of forest are destroyed by wildland fires. It is necessary to investigate the mechanisms that influence the ignition and propagation of wildland fires in order to successfully devise strategies for fighting wildland fires and to establish plans for managing forest areas or grasslands. Researchers have been formulating models to describe surface fires and, to a lesser extent, crown fires, for more than sixty years. However, these models have a significant shortcoming: none of them has been developed for use as a tool to predict fire behavior after indirect attack operations with long-term retardants. Furthermore, most of the work done to date on long-term retardants has been with the goal of evaluating these products for commercial purposes.The goal of the present study was to improve knowledge of the effects of long-term retardants on the spread of forest fires. Retardants' effects on fire intensity were quantified for varying fire situations (no-slope/no-wind, upslope, upwind), together with retardants' effects on the heat of combustion of the fuel and flame emissivity. Assessing how these last two parameters change due to the presence of retardants on the fuel is a first step towards including the effects of indirect attack operations with long-term retardants in propagation models. We found that the presence of retardants reduced fire intensity by a factor of 0.8 under the experimental conditions tested in this study. The amount of heat effectively released during flaming combustion under the presence of retardants was observed to decrease by a factor of 0.18 in comparison with untreated samples and flame emissivity was observed to be unaffected by the presence of retardants. These results indicated that the presence of retardants reduces fire intensity primarily by reducing the amount of heat effectively released per unit mass of fuel, rather than by affecting the radiation properties of the flames.

O complexo telomérico, responsável pela integridade genômica, é formado pela interação de DNA com proteínas, que são responsáveis pela proteção desses terminais. O complexo RPA de eucariotos compreende um heterotrímero, que cumpre diversas funções vitais na célula, sendo uma peça fundamental na replicação, reparo e recombinação. A ausência de homólogos de proteínas que protegem o telômero em T. cruzi nos fez investigar se o complexo RPA poderia cumprir essa função. Assim, este trabalho teve como objetivo caracterizar a interação TcRPA-1-telômero. Conseguimos verificar a interação in vitro e in vivo da RPA-1 com o telômero em epimastigotas e tripomastigotas. A ausência de homólogos de proteínas que interagem com o overhang telomérico em tripanosomas, a interação específica RPA-1-telômero, e a sua presença nos telômeros da forma de vida não replicativa, bem como as peculiaridades estruturais da TcRPA-1, levam-nos a propor que essa proteína pode estar envolvida com a proteção dos telomérica neste organismo. / The telomeric complex, responsible for genomic integrity and stability , is formed by the interaction of DNA with proteins that are responsible for maintaining and protecting these terminals. The eukaryotic RPA complex comprises a heterotrimer, which fulfills several vital functions in the cell , being a fundamental player in replication , repair and recombination. The absence of homologous proteins that protect telomeres in Trypanosoma cruzi lead us to hypothesize that RPA complex could fulfill this function. Thus, this study aimed to characterize TcRPA-1-telomere interaction. We could verify in vitro and in vivo interaction of RPA - 1 with telomeres in epimastigote and trypomastigote lifeforms. The absence of homologs of proteins that interact with telomeric overhang in trypanosomes, the specific interaction RPA-1- telomere , its presence in non- replicative lifeform as well as structural peculiarities of TcRPA-1, lead us to propose that this protein may be involved in telomere protection in this organism.

