Reply to Coffino et al.: Slippery Substrates Impair ATP-dependent Protease Function by Slowing Unfolding

Abstract

This is a response to a letter by Coffino et al. (1). I appreciate the thoughtful comments made by Coffino et al. (1) in response to my reanalysis of their data (2). Although the authors welcome the revised values of the rate constants for partitioning of a kinetically stalled substrate and the finding that a slippery sequence inhibits unfolding rather than accelerating substrate release, they object to my using the terms slippery substrate and low complexity sequence more-or-less interchangeably. Coffino et al. indicate that there are two models for what makes a sequence slippery, low sequence complexity (3) versus side chains of simple shape and small size (4). I would argue that these two models are not mutually exclusive. In Too et al. (4), it was shown that in a short otherwise polyalanine sequence, individual amino acids at the central position had different tendencies to promote fragment release or inhibit domain unfolding, with smaller amino acids (Ala, Gly) leading to the largest amount of fragment formation (4). Nonetheless, all of the sequences studied remained low complexity, and all led to substantial fragment formation. Although the details of a particular sequence clearly matter in determining the extent of processing by ATP-dependent proteases, it has also been shown that low complexity sequences containing larger and more complex side chains such as Asn and Gln are slippery (3, 5), indicating that small size or simple shape is unlikely to be a complete description of the slipperiness of a sequence stretch. We have more work ahead to fully understand how these slippery sequences work.