A novel method reveals that solvent water favors
polyproline II over BETA-strand conformation in peptides
and unfolded proteins:
Conditional Hydrophobic Accessible Surface Area (CHASA)
Abstract:
In aqueous solution the ensemble of conformations sampled by
peptides and unfolded proteins is largely determined by their
interaction with water.
It has been a long-standing goal to capture these solute-water energetics
accurately and efficiently in calculations.
Historically, accessible surface area (ASA) is one of the
most useful approaches, but this method breaks down when applied to the
solvation energetics of amphipathic peptides and proteins.
Here we introduce a novel method in which hydrophobic ASA is
determined after first positioning water oxygens in
hydrogen-bonded orientations proximate to all
accessible peptide/protein backbone N and O atoms.
This conditional hydrophobic accessible surface area (termed CHASA)
successfully differentiates between previously unexplained
solvation energies in polyalanyl peptides.
Using experimental data, the CHASA method was validated
by predicting the PII and BETA-strand conformational preferences
of non-proline residues in the coil library
(i.e. non-ALPHA-helix, non-BETA-strand, non-BETA-turn library)
derived from X-ray elucidated structures.