F. Fogolari et al., PK(A) SHIFT EFFECTS ON BACKBONE AMIDE BASE-CATALYZED HYDROGEN-EXCHANGE RATES IN PEPTIDES, Journal of the American Chemical Society, 120(15), 1998, pp. 3735-3738
Amide proton exchange (HX) rates are known to depend on protein primar
y structure as well as local and global protein structure and dynamics
. Measurement of HX rates gives information on the local exposure of a
mide protons to solvent and on local rates of structural openings. It
has long been recognized that the amide pK(a) directly influences the
HX rate. Using the finite-difference solution of the Poisson-Boltzmann
equation, we investigated the electrostatic effects on HX rates, via
calculated shifts in the amide pK(a) for model compounds (N-methylacet
amide, dipeptides entailing almost all amino acid side chains, and a t
ripeptide). Rather than shifts in the same compound with varying envir
onmental conditions, we address shifts in the HX rates of different co
mpounds relative to each other. The results for selected model compoun
ds which resemble Ala and Gly residues, with a standard choice of para
meters, agree to a high degree of accuracy with experimentally determi
ned rates. Application of the same methodology to naturally occurring
amino acids is promising but requires refinement to take into account
flexibility and inductive effects.