title: Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations.
abstract: With the help of molecular-dynamics simulations, we studied the effect of urea and guanidine chloride on the thermodynamic and structural properties of the helical fragment of protein GB1, comparing them with those of its second beta hairpin. We showed that the helical fragment in different solvents populates an ensemble of states that is more complex than that of the hairpin, and thus the associated experimental observables (circular-dichroism spectra, secondary chemical shifts, m values), that we back-calculated from the simulations and compared with the actual data, are more difficult to interpret. We observed that in the case of both peptides, urea binds tightly to their backbone, while guanidine exerts its denaturing effect in a more subtle way, strongly affecting the electrostatic properties of the solution. This difference can have consequences in the way denaturation experiments are interpreted. Proteins 2017; 85:753-763. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Center for Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN, via Celoria 16, Milano, 20133, Italy.
authors.forename: R
authors.initials: R
authors.lastname: Meloni
authors.affiliation: Center for Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN, via Celoria 16, Milano, 20133, Italy.
authors.forename: G
authors.identifier: 0000-0001-9868-1809
authors.initials: G
authors.lastname: Tiana
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D019791:Guanidine / Q000737:chemistry*; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D011489:Protein Denaturation; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D013291:Streptococcus / Q000737:chemistry; D013816:Thermodynamics; D014508:Urea / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; C034284:IgG Fc-binding protein, Streptococcus; D014508:Urea; D019791:Guanidine
keywords: MD simulations; chemical shifts; circular dichroism; denaturants; m value; metadynamics