  To understand the mechanism of trimethylamine N-oxide (TMAO) induced
stabilization of folded protein states, we systematically investigated the
action of TMAO on several model dipeptides (Leucine, L2, Serine, S2, Glutamine,
Q2, Lysine, K2, and Glycine, G2) in order to elucidate the effect of
residue-specific TMAO interactions on small fragments of solvent-exposed
conformations of the denatured states of proteins. We find that TMAO
preferentially hydrogen bonds with the exposed dipeptide backbone, but
generally not with nonpolar or polar side chains. However, interactions with
the positively charged Lys are substantially greater than with the backbone.
The dipeptide G2, is a useful model of pure amide backbone, interacts with TMAO
by forming a hydrogen bond between the amide nitrogen and the oxygen in TMAO.
In contrast, TMAO is depleted from the protein backbone in the hexapeptide G6,
which shows that the length of the polypeptide chain is relevant in aqueous
TMAO solutions. These simulations lead to the hypothesis that TMAO-induced
stabilization of proteins and peptides is a consequence of depletion of the
solute from the protein surface provided intramolecular interactions are more
favorable than those between TMAO and the backbone. To test our hypothesis we
performed additional simulations of the action of TMAO on an intrinsically
disordered A{\beta}16-22 (KLVFFAE) monomer. In the absence of TMAO
A{\beta}16-22 is a disordered random coil. However, in aqueous TMAO solution
A{\beta}16-22 monomer samples compact conformations. A transition from random
coil to {\alpha}-helical secondary structure is observed at high TMAO
concentrations. Our work highlights the potential similarities between the
action of TMAO on long polypeptide chains and entropic stabilization of
proteins in a crowded environment due to excluded volume interactions. In this
sense TMAO is a nano-crowding particle.
