Ricerc@Sapienza

In this paper we review our recent findings on the different interaction mechanisms of the C-terminal domain of the nucleoprotein (N) of measles virus (MeV) NTAIL, a model viral intrinsically disordered protein (IDP), with two of its known binding partners, i.e., the C-terminal X domain of the phosphoprotein of MeV XD (a globular viral protein) and the heat-shock protein 70 hsp70 (a globular cellular protein). The NTAIL binds both XD and hsp70 via a molecular recognition element (MoRE) that is flanked by two fuzzy regions.

Metamorphic proteins are biomolecules prone to adopting alternative conformations. Because of this feature, they represent ideal systems to investigate the general rules allowing primary structure to dictate protein topology. A comparative molecular dynamics study was performed on the denatured states of two proteins, sharing nearly identical amino-acid sequences (88%) but different topologies, namely an all-a-helical bundle protein named GA88 and an a + b- protein named GB88.

A set of missense mutations in the gene encoding profilin-1 has been linked to the onset of familial forms of ALS (fALS), also known as Lou Gehrig’s disease. The pathogenic potential of these mutations is linked to the formation of intracellular inclu- sions of the mutant proteins and correlates with the mutation- induced destabilization of its native, fully folded state. However, the mechanism by which these mutations promote misfolding and self-assembly is yet unclear.

InSiDDe (In Silico Disorder Design) is a program for the in silico design of intrinsically disordered proteins of desired length and disorder probability. The latter is assessed using IUPred and spans values ranging from 0.55 to 0.95 with 0.05 increments. One to ten artificial sequences per query, each made of 50 to 200 residues, can be generated by InSiDDe. We describe the rationale used to set up InSiDDe and show that an artificial sequence of 100 residues with an IUPred score of 0.6 designed by InSiDDe could be recombinantly expressed in E.

The mechanism of interaction of an intrinsically disordered protein (IDP) with its physiological partner is characterized by a disorder-to-order transition in which a recognition and a binding step take place. Even if the mechanism is quite complex, IDPs tend to bind their partner in a cooperative manner such that it is generally possible to detect experimentally only the disordered unbound state and the structured complex.

The essence of any biological processes relies on the conformational states of macromolecules and their interactions. It comes therefore with no surprises that the study of folding and binding has been centre stage since the birth of structural biology. In this context, the collaborative efforts of experimen- talists and theoreticians have tremendously increased our current knowl- edge on macromolecular structure and recognition.

Beta-2 microglobulin (β2m) is a protein responsible for a pathologic condition, known as dialysis-related amyloidosis (DRA), caused by its aggregation and subsequent amyloid formation. A naturally occurring mutation of β2m, D76N, presents a higher amyloidogenic propensity compared to the wild type counterpart. Since the three-dimensional structure of the protein is essentially unaffected by the mutation, the increased aggregation propensity of D76N has been generally ascribed to its lower thermodynamic stability and increased dynamics.

In several data-centric application domains, the need arises to extract valuable information from unstructured text documents. The recent paradigm of Ontology Mediated Information Extraction (OMIE) faces this problem by taking into account the knowledge expressed by a domain ontology, and reasoning over it to improve the quality of extracted data. MASTRO SYSTEM-T is a novel tool for OMIE, developed by Sapienza University and IBM Almaden Research. In this work, we demonstrate its usage for information extraction over real-world financial text documents from the U.S. EDGAR system.

Ground stone tool (GST) technology includes artefacts utilized in pounding or grinding
activities and characterized by long life cycles and multiple uses. The introduction of
such technology dates back to early prehistory, and for this reason, it is used as prime
evidence for tackling a wide range of archaeological questions such as the origins of
technology, patterns of daily subsistence and lifeways. In this paper, we contribute to
the field of study of GSTs by discussing the application of a novel multi-level analytical