Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2017-04, Vol.85 (4), p.753-763
• Main Authors: Meloni, R., Tiana, G.
• Format: Article
• Language: English
• Subjects: Backbone; Bacterial Proteins - chemistry; Binding Sites; chemical shifts; Chlorides; circular dichroism; Circularity; denaturants; Denaturation; Dichroism; Electrostatic properties; Fragmentation; Guanidine - chemistry; Guanidine hydrochloride; m value; Mathematical analysis; MD simulations; metadynamics; Molecular dynamics; Peptides; Properties (attributes); Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Denaturation; Protein Folding; Protein Interaction Domains and Motifs; Proteins; Simulation; Solvents; Spectra; Streptococcus - chemistry; Thermodynamics; Urea; Urea - chemistry
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.25255

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.