title: Simulation of urea-induced protein unfolding: a lesson from bovine β-lactoglobulin.
abstract: To investigate the molecular mechanisms involved in the very initial stages of protein unfolding, we carried out one long (1 μs) simulation of bovine β-lactoglobulin (BLG) together with three (500 ns) supporting MD runs, in which the unfolding conditions were produced by adding the osmolyte urea to the simulated systems and/or by increasing the thermal energy raising the temperature from 300 to 350 K. BLG was chosen, since it is a well-characterized model protein, for which structural and folding properties have been widely investigated by X-ray and NMR. MD trajectories were analyzed not only in terms of standard progress variables, such as backbone H-bonds, gyration radius width, secondary structure elements, but also through the scrutiny of interactions and dynamical behavior of specific key residues previously pointed out and investigated by NMR and belonging to a well known hydrophobic cluster. MD trajectories simulated in different unfolding conditions suggest that urea destabilizes BLG structure weakening protein::protein hydrophobic interactions and the hydrogen bond network. The early unfolding events, better observed at higher temperature, affect both secondary and tertiary structure of the protein.
authors: Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano, via Giuseppe Balzaretti 9, 20133 Milano, Italy. ivano.eberini@gmail.com
authors: Ivano
authors: I
authors: Eberini
authors: Andrew
authors: A
authors: Emerson
authors: Cristina
authors: C
authors: Sensi
authors: Laura
authors: L
authors: Ragona
authors: Piero
authors: P
authors: Ricchiuto
authors: Alessandro
authors: A
authors: Pedretti
authors: Elisabetta
authors: E
authors: Gianazza
authors: Anna
authors: A
authors: Tramontano
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D002417:Cattle; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007782:Lactoglobulins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011489:Protein Denaturation; D017434:Protein Structure, Tertiary; D011522:Protons; D012997:Solvents / Q000737:chemistry; D014508:Urea / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D000596:Amino Acids; D007782:Lactoglobulins; D011522:Protons; D012997:Solvents; D014867:Water; D014508:Urea