Sequence-based study of two related proteins with different folding behaviors

ZSPA-1 is an engineered protein that binds to its parent, the three-helix-bundle Z domain of staphylococcal protein A. Uncomplexed ZSPA-1 shows a reduced helix content and a melting behavior that is less cooperative, compared with the wild-type Z domain. Here we show that the difference in folding behavior between these two sequences can be partly understood in terms of an off-lattice model with 5-6 atoms per amino acid and a minimalistic potential, in which folding is driven by backbone hydrogen bonding and effective hydrophobic attraction.Comment: 12 pages, 5 figure

The Young Classic

2017 Jan Rehner Writing Prize Finalists, 4th Year Honourable MentionWRIT 470

Monte Carlo Update for Chain Molecules: Biased Gaussian Steps in Torsional Space

We develop a new elementary move for simulations of polymer chains in torsion angle space. The method is flexible and easy to implement. Tentative updates are drawn from a (conformation-dependent) Gaussian distribution that favors approximately local deformations of the chain. The degree of bias is controlled by a parameter b. The method is tested on a reduced model protein with 54 amino acids and the Ramachandran torsion angles as its only degrees of freedom, for different b. Without excessive fine tuning, we find that the effective step size can be increased by a factor of three compared to the unbiased b=0 case. The method may be useful for kinetic studies, too.Comment: 14 pages, 4 figure

Beyond e-learning: from blended methodology to transmedia education

Nowadays, at the time of convergence culture, social network, and transmedia storytelling – when social interactions are constantly remediated – e-learning, especially in universities, should be conceived as a sharing educational activity. Different learning experiences should become smoother and able to fade out the closed learning environments (as software platform and classrooms (either virtual or not)). In this paper, we will show some experiences of the Communication Sciences degree program of the University of Cagliari, which is supplied through an e-learning method. In the ten years since its foundation, the approach has evolved from a blended learning with two kinds of traditional activity (online activities and face-to-face lessons) to a much more dynamic learning experience. Many new actors (communication companies, local government, public-service corporations, new media and social media) – indeed – have been involved in educational and teaching process. But also these processes changed: collaborative working, new media comprehension, self-guided problem solving are examples of the new literacies and approaches that can be reached as new learning objectives

Interazioni tra fumi e sistemi sprinkler: analisi fluidodinamica durante un incendio

Gli incendi in galleria costituiscono uno degli scenari incidentali di maggior rischio e sono stati oggetto di ampi studi in letteratura, volti ad indagarne lo sviluppo o l’influenza di vari parametri, come ad esempio l’effetto delle ostruzioni sulla velocità critica di ventilazione. Uno sviluppo minore è invece riscontrabile per quanto riguarda l’utilizzo e gli effetti di impianti di tipo sprinkler per migliorare la sicurezza dei tunnel stradali. Un esempio recente è costituito dallo studio di Zheng e Ingason, in cui l’impiego di sprinkler è stato testato su una riproduzione in scala di una galleria stradale. Questo studio si propone di indagare l’interazione tra i fumi e i sistemi antincendio fissi ad acqua in galleria, problema che risulta essere tuttora non completamente risolto

Preliminary CFD analysis of a ventilated chamber for candles testing

As candles have grown in popularity with consumers over the last few years, so has the potential safety concern with their use in indoor environments. Carbon monoxide, particulate matter and different volatile and semi-volatile species can be found in candles emissions. Currently it is not possible to predict theoretically which emissions will be produced by a specific candle and in order to quantify real emissions is still necessary to proceed with experimental tests. A common way to quantify released pollutants is to burn candles in a well-controlled environment, such as a laboratory-scale test chambers. Obviously, it is required that these chambers are able to reproduce the environmental combustion regime of the candles, so as to guarantee that an equal level of emissions is produced and measured. Another crucial point is related to the measurements themselves: generally, air quality is measured in a single point inside the chamber with the assumption that the air and the exhausts in that point are representative of the whole ambient. This work aims to reproduce one of these chambers by means of a CFD (Computational Fluid Dynamics) model, with the purpose of obtaining an adequate tool to analyze and design more efficient test chambers. A comparison with an ad hoc experiment is performed to validate the CFD model

Thermodynamics of alpha- and beta-structure formation in proteins

An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good approximation can be described by a simple two-state model, with parameters that are in reasonable quantitative agreement with experimental data. Despite the apparent two-state character of the melting curves, the energy distributions are found to lack a clear bimodal shape, which is discussed in some detail. We also perform a Monte Carlo-based kinetic study and find, in accord with experimental data, that the alpha-helix forms faster than the beta-hairpin.Comment: 18 pages, 4 figure

Two-state folding over a weak free-energy barrier

We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded states of this protein is found to be weak, even at the folding temperature. Nevertheless, we find that melting curves to a good approximation can be described in terms of a simple two-state system, and that the relaxation behavior is close to single exponential. The motion along individual reaction coordinates is roughly diffusive on timescales beyond the reconfiguration time for an individual helix. A simple estimate based on diffusion in a square-well potential predicts the relaxation time within a factor of two.Comment: 22 pages, 5 figure

Oligomerization of amyloid Abeta peptides using hydrogen bonds and hydrophobicity forces

The 16-22 amino acid fragment of the beta-amyloid peptide associated with the Alzheimer's disease, Abeta, is capable of forming amyloid fibrils. Here we study the aggregation mechanism of Abeta(16-22) peptides by unbiased thermodynamic simulations at the atomic level for systems of one, three and six Abeta(16-22) peptides. We find that the isolated Abeta(16-22) peptide is mainly a random coil in the sense that both the alpha-helix and beta-strand contents are low, whereas the three- and six-chain systems form aggregated structures with a high beta-sheet content. Furthermore, in agreement with experiments on Abeta(16-22) fibrils, we find that large parallel beta-sheets are unlikely to form. For the six-chain system, the aggregated structures can have many different shapes, but certain particularly stable shapes can be identified.Comment: 19 pages, 7 figures (to appear in Biophys. J.