O complexo telomérico, responsável pela integridade genômica, é formado pela interação de DNA com proteínas, que são responsáveis pela proteção desses terminais. O complexo RPA de eucariotos compreende um heterotrímero, que cumpre diversas funções vitais na célula, sendo uma peça fundamental na replicação, reparo e recombinação. A ausência de homólogos de proteínas que protegem o telômero em T. cruzi nos fez investigar se o complexo RPA poderia cumprir essa função. Assim, este trabalho teve como objetivo caracterizar a interação TcRPA-1-telômero. Conseguimos verificar a interação in vitro e in vivo da RPA-1 com o telômero em epimastigotas e tripomastigotas. A ausência de homólogos de proteínas que interagem com o overhang telomérico em tripanosomas, a interação específica RPA-1-telômero, e a sua presença nos telômeros da forma de vida não replicativa, bem como as peculiaridades estruturais da TcRPA-1, levam-nos a propor que essa proteína pode estar envolvida com a proteção dos telomérica neste organismo. / The telomeric complex, responsible for genomic integrity and stability , is formed by the interaction of DNA with proteins that are responsible for maintaining and protecting these terminals. The eukaryotic RPA complex comprises a heterotrimer, which fulfills several vital functions in the cell , being a fundamental player in replication , repair and recombination. The absence of homologous proteins that protect telomeres in Trypanosoma cruzi lead us to hypothesize that RPA complex could fulfill this function. Thus, this study aimed to characterize TcRPA-1-telomere interaction. We could verify in vitro and in vivo interaction of RPA - 1 with telomeres in epimastigote and trypomastigote lifeforms. The absence of homologs of proteins that interact with telomeric overhang in trypanosomes, the specific interaction RPA-1- telomere , its presence in non- replicative lifeform as well as structural peculiarities of TcRPA-1, lead us to propose that this protein may be involved in telomere protection in this organism.

Conservation corridors, areas of land connecting patches of natural land cover, are frequently cited and implemented as a restorative strategy to counteract fragmentation. Current corridor ecology focuses on experimental corridor systems or designed and built conservation corridors to assess functionality. Such systems and designs are typically short, straight swaths of homogenous land cover with unambiguous transitions between patches. Quantifying the degree to which amorphous landscape configurations, tortuosity, and heterogeneity of land cover and land uses within the corridor has on functional connectedness is a crucial yet overlooked component of corridor efficacy studies. Corridor literature lacks a robust and repeatable methodology for delineating existing landscape elements, recognizing arbitrary edges, and identifying the start and end of ambiguous transitions between the patches and corridor. Using a set of landscapes being studied as part of a global assessment of corridor efficacy, I designed a workflow that standardizes the boundary of corridor-patch interfaces. The proposed method is a quantitative and repeatable approach that minimizes the subjectivity in corridor delineations. This research investigates the degree to which the existence of a corridor modifies the structural and functional connectivity between patches connected by a corridor compared to an intact reference area.

The kinesin-14 Kar3 from Saccharomyces cerevisiae (Sc) is a C-terminal motor that forms a heterodimer with the kinesin-accessory protein Vik1. Although Vik1 possesses a typical kinesin motor domain (MD) fold, it lacks a nucleotide-binding site. However, it binds microtubules with affinities that can be regulated Kar3’s nucleotide state. This implies intermolecular communication between its subunits. This thesis aimed to understand this communication by studying the structures and functions of Kar3Vik1 orthologs. First, we biochemically characterized Kar3 from Ashbya gossypii (Ag) and determined the crystal structure of its MD. It was shown that the active site features of the AgKar3MD are similar to that of the ScKar3 R598A mutant, and that the β1 lobe at the edge of the MD was unique in structure and amino acid content. These results may provide a rationale for the unique enzymatic properties of this motor that could be relevant to its interaction with AgVik1 and function in Ashbya gossypii. We also determined the crystal structures of Kar3 and Vik1 orthologs from Candida glabrata (Cg). While the CgKar3MD structure was very similar to that of ScKar3MD, crystals of CgVik1 captured three novel conformations of the Vik1 motor homology domain (MHD). We observed that when the N-terminal neck helix docks against the MHD core in two unique positions, the C-terminus resembling neck mimics of kinesin-14 motors also docks against the neck-core junction. However, when the neck is non-helical and disengaged from the MHD, the C-terminus is undocked and disordered. To assess the functional importance of these N- and C-terminal segments of Vik1 MHD, we created CgKar3Vik1 constructs whose Vik1 subunit contained either a point mutation or complete truncation of the C-terminus (neck mimic), and analyzed their biophysical properties. All mutants showed defective ATPase activity and microtubule-gliding ability. Characterization of the mutations in CgVik1MHD by molecular dynamics simulations showed that residues Ile578 and Asn580 are not only involved in stabilizing interactions between the neck and neck mimic but they also influence and respond to conformational changes of the neck. These observations implicate the N- and C-termini of Vik1 as a key element of Kar3Vik1 function and communication. / Thesis (Ph.D, Biochemistry) -- Queen's University, 2013-07-23 10:31:52.885

