Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Profili critici in materia di transnational group action

La presente tesi di dottorato ha ad oggetto l’analisi dei profili critici emersi nella prassi in relazione alle transnational damages group actions. All’interno di tale esteso ambito di ricerca, senza pretese di esaustività, si affronteranno determinati aspetti, tenendo in considerazione quanto accaduto negli ordinamenti che, sebbene in modo assai limitato, hanno già conosciuto tali problematiche. A seguito di una prima parte meramente introduttiva, nel secondo capitolo, si inquadreranno brevemente gli strumenti di tutela collettiva risarcitoria, indicando in che cosa consistano, a quali esigenze rispondano e quale origine abbiano; si indicheranno altresì i criteri distintivi e di classificazione che maggiormente possono rilevare nell’ottica di una cross border litigation. Nel terzo capitolo si analizzerà in termini essenziali la disciplina delle azioni collettive di alcuni Paesi, al fine di porre le basi necessarie per comprendere in quale contesto normativo si pongano le problematiche inerenti alle multi-jurisdictional collective redress actions. Nel quarto capitolo, si prenderà in considerazione la dimensione transnazionale delle azioni collettive, tenendo presenti le categorie e le regole affermatesi nel diritto internazionale privato e processuale e, soprattutto, quelle esistenti nell’ordinamento italiano e comunitario. Si individueranno poi gli obiettivi prioritari che si deve porre il giudice richiesto di giudicare sull’azione collettiva nella necessità di rendere una pronuncia o approvare una transazione che, da un lato, sia riconosciuta ed eseguita nei Paesi in cui dovrà essere riconosciuta ed eseguita e che, dall’altro lato, in ipotesi di opt out procedure, precluda ai soggetti che la pronuncia o la transazione dovrebbe vincolare successive azioni individuali e/o collettive in altri Paesi. Nel quinto capitolo, alla luce dei dati indicati nel terzo capitolo e delle considerazioni effettuate nel quarto capitolo, si analizzeranno alcuni dei profili critici posti dalla dimensione transnazionale delle azioni collettive; a tal fine, la trattazione verrà suddivisa in diversi punti che, pur essendo necessariamente connessi tra loro, nella loro individualità riescano ad evidenziare l’importanza e la centralità di determinate questioni. Peraltro, nell’intento di rispondere in modo adeguato alle problematiche analizzate, si indicheranno alcune delle soluzioni sperimentate dalla pratica giudiziaria o proposte dalla recente letteratura sul tema. Seguirà, infine, un ultimo capitolo contenente le osservazioni conclusive sugli esiti del lavoro.

New insight on a Group A Streptococcus protective antigen contributing to bacterial cell division

Bioinformatic analysis of Group A Streptococcus (GAS) genomes aiming at the identification of new vaccine antigens, revealed the presence of a gene coding for a putative surface-associated protein, named GAS40, inducing protective antibodies in an animal model of sepsis. The aim of our study was to unravel the involvement of GAS40 in cell division processes and to identify the putative interactor. Firstly, bioinformatic analysis showed that gas40 shares homology with ezrA, a gene coding for a negative regulator of Z-ring formation during cell division process. Both scanning and transmission electron microscopy indicated morphological differences between wild-type and the GAS40 knock-out mutant strain, with the latter showing an impaired capacity to divide resulting in the formation of very long chains. Moreover, when the localization of the antigen on the bacterial surface was analyzed, we found that in bacteria grown at exponential phase GAS40 specifically localized at septum, indicating a possible role in cell division. Furthermore, by ELISA and co-sedimentation assays, we found that GAS40 is able to interact with FtsZ, a protein involved in Z-ring formation during cell division process. These data together with the co-localization of GAS40/FtsZ at bacterial septum demonstrated by by confocal microscopy, strongly support the hypothesis for a key role of GAS40 in bacterial cell division.

Analysis of Two Component Systems in Group B Streptococcus Shows that RgfAC and the Novel FspSR Modulate Virulence and Bacterial Fitness

Group B Streptococcus (GBS), in its transition from commensal to pathogen, will encounter diverse host environments and thus require coordinately controlling its transcriptional responses to these changes. This work was aimed at better understanding the role of two component signal transduction systems (TCS) in GBS pathophysiology through a systematic screening procedure. We first performed a complete inventory and sensory mechanism classification of all putative GBS TCS by genomic analysis. Five TCS were further investigated by the generation of knock-out strains, and in vitro transcriptome analysis identified genes regulated by these systems, ranging from 0.1-3% of the genome. Interestingly, two sugar phosphotransferase systems appeared differently regulated in the knock-out mutant of TCS-16, suggesting an involvement in monitoring carbon source availability. High throughput analysis of bacterial growth on different carbon sources showed that TCS-16 was necessary for growth of GBS on fructose-6-phosphate. Additional transcriptional analysis provided further evidence for a stimulus-response circuit where extracellular fructose-6-phosphate leads to autoinduction of TCS-16 with concomitant dramatic up-regulation of the adjacent operon encoding a phosphotransferase system. The TCS-16-deficient strain exhibited decreased persistence in a model of vaginal colonization and impaired growth/survival in the presence of vaginal mucoid components. All mutant strains were also characterized in a murine model of systemic infection, and inactivation of TCS-17 (also known as RgfAC) resulted in hypervirulence. Our data suggest a role for the previously unknown TCS-16, here named FspSR, in bacterial fitness and carbon metabolism during host colonization, and also provide experimental evidence for TCS-17/RgfAC involvement in virulence.

The Making of a Shiite Bourgeoisie in Lebanon Political Mobilisation, Economic Resources and Formation of a Social Group

The thesis analyses the making of the Shiite middle- and upper/entrepreneurial-class in Lebanon from the 1960s till the present day. The trajectory explores the historical, political and social (internal and external) factors that brought a sub-proletariat to mobilise and become an entrepreneurial bourgeoisie in the span of less than three generations. This work proposes the main theoretical hypothesis to unpack and reveal the trajectory of a very recent social class that through education, diaspora, political and social mobilisation evolved in a few years into a very peculiar bourgeoisie: whereas Christian-Maronite middle class practically produced political formations and benefited from them and from Maronite’s state supremacy (National Pact, 1943) reinforcing the community’s status quo, Shiites built their own bourgeoisie from within, and mobilised their “cadres” (Boltanski) not just to benefit from their renovated presence at the state level, but to oppose to it. The general Social Movement Theory (SMT), as well as a vast amount of the literature on (middle) class formation are therefore largely contradicted, opening up new territories for discussion on how to build a bourgeoisie without the state’s support (Social Mobilisation Theory, Resource Mobilisation Theory) and if, eventually, the middle class always produces democratic movements (the emergence of a social group out of backwardness and isolation into near dominance of a political order). The middle/upper class described here is at once an economic class related to the control of multiple forms of capital, and produced by local, national, and transnational networks related to flows of services, money, and education, and a culturally constructed social location and identity structured by economic as well as other forms of capital in relation to other groups in Lebanon.