Mechanisms of Protein Folding

Proteins are linear polymers of amino-acids responsible for catalyzing specific reactions in the the cell. This high specificity of proteins towards particular reactions in the cell is the result of an evolution process on the design of each protein active native state. In nature this native state corresponds to the minimum free energy conformation (or ensemble of conformations) for each protein. I study of the mechanisms involved in the process of proteins spontaneously achieving the native state from the low structured denatured state. We theoretically investigate and characterize the transition state of the folding process as a function of the native contact order, while keeping close contact with current experimental techniques, helping to interpret their results and approaches. This work is done in collaboration with



Why do proteins folding rates correlate with metrics of native topology?, Patrícia F N Faísca, Rui D M Travasso, Andrea Parisi, and Antonio Rey, PLoS ONE, 7, e35599 (2012)

Non-native interactions play an effective role in protein folding dynamics, Patrícia F. N. Faísca, Ana Nunes, Rui D.M. Travasso, and Eugene I. Shakhnovich, Protein Science 19, 2196-2209 (2010)

The folding of knotted proteins: insights from lattice simulations, Patrícia F N Faísca, Rui D M Travasso, Tiago Charters, Ana Nunes and Marek Cieplak, Physical Biology 7, 016009 (2010)

The protein folding transition state: Insights from kinetics and thermodynamics, Rui D. M. Travasso, Patrícia F. N. Faísca, Antonio Rey, J. Chem. Phys. 133, 125102 (2010)

Identifying critical residues in protein folding: Insights from ϕ-value and Pfold analysis, Patricia F.N. Faisca, Rui D.M. Travasso, Robin C. Ball, and Eugene I. Shakhnovich, J. Chem Phys 129, 095108 (2008)

Pathways to folding, nucleation events and native geometry, Rui D. M. Travasso, Margarida M. Telo da Gama, and Patricia Faisca, J Chem Phys 127, 145106 (2007)

Nucleation phenomena in protein folding: the modulating role of protein sequence, Rui D. M. Travasso, Patricia Faisca, and Margarida M Telo da Gama, J. Phys.: Condens. Matter 19, 285212 (2007)