El nostre país ha estat devastat seriosament pels incendis forestals durant els darrers anys, causant greus conseqüències sobre les persones i el medi ambient i destruint una de les fonts de riquesa i equilibri més preuades del territori. A més, les repercussions econòmiques i socials han estat de gran importància.Aquesta tesi doctoral pretén trobar solucions als greus problemes que els incendis forestals representen al nostre país. Se centra en el camp de l'extinció, i més concretament, en l'aplicació de productes retardants a llarg terminiactuant com a tallafocs químics del front d'incendi. Aquesta és una tècnica d'extinció que ofereix enormes possibilitats d'èxit; amb tot, presenta grans incògnites pel que fa a la seva eficàcia i operativitat, a causa de les importants llacunes existents en el seu coneixement sobretot a mitjana i gran escala.Aquesta tesi té dos objectius específics; d'una banda, el de dissenyar una nova metodologia experimental per a l'estudi de l'efecte dels retardants a llarg termini, que permeti extreure la màxima informació sobre les principals variables que determinen el comportament d'un incendi, i de l'altra, el d'obtenir un model matemàtic que predigui l'efecte d'un tractament retardant sobre un front d'incendi, donats els paràmetres d'aplicació.Per a la consecució d'aquests objectius, ha estat dut a terme un extens programa experimental de laboratori a la Universitat de Coimbra (Portugal) i a la Universitat Politècnica de Catalunya (on ha estat dissenyada i posada en funcionament una instal·lació a tal efecte) i també han estat realitzades dues campanyes experimentals a camp, amb vegetació típicament mediterrània. En aquests experiments han estat implementats diferents sistemes d'adquisició de dades de la velocitat de propagació, la velocitat de combustió, la temperatura i la potència calorífica radiant del front d'incendi.Amb el tractament i anàlisi de les dades experimentals han estat detallats els principals fenòmens físics que ocorren quan un front d'incendi transcorre sota l'efecte duna formulació retardant. Finalment, a partir d'aquesta anàlisi, ha estat validat un model teòric de propagació d'incendis forestals basat en el mecanisme de transferència de calor per radiació. Aquest model ha estat adaptat per tal que pugui contemplar l'efecte del tractament retardant i esdevingui una eina predictiva en aquest sentit. / Forest fires have seriously devastated our region during the last years, causing human and environmental damage and destroying one of the most valuable source of wealth and balance of our country. Their economic and social consequences have been very important.This thesis tries to find solutions to the serious problems originated by wildland fires represent in our country. It is focused on the field of extinction and more specifically on the application of long-term fire retardants, which acts as firebreaks of the fire front. This is an extinction technique that offers great possibilities of success; however, it presents many uncertainties related to its efficacy and operational capacity, due to the lack of knowledge at medium and large scale.This PhD thesis has two main objectives; the first one involves designing a new experimental methodology for the study of the effect of long-term fire retardants, which allows extracting the maximum information on the main fire behaviour variables. The later aims at the achievement of a mathematical model to predict the effect of a certain retardant treatment, applied to a fire front, given its application parameters.Wide laboratory experimental programs have been carried out in the University of Coimbra (Portugal) and in the Politechnic University of Catalunya (where an experimental installation had to be designed and started) and two field experimental campaigns with typical Mediterranean vegetation have been realised as well, in order to achieve these objectives. Different data acquisition systems have been implemented so that rate of spread, combustion velocity, temperatures and heat flux by radiation of the fire front could have been recorded.The main physical phenomena that take place in a fire front treated with a retardant formulation have been detailed by means of data analysis.Finally, a theoretical mathematical model based on the radiative heat transfer mechanism has been validated through this analysis. This model has been adapted aiming at the consideration of retardant treatment effects and the achievement of a predictive tool to evaluate them.

