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Role of conformation transitions in adenylate kinase

A recent paper by Pisliakov et al. (1) asserts that it is a response to several papers, which, according to the authors (1), imply that “motions along conformational coordinates play an important role in the chemical step” (1). Because ref. 1 and most of the cited papers in ref. 1 [references 3,6,7, and 14 in Pisliakov et al. (1)] are concerned with adenylate kinase (AdK), my comments refer to this enzyme. AdK has an open state, to which the substrates bind and from which the products are released, as well as a closed state, in which catalysis takes place. None of these cited references are concerned with the chemical reaction or suggest that there is coupling between the closing/opening conformational transitions and the chemistry; catalysis in these papers refers to the overall rate and not to the chemical step. They show that the opening transition after the chemical reaction is the rate-determining step [reference 14 in (1); i.e., in AdK, like triosephosphate isomerase, the chemistry has reached perfection] (2). The two other papers, of which I am a coauthor, study the closing transition encoded in the structure [references 6 and 7 in (1)] and the role of fast motions as lubricants (3) for hinge regions.