Monthly Archives: May 2017

Molecular Machines within us: Folding/Unfolding Mechanism of the Cytochrome c

The Cytochrome c (Cytc) is a small heme protein of ~100 amino acids. It presents in the mitochondrion of eukaryotic cells and it is loosely associated with their inner membrane. Cytc is highly water-soluble and is an essential component of … Continue reading

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Fluorinated solvents models for MD simulations

Experimental studies on peptides and proteins stability and folding in solution are usually made in the presence of membrane mimic nonaqueous solvents. These conditions facilitate the study of hydrophobic stabilization effects.

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Secondary structure forming peptides in solution: ß-turns, ß-hairpins and three-stranded peptides

sMy research on peptides is focused on those that are able to form secondary structure elements in solution like -turn, -helix and -strands. The purpose of these investigations was to establish the stability of this peptide in view of its … Continue reading

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Effect of the fluorinated solvents on the stability of secondary structure forming peptides

The effect of 2,2,2-trifluoroethanol (TFE) as a cosolvent on the stability of three different secondary structure-forming peptides, the Melittin, the Betanova, and the β-hairpin II from the bacterial protein GB1 (see the crystal structures in Figure 1), was studied using … Continue reading

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Study of the conformational transition in amyloidogenic peptides

Understanding the conformational transitions that trigger the aggregation and amyloidogenesis of otherwise soluble peptides at atomic resolution is of fundamental relevance for the design of effective therapeutic agents against amyloid-related disorders.

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Application of Quasi-Gaussian entropy theory to predict the properties of simple fluids and biomolecules in solution

The Quasi-Gaussian Entropy theory (QGE) is a new statistical mechanics theory (Amadei et al., J. Chem. Phys. (1996), 104, 1560-1574), that can be used to predict the physical-chemistry properties of real and simulated systems in a very wide temperature range. A … Continue reading

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Molecular Dynamics Simulations Combined to X-Ray Spectroscopies XANES and EXAFS

In my Tesi di Laurea (equivalent to M.Sc. Diploma Thesis) in 1992, I have for the first time investigated and for the first time, the combination MD simulations and theoretical spectra calculation was attempted for the interpretation of experimental XANES … Continue reading

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