Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model.
We present a physically rigorous method to calculate solvent-dependent accessible surface areas (ASAs) of amino acid residues in unfolded proteins. ASA values will be larger in a good solvent, where solute-solvent interactions dominate and promote chain extension. Conversely, they will be smaller in a poor solvent, where solute-solute interactions dominate and promote chain collapse. In the method described here, these solvent-dependent effects are modeled by Boltzmann-weighting a simulated ensemble for solvent quality-good or poor. Solvent quality is parameterized as intramolecular hydrogen bond strength, using a "hydrogen bond dial" that can be varied from "off" to "high" (i.e., from 0 to -6 kcal/mol per hydrogen bond). When plotted as a function of hydrogen bond strength, the Boltzmann-weighted distribution of conformers describes a sigmoidal curve, with a transition midpoint near 1.5 kcal/mol per hydrogen bond. ASA tables for the 20 residues are provided under good solvent conditions and at this transition midpoint. For the backbone, these midpoint ASA values are found to be in good agreement with the earlier estimate of unfolded state ASA given by the mean of Creamer's upper and lower bounds [Creamer TP, et al. (1997) Biochemistry 36:2832-2835], a gratifying result in that cosolvents of experimental interest, such as urea (good solvent) and trimethylamine N-oxide (poor solvent), are known to affect the backbone predominantly. Unanticipated results from our simulations predict that a significant population of three-residue, hydrogen-bonded turns (inverse gamma-turns) will be detectable in blocked polyalanyl heptamers in poor solvent-an experimentally verifiable conjecture.
Gong
Haipeng
H
T. C. Jenkins Department of Biophysics, The Johns Hopkins University, Jenkins Hall, 3400 North Charles Street, Baltimore, MD 21218, USA.
Rose
George D
GD
D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides; D011487:Protein Conformation / Q000187:drug effects; D011489:Protein Denaturation / Q000187:drug effects*; D017433:Protein Structure, Secondary; D012995:Solubility; D012997:Solvents / Q000494:pharmacology*
D009842:Oligopeptides; D010455:Peptides; D012997:Solvents; C019529:polyalanine