Biological messiness vs. biological genius: Mechanistic aspects and roles of protein promiscuity

Abstract

In contrast to the traditional biological paradigms focused on 'specificity', recent research and theoretical efforts have focused on functional 'promiscuity' exhibited by proteins and enzymes in many biological settings, including enzymatic detoxication, steroid biochemistry, signal transduction and immune responses. In addition, divergent evolutionary processes are apparently facilitated by random mutations that yield promiscuous enzyme intermediates. The intermediates, in turn, provide opportunities for further evolution to optimize new functions from existing protein scaffolds. In some cases, promiscuity may simply represent the inherent plasticity of proteins resulting from their polymeric nature with distributed conformational ensembles. Enzymes or proteins that bind or metabolize noncognate substrates create 'messiness' or noise in the systems they contribute to. With our increasing awareness of the frequency of these promiscuous behaviors it becomes interesting and important to understand the molecular bases for promiscuous behavior and to distinguish between evolutionarily selected promiscuity and evolutionarily tolerated messiness. This review provides an overview of current understanding of these aspects of protein biochemistry and enzymology.

Keywords: Detoxication enzymes; Enzyme evolution; Enzyme promiscuity; Evolvability; Intrinsically Disordered proteins.

Fig. 1

Types of promiscuous behavior exhibited by enzymes, receptors and other proteins. The specific types of promiscuous behavior summarized are described in the text. The relative sizes of the compartments do not reflect their relative frequency or abundance. For example, promiscuous binding is more frequent than catalytic promiscuity, but this is not reflected in this figure.

Fig. 2

Chemical representation of promiscuous enzyme behaviors. Top: catalytic promiscuity includes structurally distinct transition states (in brackets) within the same active site. Structural differences also naturally occur remote from the transitions state for the different substrates (R vs. R′). Middle: substrate promiscuity refers to similar types of reactions, and hence similar local transition states (in brackets), for a single enzyme with a series of substrates that have structural differences remote from the local transition state (R, R′, R″). Bottom: bottom depicts the combination of catalytic and substrate promiscuity for detoxication enzymes that catalyze multiple types of reactions, with different local transition state structures (in brackets), and with variable structures remote from the transition state for any specific reaction type. For example the GSTs catalyze Michael type additions, addition to aryl epoxides (which subsequently aromatizes via dehydration), and cis-trans isomerization via addition–elimination, each for a wide range of substrate structures.

Fig. 3

Schematized summary for calculating the promiscuity index, J. For a series of substrates the enzyme efficiency, e_i = (k_cat/K_M) is determined and the term ‘I’ is calculated. I reflects the normalized probability that any given substrate will be chosen by an enzyme, when the enzyme is exposed simultaneously to low concentrations of each substrate, or the relative preference for any substrate. ‘I’ reflects the distribution of these preferences; a promiscuous enzyme with little preference (e₁ = e₂ = e_n) yields an I = 1 and a specific enzyme with a large e for only one substrate yields I = 0. It may be necessary to scale I to account for the chemical similarity or difference among the substrates used; if an enzyme has the same e_i for all substrates that are far from one another in chemical space (chemically very different) than it is more promiscuous than an enzyme that has the same e_i for substrates that sample a narrow range of chemical space (chemically similar). Substrates far away from others in chemical space, large <δ>_i, add more weight to the calculated promiscuity, J. J = 1 for a perfectly promiscuous enzyme (no preference for any substrate) and J = 0 for a completely specific enzyme.