Membrane proteins roughly constitute 30% of open reading frames in a genome and form 70% of current drug targets. They are classified as integral, peripheral membrane proteins and polypeptide toxins. α-helices and β -strands are the principal secondary structures observed in integral membrane proteins. This thesis presents the results of studies on analysis and correlation of sequence and structure of helices constituting integral helical membrane proteins. The aim of this work is to understand the helix stabilization, distortion as well as packing in terms of amino acid sequences and the correlated structures they adopt. To this end, analyses of datasets of X-ray crystal structures of integral helical membrane proteins and their comparison with a dataset of representative folds of globular proteins was carried out. Initial analysis was carried out using a non-redundant dataset of 75 membrane proteins to understand sequence and structural preferences for stabilization of helix termini. The subsequent analysis of helix distortions in membrane proteins was carried out using an updated dataset of 90 membrane proteins. Chapter 1 of the thesis reviews experimental as well as theoretical studies that have provided insights into understanding the structure of helical membrane proteins. Chapter 2 details the methods used during the course of the present investigations. These include the protocol used for creation of the non-redundant database of membrane and globular proteins. Various statistical methods used to test significance of the position-wise representation of amino acids in helical regions and the differences in globular and membrane protein datasets have been listed. Based on the tests of significance, a methodology to identify differences in propensity values that are statistically significant among two datasets has been devised. Programs used for secondary structure identification of membrane proteins namely Structure Identification (STRIDE) and Assignment of Secondary Structure in Proteins (ASSP) as well as those used for characterization of helical geometry (Helanal-Plus) have also been enlisted. In Chapter 3, datasets of 865 α-helices in 75 membrane proteins and 2680 α- helices from 626 representative folds in globular proteins defined by the STRIDE program have been analyzed to study the sequence determinants at fifteen positions within and around the α-helix. The amino acid propensities have been studied for positions that are important for the process of helix initiation, propagation, stabilization and termination. Each of the 15 positions has unique sequence characteristics reflecting their role and contribution towards the stability of the α-helix. A comparison of the sequence preferences in membrane and globular proteins revealed common residue preferences in both these datasets confirming the importance of these positions and the strict residue preferences therein. However, short/medium length α-helices that initiated/terminated within the membrane showed distinct amino acid preferences at the N-terminus (Ncap, N1, N2) as well as the C-terminus ( Ccap, Ct) when compared to α-helices belonging to membrane and globular proteins. The sequence preferences in membrane proteins were governed by the helix initiating and terminating property of the amino acids as well as the external environment of the helix. Results from our analysis also conformed well with experimentally tested amino acid preferences in a position-specific amino acid preference library of the rat neurotensin receptor (Schlinkmann et al (2012) Proc Natl Acad Sci USA 109(25):1890-5) as well as crystal structures of GPCR proteins. In the light of the environment dependent amino acid preferences found at α- helix termini, a survey was carried out to find various helix capping motifs adopted at both termini of α-helices in globular and membrane proteins to stabilize these helix termini. The results from these findings have been reported in Chapter 4. A sequence dependent structural preference is found for capping motifs at helix termini embedded inside and protruding outside the membrane. The N-terminus of α-helices was capped by hydrogen bonds involving free main chain amide groups of the first helical turn as donors and amino acid side chains as acceptors, as against the C-terminus which showed position-dependent characteristic backbone conformations to cap the helix. Overall helix termini inside the membrane did not show a very high number of capping motifs; instead these termini were stabilized by helix- helix interactions contributed by the neighboring helices of the helical bundle. In Chapter 5, we examine transmembrane helical (TMH) regions to identify as well as characterize the various types of helix perturbations in membrane proteins using ASSP and Helanal-Plus. A survey of literature shows that the term ‘helix kink’ has been used rather loosely when in fact helical regions show significant amounts of variation and transitions in helical parameters. Hence a systematic analysis of TMH regions was undertaken to quantify different types of helix perturbations, based on geometric parameters such as helical twist, rise per residue and local bending angle. Results from this analysis indicated that helices are not only kinked but undergo transitions