MODELING UNFOLDED STATES OF PROTEINS AND PEPTIDES .2. BACKBONE SOLVENT ACCESSIBILITY

Buried surface area is often used as a measure of the contribution to protein folding from the hydrophobic effect. Quantitatively, the surfa ce buried upon folding is reckoned as the difference in area between t he native and unfolded states. This calculation is well defined for a known structure but model-dependent for the unfolded state. In a previ ous paper [Creamer, T. P., Srinivasan, R., & Rose, G. D. (1995) Bioche mistry 34, 16245-16250], we developed two models that bracket the surf ace area of the unfolded state between Limiting extremes. Using these extrema, it was shown that earlier models, such as an extended tripept ide, overestimate the surface area of side chains in the unfolded stat e. In this sequel to our previous paper, we focus on backbone surface in the unfolded state, again adopting the strategy of trapping the are a between limiting extrema. A principal conclusion of this present stu dy is that most backbone surface in proteins is buried within local st ructure.