The solvation free energy of the peptide backbone is
conformation-dependent.
Abstract:
Does aqueous solvent discriminate
among peptide conformers? To address this
question, we computed the solvation free energy of
a blocked, 12-residue polyalanyl-peptide in explicit
water and analyzed its solvent structure. The peptide
was modeled in each of 4 conformers: ALPHA-helix,
antiparallel BETA-strand, parallel BETA-strand, and polyproline
II helix (PII). Monte Carlo simulations in the
canonical ensemble were performed at 300 K using
the CHARMM 22 force field with TIP3P water. The
simulations indicate that the solvation free energy
of PII is favored over that of other conformers for
reasons that defy conventional explanation.
Specifically, in these 4 conformers, an almost perfect correlation
is found between a residue's solvent-accessible
surface area and the volume of its first solvent
shell, but neither quantity is correlated with the
observed differences in solvation free energy. Instead,
solvation free energy tracks with the interaction
energy between the peptide and its first-shell
water. An additional, previously unrecognized contribution
involves the conformation-dependent perturbation
of first-shell solvent organization. Unlike
PII, BETA-strands induce formation of entropically disfavored
peptide:water bridges that order vicinal water
in a manner reminiscent of the hydrophobic
effect. The use of explicit water allows us to capture
and characterize these dynamic water bridges that
form and dissolve during our simulations.