Title
Sequence, structure, and cooperativity in folding of elementary protein structural motifs
Author
Jason K. Lai, Ginka S. Kubelka, Jan Kubelka
Year
2015
Journal
PNAS
Abstract
Residue-level unfolding of two helix-turn-helix proteins—one naturally occurring and one de novo designed—is reconstructed from multiple sets of site-specific 13C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa–Jernigan statistical potentials), local structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako–Saitô–Muñoz–Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model proteins and their fragments and 13C-amide I′ bands for multiple isotopologues of each protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two motifs is different, reflecting the order of local stability. We introduce free energy profiles for “experimental” reaction coordinates—namely, the degree of local folding as sensed by site-specific 13C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture.
Full Article
Instrument
J-815
Keywords
Circular dichroism, Secondary structure, Thermal stability, Thermodynamics, Biochemistry