to form interspersed stretches of 310 helices and π-bulges within the bilayer. These interspersed 310 and π-helices showed unique sequence preferences within and around their helical body, and also assisted in main- taining the helical structure within the bilayer. We found that Proline not only kinked the helical regions in a characteristic manner but also caused a tightening or unwinding in a helical region to form 310 and π-helix fragments respectively. The helix distortions also resulted in backbone hydrogen bonds to be missed which were stabilized by hydrogen bonds from neighboring residues mediated by their side chain atoms. Furthermore, a packing analysis showed that helical regions with distortions were able to establish inter-helical interactions with more number of transmembrane segments in the helical bundle. The study on helix perturbations presented in the previous chapter, brought to light a previously unreported 19 amino acid π-helix fragment interspersed between α-helices in the functionally important transmembrane helix 2 (TM2) belonging to Mitochondrial cytochrome-c-oxidase (1v55). Chapter 6 describes a case study of the structurally similar but functionally different members within the Heme-Copper- Superoxidases (HCO) superfamily that were considered for a comparative analysis of TM2. An analysis of 7 family members revealed that the π-helix shortens, fragments in two shorter π-helices or was even absent in some family members. The long π-helix significantly decreased the total twist and rise of the entire helical fragment thus accommodating more hydrophobic amino acids within the bilayer to avoid hydrophobic mismatch with the bilayer. The increased radius of the TM2 helical fragment also assisted in helix packing interactions by increasing the number of residues involved in helix-helix interactions and hydrogen bonds. Chapter 7 documents the conclusions from the different analyses presented in each of the above chapters. Overall, it is found that membrane proteins optimize the biophysical and chemical constraints of the external environment to strategically place select amino acids at helix termini to ‘start’ and ‘stop’ α-helices. The stabilization of these helix termini is a consequence of sequence dependent structural preferences to form helix capping motifs. The studies on helix transitions and distortions highlight that membrane proteins are not only packed as α-helices but also accomodate 310- and π-helical fragments. These transitions and distortions help in harboring more hydrophobic amino acids and aiding inter-helical interactions important for maintaining the fold of the membrane protein. Appendix A describes a comparison of α-helix assignments in globular and membrane proteins by two algorithms, one based on Cα trace (ASSP) and the other using a combination of hydrogen bond pattern along with backbone torsion angles φ and ψ (STRIDE).

La ricerca intende illustrare le modalità applicative attraverso le quali si possono esprimere in lingua cinese le terminologie specialistiche dei campi tecnici e scientifici del XXI secolo. Un percorso che attraversa la storia delle scienze in Cina dal terzo secolo a.C. fino ai nostri giorni, ricostruisce le regole che passo dopo passo, non senza deviazioni e ripensamenti, gli studiosi cinesi hanno stabilito per creare e gestire le loro “parole” composte con innumerevoli caratteri, gli hanzi, simbolo della cultura e della civiltà cinese, icone che ancora oggi “parlano” ai lettori, espressioni grafiche di oggetti e di concetti. La presentazione dell'opera di Feng Zhiwei, uno tra i maggiori esponenti della terminologia cinese contemporanea, ci accompagna nell'approfondimento degli orientamenti degli studi terminologici cinesi e nel confronto con quelli euro americani, a partire dagli studi svolti da Eugen Wüster all'inizio del XX secolo. L'analisi della terminologia cinese nella tecnologia del fotovoltaico e nel mondo economico-finanziario, costituisce il terreno di verifica delle pratiche terminologiche in essere nella lingua cinese e delle tendenze nella costruzione neologica e neonimica. / This research aims to illustrate the methodes used for creation of the specialized terminologies in the technical and scientific fields in the XXI century’s Chinese language. A pathway crossing the history of sciences in China from the III century B.C. until our days, reconstructs the rules that step after step the Chinese scholars have established in order to create and manage their “words” with the lot of characters, the hanzi, symbol of the Chinese culture and civilization, icons that still today “speak” to the readers, graphical expressions of objects and concepts. The presentation of the work of Feng Zhiwei, one among the greatest exponents of the contemporary Chinese terminology, is our guideline in a close examination of the Chinese terminological studies’ orientations, in comparison with the euro-americans ones, starting from the studies developed by Eugen Wüster at the beginning of the XX century. The analysis of the Chinese terminology in the photovoltaic technology and in the economic-financial world, constitutes the ground of verification of the actual terminological practices in the Chinese language and the tendencies in the neological and neonymical construction.

