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.

Microwave-Mediated Hetero Diels-Alder reaction: Synthesis of biologically active compounds

Heterocyclic compounds represent almost two-thirds of all the known organic compounds: they are widely distributed in nature and play a key role in a huge number of biologically important molecules including some of the most significant for human beings. A powerful tool for the synthesis of such compounds is the hetero Diels-Alder reaction (HDA), that involve a [4+2] cycloaddition reaction between heterodienes and suitable dienophiles. Among heterodienes to be used in such six-membered heterocyclic construction strategy, 3-trialkylsilyloxy-2-aza-1,3-dienes (Fig 1) has been demonstrated particularly attractive. In this thesis work, HDA reactions between 2-azadienes and carbonylic and/or olefinic dienophiles, are described. Moreover, substitution of conventional heating by the corresponding dielectric heating as been explored in the frame of Microwave-Assisted-Organic-Synthesis (MAOS) which constitutes an up-to-grade research field of great interest both from an academic and industrial point of view. Reaction of the azadiene 1 (Fig 1) will be described using as dienophiles carbonyl compounds as aldehyde and ketones. The six-membered adducts thus obtained (Scheme 1) have been elaborated to biologically active compounds like 1,3-aminols which constitutes the scaffold for a wide range of drugs (Prozac®, Duloxetine, Venlafaxine) with large applications in the treatment of severe diseases of nervous central system (NCS). Scheme 1 The reaction provides the formation of three new stereogenic centres (C-2; C-5; C-6). The diastereoselective outcome of these reactions has been deeply investigated by the use of various combination of achiral and chiral azadienes and aliphatic, aromatic or heteroaromatic aldehydes. The same approach, basically, has been used in the synthesis of piperidin-2-one scaffold substituting the carbonyl dienophile with an electron poor olefin. Scheme 2 As a matter of fact, this scaffold is present in a very large number of natural substances and, more interesting, is a required scaffold for an huge variety of biologically active compounds. Activated olefins bearing one or two sulfone groups, were choose as dienophiles both for the intrinsic characteristic flexibility of the “sulfone group” which may be easily removed or elaborated to more complex decorations of the heterocyclic ring, and for the electron poor property of this dienophiles which makes the resulting HDA reaction of the type “normal electron demand”. Synthesis of natural compounds like racemic (±)-Anabasine (alkaloid of Tobacco’s leaves) and (R)- and (S)-Conhydrine (alkaloid of Conium Maculatum’s seeds and leaves) and its congeners, are described (Fig 2).

Microfluidic device and interfacial transport: application to biomolecules and nanostructures

The aim of my dissertation is to provide new knowledge and applications of microfluidics in a variety of problems, from materials science, devices, and biomedicine, where the control on the fluid dynamics and the local concentration of the solutions containing the relevant molecules (either materials, precursors, or biomolecules) is crucial. The control of interfacial phenomena occurring in solutions at dierent length scales is compelling in nanotechnology for devising new sensors, molecular electronics devices, memories. Microfluidic devices were fabricated and integrated with organic electronics devices. The transduction involves the species in the solution which infills the transistor channel and confined by the microfluidic device. This device measures what happens on the surface, at few nanometers from the semiconductor channel. Soft-lithography was adopted to fabricate platinum electrodes, starting from platinum carbonyl precursor. I proposed a simple method to assemble these nanostructures in periodic arrays of microstripes, and form conductive electrodes with characteristic dimension of 600 nm. The conductivity of these sub-microwires is compared with the values reported in literature and bulk platinum. The process is suitable for fabricating thin conductive patterns for electronic devices or electrochemical cells, where the periodicity of the conductive pattern is comparable with the diusion length of the molecules in solution. The ordering induced among artificial nanostructures is of particular interest in science. I show that large building blocks, like carbon nanotubes or core-shell nanoparticles, can be ordered and self-organised on a surface in patterns due to capillary forces. The eective probability of inducing order with microfluidic flow is modeled with finite element calculation on the real geometry of the microcapillaries, in soft-lithographic process. The oligomerization of A40 peptide in microconfined environment represents a new investigation of the extensively studied peptide aggregation. The added value of the approach I devised is the precise control on the local concentration of peptides together with the possibility to mimick cellular crowding. Four populations of oligomers where distinguished, with diameters ranging from 15 to 200 nm. These aggregates could not be addresses separately in fluorescence. The statistical analysis on the atomic force microscopy images together with a model of growth reveal new insights on the kinetics of amyloidogenesis as well as allows me to identify the minimum stable nucleus size. This is an important result owing to its implications in the understanding and early diagnosis and therapy of the Alzheimer’s disease

