Alfredo Di Nola

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A new method for simulating the folding process of a protein is reported. The method is based on the essential dynamics sampling technique. In essential dynamics sampling, a usual molecular dynamics simulation is performed, but only those steps, not increasing the distance from a target structure, are accepted. The distance is calculated in a(More)
In this paper we address the question of how a protein environment can modulate the absorption spectrum of a chromophore during a molecular dynamics simulation. The effect of the protein is modeled as an external field acting on the unperturbed eigenstates of the chromophore. Using a first-principles method recently developed in our group, we calculated the(More)
The effect of temperature on the activation of native fluctuation motions during molecular dynamics unfolding simulations of horse heart cytochrome c has been studied. Essential dynamics analysis has been used to analyze the preferred directions of motion along the unfolding trajectories obtained by high temperature simulations. The results of this study(More)
In this article we use the recently developed perturbed matrix method (PMM) to investigate the effect of conformational fluctuations on the electronic properties of heme in Myoglobin. This widely studied biomolecule has been chosen as a benchmark for evaluating the accuracy of PMM in a large and complex system. Using a long, 80-ns, molecular dynamics(More)
The dynamical aspects of the fully hydrated TEM-1 beta-lactamase have been determined by a 5 ns Molecular Dynamics simulation. Starting from the crystallographic coordinates, the protein shows a relaxation in water with an overall root mean square deviation from the crystal structure increasing up to 0.17 nm, within the first nanosecond. Then a plateau is(More)
The calculation of free energies by computer simulation represents one of the most promising areas in molecular modeling. While the computational methods developed so far give reliable results for liquids or solutions, they are not satisfactory for globular proteins. The reproducibility of the data is poor due to several sources of error. The most important(More)
In 2000 in Italy about 470,000 workers found jobs provided by Temporary Work Agencies, i.e., more than twice the number in 1999. Temporary Work is an expanding phenomenon since it well suits the flexibility requirements of business: 77% of Temporary Work is in the manufacturing industry, involving mostly unskilled workers. The young age, low level of(More)
In recent years several implementations of molecular dynamics Ž. Ž. MD codes have been reported on multiple instruction multiple data MIMD machines. However, very few implementations of MD codes on single instruction Ž. multiple data SIMD machines have been reported. The difficulty in using pair lists of nonbonded interactions is the major problem with MD(More)
Oxidative stress is a widespread challenge for living organisms, and especially so for parasitic ones, given the fact that their hosts can produce reactive oxygen species (ROS) as a mechanism of defense. Thus, long lived parasites, such as the flatworm Schistosomes, have evolved refined enzymatic systems capable of detoxifying ROS. Among these, glutathione(More)
Human neutrophil collagenase (HNC, MMP-8) is one of the target enzymes for drug treatment of pathologic extracellular matrix degradation. Peptidomimetic inhibitors bind in the S'-side of the enzyme active site occupying the S'1 primary specificity pocket by their large hydrophobic side-chains. The crystal structure of the complex between the catalytic(More)