, 131:1288
Date: 23 Nov 2012

Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting

Abstract

In the preceding article, “Perspective: Pre-chemistry conformational changes in DNA polymerase mechanisms” contributed by Schlick and coworkers as well as previous studies of these workers (Schlick et al. in Theor Chem Acc 131:1287, 2012; Radhakrishnan and Schlick in J Am Chem Soc 127:13245–13252, 2005; Radhakrishnan and Schlick in Biochem Biophys Res Commun 350:521–529, 2006; Radhakrishnan et al. in Biochemistry 45:15142–15156, 2006; Radhakrishnan and Schlick in Proc Natl Acad Sci USA 101:5970–5975, 2004) have argued that the conformational changes preceding the chemical step contribute to DNA synthesis and to the fidelity of DNA polymerases. In one of our previous investigations (Ram Prasad and Warshel in Proteins 79:2900–2919, 2011), we argued and showed that as long as the free energy barriers associated with any of the prechemistry steps are not rate limiting, they could not contribute to the catalysis and then to the fidelity. Though all our arguments are based on exact and well-defined scientific logics, Schlick and coworkers seem to overlook some of the clear conditions in these arguments and in particular the requirement that the chemical step is rate limiting in their arguments that the prechemistry barriers contribute to the catalysis. In fact, as long as the prechemistry steps are not rate limiting, we have shown that the enzymes cannot carry the memory of the previous steps. We also address other potential misunderstandings about several key issues; First, we clarify that it is misleading to relate the prechemistry proposal to the clear fact that the substrate-induced conformational changes determine the final preorganization (the issue is the height of the barrier of the enzyme substrate system and not the trivial fact that the enzyme has to change its structure when the substrate binds). Second, we address the presumed role of dynamical effects in enzyme catalysis and the assumption that any observable should be explored in studies of biological function even if they are not relevant to the given effect. Third, we clarify that the fidelity cannot be explained or quantified by invoking the induced fit or conformational selection effects but by evaluating the free energy contributions to the rate-limiting steps from the structures of the corresponding systems (that of course can reflect the induce fit structural changes). Overall, we put a major emphasis on clarifying what is the prechemistry proposal and thus on trying to force the reader to focus on the only real controversy. We of course dismiss any implication that our studies cannot explore mutational effects as we actually pioneered such computational studies and we clarify that in studies of chemical rates, the focus must be placed on evaluating the chemical barriers, rather than on irrelevant factors, but that the calculations of the chemical barriers must consider all the factors that determine this barrier (including metal ions) and also examine if needed different problematic proposals such as dynamical effects, tunneling, and prechemistry.

Editor’s Note: This paper and papers by Mulholland AJ, Roitberg AE, Tuñón I (doi:10.1007/s00214-012-1286-8) and Schlick T, Arora K, Beard WA, Wilson SH (doi:10.1007/s00214-012-1287-7) document and discuss contrasting outlooks on the questions of prechemistry and catalysis in DNA polymerase. All authors were initially provided with one another’s manuscripts, at which point opportunities to make revisions were offered, and finally, Mulholland, Roitberg, and Tuñón were given the ‘last word’ on the revised manuscripts in their role as commentators. The editors of TCA hope that this discussion will illuminate key issues affecting ongoing work in this area.