Potential Analysis for Hypoelliptic Second Order PDEs with Nonnegative Characteristic Form

In this Thesis we consider a class of second order partial differential operators with non-negative characteristic form and with smooth coefficients. Main assumptions on the relevant operators are hypoellipticity and existence of a well-behaved global fundamental solution. We first make a deep analysis of the L-Green function for arbitrary open sets and of its applications to the Representation Theorems of Riesz-type for L-subharmonic and L-superharmonic functions. Then, we prove an Inverse Mean value Theorem characterizing the superlevel sets of the fundamental solution by means of L-harmonic functions. Furthermore, we establish a Lebesgue-type result showing the role of the mean-integal operator in solving the homogeneus Dirichlet problem related to L in the Perron-Wiener sense. Finally, we compare Perron-Wiener and weak variational solutions of the homogeneous Dirichlet problem, under specific hypothesis on the boundary datum.

Circadian rhythms, sleep and autonomic function in progressive supranuclear palsy: characteristic features and reciprocal interactions

Background: Progressive supranuclear palsy (PSP) is a rare neurodegenerative condition. The aims of this study were to evaluate the association between sleep, the circadian system and autonomic function in a cohort of PSP patients. Methods: Patients with PSP diagnosed according to consensus criteria were recruited prospectively and retrospectively and performed the following tests: body core temperature (BcT), sleep-wake cycle, systolic and diastolic blood pressure (SBP, DBP) continuous monitoring for 48 h under controlled environmental conditions; cardiovascular reflex tests (CRTs). The analysis of circadian rhythmicity was performed with the single cosinor method. For state-dependent analysis, the mean value of variables in each sleep stage was calculated as well as the difference to the value in wake. Results: PSP patients presented a reduced total duration of night sleep, with frequent and prolonged awakenings. During daytime, patients had very short naps, suggesting a state of profound sleep deprivation across the 24-h. REM sleep behaviour disorder was found in 15%, restless legs syndrome in 46%, periodic limb movements in 52% and obstructive sleep apnea in 54%. BcT presented the expected fall during night-time, however, compared to controls, mean values during day and night were higher. However BcT state-dependent modulation was maintained. Increased BcT could be attributed to an inability to properly reduce sympathetic activity favoured by the sleep deprivation. At CRTs, PSP presented mild cardiovascular adrenergic impairment and preserved cardiovagal function. 14% had non-neurogenic orthostatic hypotension. Only 2 PSP presented the expected BP dipping pattern, possibly as a consequence of sleep disruption. State-dependent analysis showed a partial loss of the state-dependent modulation for SBP. Discussion: This study showed that PSP presented abnormalities of sleep, circadian rhythms and cardiovascular autonomic function that are likely to be closely linked one to another.

Variety, flexibility, and use of abstract concepts. A multiple grounded perspective.

