Abstract
Key enzymatic processes use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. The applicability of traditional proofreading schemes, however, is limited because they typically require dedicated structural features in the enzyme, such as a nucleotide hydrolysis site or multiple intermediate conformations. Here, we explore an alternative conceptual mechanism that achieves error correction by having substrate binding and subsequent product formation occur at distinct physical locations. The time taken by the enzyme-substrate complex to diffuse from one location to another is leveraged to discard wrong substrates. This mechanism does not have the typical structural requirements, making it easier to overlook in experiments. We discuss how the length scales of molecular gradients dictate proofreading performance, and quantify the limitations imposed by realistic diffusion and reaction rates. Our work broadens the applicability of kinetic proofreading and sets the stage for studying spatial gradients as a possible route to specificity.
Highlights
We introduce an effective number of extra biochemical intermediates (n) that a traditional proofreading scheme would need to have in order to yield the same fidelity, that is h=heq 1⁄4 hneq
The baseline cost in our case is analogous to the work that ATP synthase needs to perform to maintain a nonequilibrium [ATP]/[ADP] ratio in the cell, whereas our calculated power is analogous to the rate of ATP hydrolysis by a traditional proofreading enzyme
Our proposed spatial proofreading scheme is based on a time delay; but unlike the classic model, here the delay is due to spatial transport rather than transitions through biochemical intermediates
Summary
The nonequilibrium mechanism called kinetic proofreading (Hopfield, 1974; Ninio, 1975) is used for reducing the error rates of many biochemical processes important for cell function (e.g. DNA replication [Kunkel, 2004], transcription [Sydow and Cramer, 2009], translation [Rodnina and Wintermeyer, 2001; Ieong et al, 2016], signal transduction [Swain and Siggia, 2002], or pathogen recognition [McKeithan, 1995; Goldstein et al, 2004; Cui and Mehta, 2018]). PPPP used to discard the wrong substrates, which are assumed to unbind from the enzyme more readily than the right substrates (Figure 1b) When this delay is longer than substrate unbinding time scales, very low error rates of product formation can be achieved, allowing this spatial chemical state space (b) time delay through spatial localization of substrates proofreading scheme to outperform biochemical mechanisms with a finite number of proofreading steps. In contrast to traditional proofreading, the binding activation nonequilibrium mechanism here does not require any direct energy consumption by the kon koff r enzyme or substrate itself (e.g. through ATP λS effector hydrolysis) This liberates the enzyme from any proofreading-specific molecular features; physical space any ‘equilibrium’ enzyme with a localized effector can proofread using our scheme if appropriate concentration gradients of the sub-. Our work motivates a detailed investigation of spatial structures and compartmentalization in living cells as possible delay mechanisms for proofreading enzymatic reactions
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