title: Comparison of chemical and thermal protein denaturation by combination of computational and experimental approaches. II.
abstract: Chemical and thermal denaturation methods have been widely used to investigate folding processes of proteins in vitro. However, a molecular understanding of the relationship between these two perturbation methods is lacking. Here, we combined computational and experimental approaches to investigate denaturing effects on three structurally different proteins. We derived a linear relationship between thermal denaturation at temperature T(b) and chemical denaturation at another temperature T(u) using the stability change of a protein (ΔG). For this, we related the dependence of ΔG on temperature, in the Gibbs-Helmholtz equation, to that of ΔG on urea concentration in the linear extrapolation method, assuming that there is a temperature pair from the urea (T(u)) and the aqueous (T(b)) ensembles that produces the same protein structures. We tested this relationship on apoazurin, cytochrome c, and apoflavodoxin using coarse-grained molecular simulations. We found a linear correlation between the temperature for a particular structural ensemble in the absence of urea, T(b), and the temperature of the same structural ensemble at a specific urea concentration, T(u). The in silico results agreed with in vitro far-UV circular dichroism data on apoazurin and cytochrome c. We conclude that chemical and thermal unfolding processes correlate in terms of thermodynamics and structural ensembles at most conditions; however, deviations were found at high concentrations of denaturant.
authors: Department of Physics, University of Houston, Houston, Texas 77204-5005, USA.
authors: Qian
authors: Q
authors: Wang
authors: Alexander
authors: A
authors: Christiansen
authors: Antonios
authors: A
authors: Samiotakis
authors: Pernilla
authors: P
authors: Wittung-Stafshede
authors: Margaret S
authors: MS
authors: Cheung
mesh_terms: D001059:Apoproteins / Q000737:chemistry*; D001400:Azurin / Q000737:chemistry*; D002942:Circular Dichroism; D045304:Cytochromes c / Q000737:chemistry*; D005418:Flavodoxin / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011489:Protein Denaturation; D017510:Protein Folding; D012997:Solvents / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics; D014508:Urea / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D001059:Apoproteins; D005418:Flavodoxin; D012997:Solvents; C038778:apoazurin; C026932:apoflavodoxin; D014867:Water; D001400:Azurin; D014508:Urea; D045304:Cytochromes c