title: Exploring early stages of the chemical unfolding of proteins at the proteome scale.
abstract: After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein unfolding or passively stabilize the unfolded state? By analyzing a set of 30 proteins (representative of all native folds) through extensive molecular dynamics simulations in denaturant (using a range of force-fields), we derived robust rules for urea unfolding that are valid at the proteome level. Irrespective of the protein fold, presence or absence of disulphide bridges, and secondary structure composition, urea concentrates in the first solvation shell of quasi-native proteins, but with a density lower than that of the fully unfolded state. The presence of urea does not alter the spontaneous vibration pattern of proteins. In fact, it reduces the magnitude of such vibrations, leading to a counterintuitive slow down of the atomic-motions that opposes unfolding. Urea stickiness and slow diffusion is, however, crucial for unfolding. Long residence urea molecules placed around the hydrophobic core are crucial to stabilize partially open structures generated by thermal fluctuations. Our simulations indicate that although urea does not favor the formation of partially open microstates, it is not a mere spectator of unfolding that simply displaces to the right of the folded ←→ unfolded equilibrium. On the contrary, urea actively favors unfolding: it selects and stabilizes partially unfolded microstates, slowly driving the protein conformational ensemble far from the native one and also from the conformations sampled during thermal unfolding.
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain ; Joint Research Program in Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Michela
authors.initials: M
authors.lastname: Candotti
authors.affiliation: Laufer Center, Stony Brook University, Stony Brook, New York, United States of America.
authors.forename: Alberto
authors.initials: A
authors.lastname: Pérez
authors.affiliation: Joint Research Program in Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Carles
authors.initials: C
authors.lastname: Ferrer-Costa
authors.affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Manuel
authors.initials: M
authors.lastname: Rueda
authors.affiliation: Theoretische und Computergestützte Biophysik, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany.
authors.forename: Tim
authors.initials: T
authors.lastname: Meyer
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain.
authors.forename: Josep Lluís
authors.initials: JL
authors.lastname: Gelpí
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain ; Joint Research Program in Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
mesh_terms: D058767:Protein Unfolding; D020543:Proteome
chemical_list: D020543:Proteome