  The contribution of a specific hydrogen bond in apoflavodoxin to protein
stability is investigated by combining theory, experiment and simulation.
Although hydrogen bonds are major determinants of protein structure and
function, their contribution to protein stability is still unclear and widely
debated. The best method so far devised to estimate the contribution of
side-chain interactions to protein stability is double-mutant-cycle analysis,
but the interaction energies so derived are not identical to incremental
binding energies (the energies quantifying net contributions of two interacting
groups to protein stability). Here we introduce double-deletion analysis of
isolated residue pairs as a means to precisely quantify incremental binding.
The method is exemplified by studying a surface-exposed hydrogen bond in a
model protein (Asp96/Asn128 in apoflavodoxin). Combined substitution of these
residues by alanines slightly destabilizes the protein, due to a decrease in
hydrophobic surface burial. Subtraction of this effect, however, clearly
indicates that the hydrogen-bonded groups in fact destabilize the native
conformation. In addition, Molecular Dynamics simulations and classic
double-mutant-cycle analysis explain quantitatively that, due to frustration,
the hydrogen bond must form in the native structure because, when the two
groups get approximated upon folding their binding becomes favorable. We would
like to remark two facts: that this is the first time the contribution of a
specific hydrogen bond to protein stability has been measured from experiment,
and that more hydrogen bonds need to be analyzed in order to draw general
conclusions on protein hydrogen bonds energetics. To that end, the double
deletion method should be of help.
