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.

Characterization of the Staphylococcus aureus bone sialoprotein-binding protein SdrE and the serine protease EpiP

In an attempt to develop a Staphylococcus aureus vaccine, we have applied reverse vaccinology approach, mainly based on in silico screening and proteomics. By using this approach SdrE, a protein belonging to serine-aspartate repeat protein family was identified as potential vaccine antigen against S. aureus. We have investigated the biochemical properties as well as the vaccine potential of SdrE and its highly conserved CnaBE3 domain. We found the protein SdrE to be resistant to trypsin. Further analysis of the resistant fragment revealed that it comprises a CnaBE3 domain, which also showed partial trypsin resistant behavior. Furthermore, intact mass spectrometry of rCnaBE3 suggested the possible presence of isopeptide bond or some other post-translational modification in the protein.However, this observation needs further investigation. Differential Scanning Fluorimetry study reveals that calcium play role in protein folding and provides stability to SdrE. At the end we have demonstrated that SdrE is immunogenic against clinical strain of S. aureus in murine abscess model. In the second part, I characterized a protein, annotated as epidermin leader peptide processing serine protease (EpiP), as a novel S. aureus vaccine candidate. The crystal structure of the rEpiP was solved at 2.05 Å resolution by x-ray crystallography . The structure showed that rEpiP was cleaved somewhere between residues 95 and 100 and cleavage occurs through an autocatalytic intra-molecular mechanism. In addition, the protein expressed by S. aureus cells also appeared to undergo a similar processing event. To determine if the protein acts as a serine protease, we mutated the catalytic serine 393 residue to alanine, generating rEpiP-S393A and solved its crystal structure at a resolution of 1.95 Å. rEpiP-S393A was impaired in its protease activity, as expected. Protective efficacy of rEpiP and the non-cleaving mutant protein was comparable, implying that the two forms are interchangeable for vaccination purposes.

Metodi computazionali per l'annotazione di genomi e proteomi

Il progresso tecnologico nel campo della biologia molecolare, pone la comunità scientifica di fronte all’esigenza di dare un’interpretazione all’enormità di sequenze biologiche che a mano a mano vanno a costituire le banche dati, siano esse proteine o acidi nucleici. In questo contesto la bioinformatica gioca un ruolo di primaria importanza. Un nuovo livello di possibilità conoscitive è stato introdotto con le tecnologie di Next Generation Sequencing (NGS), per mezzo delle quali è possibile ottenere interi genomi o trascrittomi in poco tempo e con bassi costi. Tra le applicazioni del NGS più rilevanti ci sono senza dubbio quelle oncologiche che prevedono la caratterizzazione genomica di tessuti tumorali e lo sviluppo di nuovi approcci diagnostici e terapeutici per il trattamento del cancro. Con l’analisi NGS è possibile individuare il set completo di variazioni che esistono nel genoma tumorale come varianti a singolo nucleotide, riarrangiamenti cromosomici, inserzioni e delezioni. Va però sottolineato che le variazioni trovate nei geni vanno in ultima battuta osservate dal punto di vista degli effetti a livello delle proteine in quanto esse sono le responsabili più dirette dei fenotipi alterati riscontrabili nella cellula tumorale. L’expertise bioinformatica va quindi collocata sia a livello dell’analisi del dato prodotto per mezzo di NGS ma anche nelle fasi successive ove è necessario effettuare l’annotazione dei geni contenuti nel genoma sequenziato e delle relative strutture proteiche che da esso sono espresse, o, come nel caso dello studio mutazionale, la valutazione dell’effetto della variazione genomica. È in questo contesto che si colloca il lavoro presentato: da un lato lo sviluppo di metodologie computazionali per l’annotazione di sequenze proteiche e dall’altro la messa a punto di una pipeline di analisi di dati prodotti con tecnologie NGS in applicazioni oncologiche avente come scopo finale quello della individuazione e caratterizzazione delle mutazioni genetiche tumorali a livello proteico.

Exploring host-pathogen interactions through protein microarray. Large-scale protein microarray analysis revealed novel human receptors for the staphylococcal immune evasion protein FLIPr and for the neisserial adhesin NadA

Adhesion, immune evasion and invasion are key determinants during bacterial pathogenesis. Pathogenic bacteria possess a wide variety of surface exposed and secreted proteins which allow them to adhere to tissues, escape the immune system and spread throughout the human body. Therefore, extensive contacts between the human and the bacterial extracellular proteomes take place at the host-pathogen interface at the protein level. Recent researches emphasized the importance of a global and deeper understanding of the molecular mechanisms which underlie bacterial immune evasion and pathogenesis. Through the use of a large-scale, unbiased, protein microarray-based approach and of wide libraries of human and bacterial purified proteins, novel host-pathogen interactions were identified. This approach was first applied to Staphylococcus aureus, cause of a wide variety of diseases ranging from skin infections to endocarditis and sepsis. The screening led to the identification of several novel interactions between the human and the S. aureus extracellular proteomes. The interaction between the S. aureus immune evasion protein FLIPr (formyl-peptide receptor like-1 inhibitory protein) and the human complement component C1q, key players of the offense-defense fighting, was characterized using label-free techniques and functional assays. The same approach was also applied to Neisseria meningitidis, major cause of bacterial meningitis and fulminant sepsis worldwide. The screening led to the identification of several potential human receptors for the neisserial adhesin A (NadA), an important adhesion protein and key determinant of meningococcal interactions with the human host at various stages. The interaction between NadA and human LOX-1 (low-density oxidized lipoprotein receptor) was confirmed using label-free technologies and cell binding experiments in vitro. Taken together, these two examples provided concrete insights into S. aureus and N. meningitidis pathogenesis, and identified protein microarray coupled with appropriate validation methodologies as a powerful large scale tool for host-pathogen interactions studies.

