A view on the dogma of hydrophobic imperialism in protein folding

In a recent article, Ben-Naim has claimed that (a) adherence to the dominance of hydrophobic interactions is the wrong way to try to solve the Levinthal paradox and the protein folding problem; (b) recognition of the fundamental role played by hydrophilic interactions should lead to the solution of the protein folding problem (Ben-Naim, 2012). This is a somewhat strange situation by considering that Ben-Naim published a book in 1980 entitled Hydrophobic Interactions in which he provided a precise definition of hydrophobic interactions and showed their relevance for several self-assembly biological processes, such as protein folding (Ben-Naim, 1980). I have learned a lot of things on reading and studying this book. Now, I would like to comment on the Ben-Naim’s claim, emphasizing that the hydrophobic effect, when rightly re-defined, is the driving force of the collapse of polypeptide chains and provides the main contribution to the conformational stability of native structure. In this comment, I will be mainly concerned with the third sub-problem of the protein folding problem, according to Ben-Naim’s division (2012): “the molecular factors that contribute to the stability of the native structure of the protein. ” This is because the forces that speed and guide the folding come from the gradients of the Gibbs energy function that, in turn, is derived from the molecular interactions. In order to arrive at a correct understanding of the matter, one needs a clear definition of some terms that are used too freely in the current (especially biochemical) literature. The hydrophobic effect consists of two distinct processes: hydrophobic hydration and hydrophobic interaction (Blokzijl & Engberts, 1993). Hydrophobic hydration refers to the transfer of a nonpolar molecule (i.e. methane or neopentane) from a fixed position in the ideal gas phase to a fixed position in water [this is also called Ben-Naim standard (Lee, 1991)]. This process is not thermodynamically favored and has peculiar thermodynamic features: around room temperature, the large and positive Gibbs energy change is mainly due to a large and negative entropy change. This implies that the poor solubility of nonpolar species in water is ruled, at ambient temperatures, by the water entropy whose molecular origin is the crux of the matter (Ben-Naim, 1974; Lee, 1991). Hydrophobic interaction is considered to be a partial reversal of hydrophobic hydration: nonpolar molecules, being poor soluble in water in view of their inability to participate in H-bonds, are forced to associate with each other by water molecules that do not want to waste entropy (i.e. water molecules lose more entropy to solvate several nonpolar molecules than to solvate a single large aggregate formed by such molecules; see below for a molecular explanation of this fact). It is a water-induced attraction. Hydrophobic interaction cannot be studied from an experimental point of view for nonpolar solutes due to their poor solubility in water, but computer simulations indicate that it is characterized by a negative Gibbs energy change and a positive entropy change (Paschek, 2004). Kauzmann (1959) originally claimed that an intra-molecular hydrophobic interaction is operative in the folding of globular proteins because the latter possess a large fraction of nonpolar side chains. Actually, I agree that hydrophobic interaction is fundamental for protein folding, but it is operative due to basic geometric features of flexible chains, not for the presence of nonpolar side chains, as I will try to explain below. The changes in thermodynamic functions associated with a process (e.g. protein folding/unfolding) are macroscopic quantities and cannot provide microscopicmolecular information. To try to gain a molecular understanding, it is necessary to build up a reliable model of the real process, and to divide/partition, it in some steps that should be amenable to a rigorous treatment by means of statistical thermodynamics. In this respect, it is important to point out that several partitioning schemes could be adopted that apparently work well. However, a partitioning scheme has to be judged on the basis of its