The nature of concepts is a matter of intense debate in cognitive sciences. While traditional views claim that conceptual knowledge is represented in a unitary symbolic system, recent Embodied and Grounded Cognition theories (EGC) submit the idea that conceptual system is couched in our body and influenced by the environment (Barsalou, 2008). One of the major challenges for EGC is constituted by abstract concepts (ACs), like fantasy. Recently, some EGC proposals addressed this criticism, arguing that the ACs comprise multifaced exemplars that rely on different grounding sources beyond sensorimotor one, including interoception, emotions, language, and sociality (Borghi et al., 2018). However, little is known about how ACs representation varies as a function of life experiences and their use in communication. The theoretical arguments and empirical studies comprised in this dissertation aim to provide evidence on multiple grounding of ACs taking into account their varieties and flexibility. Study I analyzed multiple ratings on a large sample of ACs and identified four distinct subclusters. Study II validated this classification with an interference paradigm involving motor/manual, interoceptive, and linguistic systems during a difficulty rating task. Results confirm that different grounding sources are activated depending on ACs kind. Study III-IV investigate the variability of institutional concepts, showing that the higher the law expertise level, the stronger the concrete/emotional determinants in their representation. Study V introduced a novel interactive task in which abstract and concrete sentences serve as cues to simulate conversation. Analysis of language production revealed that the uncertainty and interactive exchanges increase with abstractness, leading to generating more questions/requests for clarifications with abstract than concrete sentences. Overall, results confirm that ACs are multidimensional, heterogeneous, and flexible constructs and that social and linguistic interactions are crucial to shaping their meanings. Investigating ACs in real-time dialogues may be a promising direction for future research.

The Hitchin map for one-nodal base curves of compact type

Studying moduli spaces of semistable Higgs bundles (E, \phi) of rank n on a smooth curve C, a key role is played by the spectral curve X (Hitchin), because an important result by Beauville-Narasimhan-Ramanan allows us to study isomorphism classes of such Higgs bundles in terms of isomorphism classes of rank-1 torsion-free sheaves on X. This way, the generic fibre of the Hitchin map, which associates to any semistable Higgs bundle the coefficients of the characteristic polynomial of \phi, is isomorphic to the Jacobian of X. Focusing on rank-2 Higgs data, this construction was extended by Barik to the case in which the curve C is reducible, one-nodal, having two smooth components. Such curve is called of compact type because its Picard group is compact. In this work, we describe and clarify the main points of the construction by Barik and we give examples, especially concerning generic fibres of the Hitchin map. Referring to Hausel-Pauly, we consider the case of SL(2,C)-Higgs bundles on a smooth base curve, which are such that the generic fibre of the Hitchin map is a subvariety of the Jacobian of X, the Prym variety. We recall the description of special loci, called endoscopic loci, such that the associated Prym variety is not connected. Then, letting G be an affine reductive group having underlying Lie algebra so(4,C), we consider G-Higgs bundles on a smooth base curve. Starting from the construction by Bradlow-Schaposnik, we discuss the associated endoscopic loci. By adapting these studies to a one-nodal base curve of compact type, we describe the fibre of the SL(2,C)-Hitchin map and of the G-Hitchin map, together with endoscopic loci. In the Appendix, we give an interpretation of generic spectral curves in terms of families of double covers.

A glassful of graphene: graphene-based materials for drinking water remediation

Modern world suffers from an intense water crisis. Emerging contaminants represent one of the most concerning elements of this issue. Substances, molecules, ions, and microorganisms take part in this vast and variegated class of pollutants, which main characteristic is to be highly resistant to traditional water purification technologies. An intense international research effort is being carried out in order to find new and innovative solutions to this problem, and graphene-based materials are one of the most promising options. Graphene oxide (GO) is a nanostructured material where domains populated by oxygenated groups alternate with interconnected areas of sp2 hybridized carbon atoms, on the surface of a one-atom thick nanosheets. GO can adsorb a great number of molecules and ions on its surface, thanks to the variety of different interactions that it can express, such as hydrogen bonding, p-p stacking, and electrostatic and hydrophobic interaction. These characteristics, added to the high superficial area, make it an optimal material for the development of innovative materials for drinking water remediation. The main concern in the use of GO in this field is to avoid secondary contaminations (i.e. GO itself must not become a pollutant). This issue can be faced through the immobilization of GO onto polymeric substrates, thus developing composite materials. The use of micro/ultrafiltration polymeric hollow fibers as substrates allows the design of adsorptive membranes, meaning devices that can perform filtration and adsorption simultaneously. In this thesis, two strategies for the development of adsorptive membranes were investigated: a core-shell strategy, where hollow fibers are coated with GO, and a coextrusion strategy, where GO is embedded in the polymeric matrix of the fibers. The so-obtained devices were exploited for both fundamental studies (i.e. molecular and ionic behaviour in between GO nanosheets) and real applications (the coextruded material is now at TRL 9).