title: Better biomolecule thermodynamics from kinetics.
abstract: Protein stability is measured by denaturation: When solvent conditions are changed (e.g., temperature, denaturant concentration, or pH) the protein population switches between thermodynamic states. The resulting denaturation curves have baselines. If the baselines are steep, nonlinear, or incomplete, it becomes difficult to characterize protein denaturation. Baselines arise because the chromophore probing denaturation is sensitive to solvent conditions, or because the thermodynamic states evolve structurally when solvent conditions are changed, or because the barriers are very low (downhill folding). Kinetics can largely eliminate such baselines: Relaxation of chromophores, or within thermodynamic states, is much faster than the transition over activation barriers separating states. This separation of time scales disentangles population switching between states (desired signal) from chromophore or population relaxation within states (baselines). We derive simple formulas to extract unfolding thermodynamics from kinetics. The formulas are tested with model data and with a difficult experimental test case: the apparent two-state folder PI3K SH3 domain. Its melting temperature T(m) can be extracted reliably by our "thermodynamics from kinetics approach," even when conventional fitting is unreliable.
authors: Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, USA.
authors: Kiran
authors: K
authors: Girdhar
authors: Gregory
authors: G
authors: Scott
authors: Yann R
authors: YR
authors: Chemla
authors: Martin
authors: M
authors: Gruebele
mesh_terms: D000595:Amino Acid Sequence; D007700:Kinetics; D008969:Molecular Sequence Data; D019869:Phosphatidylinositol 3-Kinases / Q000737:chemistry* / Q000235:genetics; D011489:Protein Denaturation; D015202:Protein Engineering; D055550:Protein Stability; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics; D013816:Thermodynamics; D018909:src Homology Domains
chemical_list: D011994:Recombinant Proteins; D019869:Phosphatidylinositol 3-Kinases