It
has been a long-standing conviction that a protein’s
native fold is selected from a vast number of conformers by the optimal
constellation of enthalpically favorable interactions. In marked contrast,
this Perspective introduces a different mechanism, one that emphasizes
conformational entropy as the principal organizer in protein folding
while proposing that the conventional view is incomplete. This mechanism
stems from the realization that hydrogen bond satisfaction is a thermodynamic
necessity. In particular, a backbone hydrogen bond may add little
to the stability of the native state, but a completely unsatisfied
backbone hydrogen bond would be dramatically destabilizing, shifting
the U(nfolded) ⇌ N(ative) equilibrium far to the left. If even
a single backbone polar group is satisfied by solvent when unfolded
but buried and unsatisfied when folded, that energy penalty alone,
approximately +5 kcal/mol, would rival almost the entire free energy
of protein stabilization, typically between −5 and −15
kcal/mol under physiological conditions. Consequently, upon folding,
buried backbone polar groups must form hydrogen bonds, and they do
so by assembling scaffolds of α-helices and/or strands of β-sheet,
the only conformers in which, with rare exception, hydrogen bond donors
and acceptors are exactly balanced. In addition, only a few thousand
viable scaffold topologies are possible for a typical protein domain.
This thermodynamic imperative winnows the folding population by culling
conformers with unsatisfied hydrogen bonds, thereby reducing the entropy
cost of folding. Importantly, conformational restrictions imposed
by backbone···backbone hydrogen bonding in the scaffold
are sequence-independent, enabling mutationand thus evolutionwithout
sacrificing the structure.