The sequence of a polypeptide chain determines its structure which in turns determines its function. A protein is stabilized by multiple forces; hydrophobic interaction, electrostatic interactions and hydrogen bond formation between residues. While the above forces are non-covalent in nature the protein structure is also stabilized by disulfide bonds. Structural features such as naturally occurring cavities in proteins also affect its stability. Studying factors which affect a protein’s structural stability helps us understand complex sequence-structure-function relationships, the knowledge of which can be applied in areas such as protein engineering. The work presented in this thesis deals with various and diverse aspects of protein structure. Chapter 1 gives an overall introduction on the topics studied in this thesis. Chapter 2 focuses on a unique, non-regular, structural feature of proteins, viz. protein cavities. Cavities directly affect the packing density of the protein. It has been shown that large to small cavity creating mutations destabilize the protein with the extent of destabilization being proportional to the size of cavity created. On the other hand, small to large cavity filling mutations have been shown to increase protein stability. Tools which analyze protein cavities are thus important in studies pertaining to protein structure and stability. The chapter presents two methods which detect and calculate cavity volumes in proteins. The first method, DEPTH 2.0, focuses on accurate detection and volume calculation of cavities. The second method, ROBUSTCAVITIES, focuses on detection of biologically relevant cavities in proteins. We then study another aspect of protein structure – the disulfide bond. Disulfide bonds confer stability to the protein by decreasing the entropy of the unfolded state. Previous studies which attempted to engineer disulfides in proteins have shown mixed results. Previously, disulfide bonds in individual secondary structures were characterized. Analysis of disulfides in α-helices and antiparallel β-strands yielded important common features of such bonds. In Chapter 3 we present a review of these studies. We then use MODIP; a tool that identifies amino acid pairs which when mutated to cysteines will most likely form a disulfide bond, to analyze disulfide bonds in parallel β-strands. A direct way to analyze sequence-structure relationships is via mutating individual residues, evaluating the effect on stability and activity of the protein and inferring its effect on protein structure. Saturation mutagenesis libraries, where all possible mutations are made at every position in the protein contain a huge amount of information pertaining to the effect of mutations on structure. Making such libraries and screening them has been an extremely resource intensive process. We combine a fast inverse PCR based method to rapidly generate saturation mutagenesis libraries with the power of deep sequencing to derive phenotypes of individual mutants without any large scale screening. In Chapter 4 we present an Illumina data analysis pipeline which analyzes sequencing data from a saturation mutagenesis library, and derives individual mutant phenotypes with high confidence. In Chapter 5 we apply the insights derived from structure-function studies and apply it to the problem of protein engineering, specifically immunogen design. The Human Immunodeficiency Virus adopts various strategies to evade the host immune system. Being able to display the conserved epitopes which elicit a broadly neutralizing response is the first step towards an effective vaccine. Grafting such an epitope onto a foreign scaffold will mitigate some of the key HIV defenses. We develop a computational protocol which grafts the broadly neutralizing antibody b12 epitope on scaffolds selected from the PDB. This chapter also describes the only experimental work presented in this thesis viz. cloning, expressing and screening the epitope-scaffolds using Yeast Surface Display. Our epitope-scaffolds show modest but specific binding. In a bid to improve binding, we make random mutant libraries of the epitope-scaffolds and screen them for better binders using FACS. This work is on-going and we aim to purify our epitope-scaffolds, characterize them biophysically and eventually test their efficacy as immunogens.