Better biomolecule thermodynamics from kinetics

Kiran Girdhar, Gregory Scott, Yann R. Chemla, Martin Gruebele

Research output: Contribution to journalArticle

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 Tm can be extracted reliably by our thermodynamics from kinetics approach, even when conventional fitting is unreliable.

Original languageEnglish (US)
Article number015102
JournalJournal of Chemical Physics
Volume135
Issue number1
DOIs
StatePublished - Jul 7 2011

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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