Physicist by training, Francesco Rao started a PhD at the University of Zurich in the Biochemistry department at the beginning of 2002. The PhD training was concluded by a thesis on protein folding and aggregation, introducing the novel technique of complex networks analysis of molecular dynamics (MD) simulations. He was then assigned a prestigious Italian fellowship from the research center "E. Fermi'' located in Rome, where he continued to work on the theory of complex networks and their application to biomolecular transitions. In 2007 he moved to the University of Strasbourg/ISIS in the group of Prof. M. Karplus as an EMBO fellow, investigating the role of dynamics in protein allostery and enzyme catalysis.
Proteins are fascinating complex systems. The traditional structure-function paradigm, "to know function study structure'' which goes back to Watson and Crick, have guided our interpretation of protein function for decades. But our mechanistic understanding of how those processes are regulated is still unclear. It is only rather recently that the possible role of dynamics in signaling, allostery and catalytic activity, per se, has been recognized. The goal of our research is to understand and elucidate the role of dynamics in the context of protein function. To this aim we use the tools of molecular dynamics simulations and complex network analysis to obtain high resolution mappings of the underlying free-energy landscape. The latter, driving the biologically relevant conformational transition, provide a quantitative insight on both the thermodynamics and kinetics of the process.
- D. Prada-Gracia, R. Shevchuk, P. Hamm, F. Rao: Towards a microscopic description of the free-energy landscape of water. J Chem Phys, 2012; 137 (14): 144504. http://dx.doi.org/10.1063/1.4755746
- R. Shevchuk, D. Prada-Gracia, F. Rao: Water Structure-Forming Capabilities are Temperature Shifted for Different Models. J Phys Chem B, 2012; 116 (25):7538-7543. http://dx.doi.org/10.1021/jp303583f
- R. Shevchuk, F. Rao: Note: Microsecond long atomistic simulation of supercooled water. J Chem Phys, 2012; 137 (3): 036101. http://dx.doi.org/10.1063/1.4737867
- S. Mostarda, D. Gfeller, F. Rao: Beyond the Binding Site: The Role of the beta2 - beta3 Loop and Extra-Domain Structures in PDZ Domains. Plos Comput Biol, 2012; 8 (3) : e1002429-e1002429. http://dx.doi.org/10.1371/journal.pcbi.1002429
- F. Rao: Protein Inherent Structures by Different Minimization Strategies J Comput Chem, 2011; 32 (6): 1113-1116
- M. Seeber, F. Rao, F. Fanelli: Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces J Comput Chem, 2011; 32 (6): 1183-1194
- S. Garrett-Roe, F. Perakis, F. Rao, P. Hamm: Three-Dimensional Infrared Spectroscopy of Isotope-Substituted Liquid Water Reveals Heterogeneous Dynamics J Phys Chem B, 2011; 115 (21): 6976-6984
- F. Rao, Local Transition Gradients Indicating the Global Attributes of Protein Energy Landscapes, J. Phys. Chem. Lett. (2010), 1, 1580-1583
- F. Rao and M. Karplus, Protein dynamics investigated by inherent structure analysis, Proc. Natl. Acad. Sci. USA (2010) 107, 9152-9157
- D. Gfeller, D. Morton de Lachapelle, P. De Los Rios, G. Caldarelli, and F. Rao, Uncovering the topology of configuration space networks, Phys. Rev. E (2007) 76, 026113
- D. Gfeller, P. De Los Rios, A. Caflisch, and F. Rao, Complex network analysis of free-energy landscapes, Proc. Natl. Acad. Sci. USA (2007) 104, 1817-1822
- M. Seeber , M. Cecchini , F. Rao , G. Settanni and A. Caflisch, Wordom: a program for efficient analysis of molecular dynamics simulations, Bionform. (2007) 23, 2625
- F. Rao and A. Caflisch, The protein folding network, J. Mol. Biol. (2004) 342, 299-306
- F. Rao and A. Caflisch, Replica exchange molecular dynamics simulations of reversible folding, J. Chem. Phys. (2003) 119, 4035-42