Statistical mechanical modeling and simulations of repeat proteins. Repeat protein domains are formed by tandem arrays of repeating structural units, constitute about 20% of the eukaryotic proteome, mediating protein-protein interactions and acting as mechano-transductors. As such they may represent the basis for the construction of mechanical nanodevices. In collaboration with experimental groups in the field, we have been working on simplified models of repeat proteins which explains both the thermodynamics and the kinetics of folding of this class of proteins. We have also been carrying out atomistic molecular dynamics (MD) simulations of several repeat protein systems to study their folding behavior and their mechanical characteristics when subjected to external pulling forces.

References:

•  Settanni G., Serquera D., Marszalek P.E., Paci E., Itzhaki L.S. Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin. PLoS Comput Biol. 2013 Jan;9(1):e1002864
• Serquera D., Lee W., Settanni G., Paci E., Marszalek P.E., Itzhaki L.S. Mechanical unfolding of an ankyrin repeat protein. Biophys. J., 2010 98(7):1294-301
  

• Wetzel S.K., Settanni G., Kenig M., Binz K., Plückthun A. Folding and Unfolding Mechanism of Highly Stable Full Consensus Ankyrin Repeat Proteins. J. Mol. Biol. 2008 376(1):241-57
• Svava K. Wetzel, Christina Ewald, Simon Jurt, Giovanni Settanni, Andreas Plückthun and Oliver Zerbe. Residue-resolved stability of full-consensus ankyrin repeat proteins probed by NMR. J. Mol. Biol., 2010 402(1):241-58

Figure Caption: (Top) Cartoon of an ankyrin repeat protein. (Bottom) Free energy landscape of a consensus designed ankyrin repeat protein (NI3C) with five repeat, at 0M [GdmHCl] obtained using an Ising-like model.

Peptide folding. Our activity focuses on the development and application of methods for the identification of the folding transition state of peptides  and, more in general, for the complete characteriztion and representation of the dynamics of peptides by using atomistic molecular dynamics simulations . This research effort is based on the application of concepts like kinetic networks and Markov models to the trajectory data of peptides collected by MD simulations. Results from this line of research are validated against available experimental data on the kinetics of folding of peptides (folding/unfolding rates, phi values).

References:

• Radford IH, Fersht AR, Settanni G. Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding. J Phys Chem B. 2011 115(22):7459-71
• Settanni G., Fersht A. R. High Temperature Unfolding Simulations of the TRPZ1 peptide
  Biophys. J. 2008 94(11):4444-53
• Settanni G., Rao F., Caflisch A. Phi-value analysis by molecular dynamics simulations of reversible folding. Proc. Natl. Acad. Scie. USA, 2005, 102:628-33.

Figure Caption: Kinetic network representation of the conformational space of TRPZ1 peptide from MD simulations. Each circle represents a set of similar conformations (cluster). The size of the circle is proportional to the number of conformations in the cluster. Pair of clusters are connected by lines when a transition from one to the other has been observed along the simulations. Clusters with similar connectivity pattern are placed close together in the plot. The network structure naturally reveals the presence of large states, the native N, the intermediate I and the denatured D state.

Transport and adsorption properties of blood proteins. Transport of nutrients to peripheral tissues and healing of damaged blood vessels are among the most important functions of blood. These functions involve the action of a series of proteins some of which are found in large amounts in the blood circulation. Fibrinogen is a multiprotein complex which, when activated, aggregate to form fibrin, a net-shaped molecular formation which is fundamental for the coagulation of blood following, i.e, a wound or when an extraneous body comes into contact with blood (i.e., graft implants). Thus, adsorption of fibrinogen on material surfaces play an important role in viability of those materials for implants. In collaboration with experimental groups in the field, we use atomistic molecular dynamics simulations to characterize the adsorption process of fibrinogen on material surfaces. Another important molecule in the blood is albumin, which mediate transport of lipids and other molecules in blood. Albumin is a multidomain protein which provides several binding sites used to bind a range of different target molecules. Target molecules (lipids, drugs, etc.) bind to albumin which act as a transporter, and are then released where needed by blood circulation. Here we use molecular dynamics simulations to study the binding modes of several lipids to Albumin and the kinetics of lipid release/uptake.

Figure Caption: Simulation box containing a water solvated fibrinogen molecule on a slab of amorphus silica.