TrimethylamineN‐oxide influence on the backbone of proteins: An oligoglycine model

Abstract

The study of organic osmolytes has been pivotal in demonstrating the role of solvent effects on the protein backbone in the folding process. Whereas a thermodynamic description of the interactions between the protein backbone and osmolyte has been well defined, the structural analysis of the effect of osmolyte on the protein backbone has been incomplete. Therefore, we have carried out simulations of a peptide backbone model, glycine 15 in protecting osmolyte TMAO solution in order to determine the effect of the solution structure on the conformation of the peptide backbone. We demonstrate that the models chosen show that the ensemble of backbone structures shifts towards a more collapsed state in TMAO solution as compared to pure water solution. The collapse is consistent with preferential exclusion of the osmolyte caused by unfavorable interactions between osmolyte and peptide backbone. The exclusion is due to strong triplet correlations of osmolyte, water, and peptide backbone. This provides a clear mechanism demonstrating that even a modest concentration of TMAO forces the protein backbone to adopt a more collapsed structure in the absence of sidechain effects.

Backbone additivity in the transfer model of protein solvation

“…41 However, the total solution-peptide hydrogen bond amounts are usually lower in TMAO, which is in part, a result of the lack of interaction of TMAO with the peptide backbone as compared to urea. 38 This is analogous to the classic interpretation of experiments by Timasheff that protecting osmolytes are preferentially excluded from the local region of the protein, whereas nonprotecting osmolytes are seen in higher amounts close by. 42,43 Recent experimental measurements have indicated hydrogen bonding of urea with the NH group of a dialanine peptide, yet urea hydrogen bonding with the carbonyl group of the peptide was not as well resolved.…”

“…For longer repeats of the backbone model the preferential interaction parameter is usually negative indicating a significant decrease in the overall amount of TMAO as compared to bulk solution, but this depends on conformation and is quite noisy. The high relative error seen is common behavior for the preferential interaction parameter as evidenced by the calculations of others, [36][37][38] because the nature of the calculation depends upon the local number fluctuations at increasing distances. The inherent nosiness of the parameter, and the subsequent lack in statistical confidence of the interpretation, caused us to look at shorter ranged events that are less susceptible to artifacts caused by large local number fluctuations.…”

“…Several previous simulations have demonstrated the direct interaction of urea with peptide or protein 22,45,46,[50][51][52] as well as the lack of interaction between TMAO and a cyclic 53 and long peptide backbone model. 38 Similarly, solution hydrogen bonds with the peptide backbone models demonstrate very little hydrogen bonding of TMAO with the peptide backbone, whereas urea forms about 1/2 hydrogen bond per glycine residue. We see the denaturing osmolyte acting as a hydrogen bond donor with far more frequency than as a hydrogen bond acceptor.…”

Microscopic insights into the protein-stabilizing effect of trimethylamine N-oxide (TMAO)

“…1, Inset) adopts a skewed tetrahedral structure with a charged oxygen capable of accepting hydrogen bonds (H bonds) and three hydrophobic (methyl) groups. This amphiphilic structural arrangement makes TMAO a rather special cosolvent, because it can form H bonds with water, self-associate in a manner similar to surfactants, and show preferential interactions with or exclusion (4)(5)(6)(7)(8)(9)(10)(11)(12) from certain protein functional groups (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23). Indeed, these molecular properties of TMAO have been used, either individually or in combination, to rationalize its biological activities.…”

Protein folding/unfolding in the presence of interacting macromolecular crowders

“…The interaction of cosolvents with proteins can be quantified in terms of preferential interaction coefficients [29], and has been modeled using simplified core-shell descriptions [30] as well as atomistically detailed representations. Two examples of cosolvents whose interaction with proteins has been investigated through atomic-level simulations are the denaturant urea and the protective osmolyte trimethylamine N-oxide, TMAO [31][32][33][34][35][36][37][38]. Simulating the interaction of large macromolecular crowders with a protein at the same level of detail is computationally demanding, because cosolvents such as urea and TMAO are significantly smaller in size than, for instance, protein crowders.…”