Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like properties.
Recently, we have proposed that, on average, the structure of the unfolded state of small, mostly alpha-helical proteins may be similar to the native structure (the 'mean-structure' hypothesis). After examining thousands of simulations of both the folded and the unfolded states of five polypeptides in atomistic detail at room temperature, we report here a result that seems at odds with the mean-structure hypothesis. Specifically, the average inter-residue distances in the collapsed unfolded structures agree well with the statistics of the ideal random-flight chain with link length of 3.8 A (the length of one amino acid). A possible resolution of this apparent contradiction is offered by the observation that the inter-residue distances in a typical alpha-helix over short stretches are close to the average distances in an ideal random-flight chain.
Zagrovic
Bojan
B
Biophysics Program and Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.
Pande
Vijay S
VS
D003198:Computer Simulation; D011489:Protein Denaturation / Q000502:physiology*; D017433:Protein Structure, Secondary / Q000502:physiology*; D013205:Staphylococcal Protein A / Q000378:metabolism
D013205:Staphylococcal Protein A