Zinco, invecchiamento e sistema immunitario: effetti sull'apoptosi e sulla proliferazione dei linfociti

Immunosenescence is characterized by a complex remodelling of the immune system, mainly driven by lifelong antigenic burden. Cells of the immune system are constantly exposed to a variety of stressors capable of inducing apoptosis, including antigens and reactive oxygen species continuously produced during immune response and metabolic pathways. The overall homeostasis of the immune system is based on the balance between antigenic load, oxidative stress, and apoptotic processes on one side, and the regenerative potential and renewal of the immune system on the other. Zinc is an essential trace element playing a central role on the immune function, being involved in many cellular processes, such as cell death and proliferation, as cofactor of enzymes, nuclear factors and hormones. In this context, the age associated changes in the immune system may be in part due to zinc deficiency, often observed in aged subjects and able to induce impairment of several immune functions. Thus, the aim of this work was to investigate the role of zinc in two essential events for immunity during aging, i.e. apoptosis and cell proliferation. Spontaneous and oxidative stress-induced apoptosis were evaluated by flow cytometry in presence of a physiological concentration of zinc in vitro on peripheral blood mononuclear cells (PBMCs) obtained from healthy subjects of different age: a group of young subjects, a group of old subjects and a group of nonagenarians. In addition, cell cycle phases were analyzed by flow cytometry in PBMCs, obtained from the subjects of the same groups in presence of different concentration of zinc. We also analyzed the influence of zinc in these processes in relation to p53 codon 72 polymorphism, known to affect apoptosis and cell cycle in age-dependent manner. Zinc significantly reduces spontaneous apoptosis in all age-groups; while it significantly increases oxidative stress-induced late apoptosis/necrosis in old and nonagenarians subjects. Some factors involved in the apoptotic pathway were studied and a zinc effect on mitochondrial membrane depolarization, cytochrome C release, caspase-3 activation, PARP cleavage and Bcl-2 expression was found. In conclusion, zinc inhibits spontaneous apoptosis in PBMCs contrasting the harmful effects due to the cellular culture conditions. On the other hand, zinc is able to increase toxicity and induce cell death in PBMCs from aged subjects when cells are exposed to stressing agents that compromise antioxidant cellular systems. Concerning the relationship between the susceptibility to apoptosis and p53 codon 72 genotype, zinc seems to affect apoptosis only in PBMCs from Pro- people suggesting a role of this ion in strengthening the mechanism responsible of the higher propensity of Pro- towards apoptosis. Regarding cell cycle, high doses of zinc could have a role in the progression of cells from G1 to S phase and from S to G2/M phase. These effect seems depend on the age of the donor but seems to be unrelated to p53 codon 72 genotype. In order to investigate the effect of an in vivo zinc supplementation on apoptosis and cell cycle, PBMCs from a group of aged subjects were studied before and after six weeks of oral zinc supplementation. Zinc supplementation reduces spontaneous apoptosis and it strongly reduces oxidative stress-induced apoptosis. On the contrary, no effect of zinc was observed on cell cycle. Therefore, it’s clear that in vitro and in vivo zinc supplementation have different effects on apoptosis and cell cycle in PBMCs from aged subjects. Further experiments and clinical trials are necessary to clarify the real effect of an in vivo zinc supplementation because this preliminary data could encourage the of this element in all that disease with oxidative stress pathogenesis. Moreover, the expression of metallothioneins (MTs), proteins well known for their zinc-binding ability and involved in many cellular processes, i.e. apoptosis, metal ions detoxification, oxidative stress, differentiation, was evaluated in total lymphocytes, in CD4+ and in CD8+ T lymphocytes from young and old healthy subjects in presence of different concentration of zinc in vitro. Literature data reported that during ageing the levels of these proteins increase and concomitantly they lose the ability to release zinc. This fact induce a down-regulation of many biological functions related to zinc, such as metabolism, gene expression and signal transduction. Therefore, these proteins may turn from protective in young-adult age to harmful agents for the immune function in ageing following the concept that several genes/proteins that increase fitness early in life may have negative effects later in life: named “Antagonistic Pleyotropy Theory of Ageing”. Data obtained in this work indicate an higher and faster expression of MTs with lower doses of zinc in total lymphocytes, in CD4+ and in CD8+ T lymphocytes from old subjects supporting the antagonistic pleiotropic role of these proteins.