The biological significance of substrate inhibition: A mechanism with diverse functions

Abstract

Many enzymes are inhibited by their own substrates, leading to velocity curves that rise to a maximum and then descend as the substrate concentration increases. Substrate inhibition is often regarded as a biochemical oddity and experimental annoyance. We show, using several case studies, that substrate inhibition often has important biological functions. In each case we discuss, the biological significance is different. Substrate inhibition of tyrosine hydroxylase results in a steady synthesis of dopamine despite large fluctuations in tyrosine due to meals. Substrate inhibition of acetylcholinesterase enhances the neural signal and allows rapid signal termination. Substrate inhibition of phosphofructokinase ensures that resources are not devoted to manufacturing ATP when it is plentiful. In folate metabolism, substrate inhibition maintains reactions rates in the face of substantial folate deprivation. Substrate inhibition of DNA methyltransferase serves to faithfully copy DNA methylation patterns when cells divide while preventing de novo methylation of methyl-free promoter regions. Keywords:.b iological function; enzyme kinetics; substrate inhibitionThe kinetics of an enzymatic reaction are typically studied by varying the concentration of substrate and plotting the rate of product formation as a function of substrate concentration. In the conventional case this yields a typical hyperbolic Michaelis-Menten curve, and a linear reciprocal LineweaverBurk plot, from which the kinetic constants of the enzyme can be calculated. A surprisingly large number of enzymes do not behave in this conventional way. Instead, their velocity curves rise to a maximum and then decline as the substrate concentration goes up. This phenomenon is referred to as substrate inhibition, and it is estimated that it occurs in some 20% of enzymes [1]. A partial list of enzymes that show substrate inhibition appears in Box 1.Substrate inhibition is often interpreted as an abnormality that comes from using artificially high substrate concentration in a laboratory setting. In a review article on the mechanisms of substrate inhibition in 1994, Kuehl [2] commented that ''although recognized early on as an almost universal phenomenon, it has nevertheless met an almost universal disinterest. Probably the main reason for this neglect is that the majority of enzymologists and many authorities in the field regard substrate inhibition as being almost always a nonphysiological phenomenon.'' There are several reasons for suspecting that substrate inhibition is not a pathological phenomenon, but a biologically relevant regulatory mechanism. First, in many cases normal substrate concentrations are to the right of the velocity maximum, which indicates that these enzymes typically operate under substrate inhibition. Second, many enzymes have specialized sites where a second substrate molecule can bind and act as an allosteric inhibitor. For those enzymes, substrate inhibition is clearly a specially evolved property. Third, evidence is accumulating that substr...

Mutational Analysis of the Integral Membrane Methyltransferase Isoprenylcysteine Carboxyl Methyltransferase (ICMT) Reveals Potential Substrate Binding Sites

“…It has been estimated that substrate inhibition occurs for ϳ20% of all wild-type enzymes, and it typically is observed at substrate concentrations that are higher than the physiological levels (27). Although the molecular basis for substrate inhibition is not always apparent, one explanation for it is that the enzyme has two binding sites for its substrate: a productive site where binding produces product and a non-productive site where binding produces the product at a reduced rate (33). A plausible explanation for the substrate inhibition observed for the ICMT mutants is that these residues line the lipid binding pocket that recognizes the isoprenyl moiety of ICMT substrates and that mutating these residues alters the substrate binding pocket slightly such that the isoprenylcysteine substrate can bind in a non-productive conformation.…”

The UDP-glucose Dehydrogenase of Escherichia coli K-12 Displays Substrate Inhibition by NAD That Is Relieved by Nucleotide Triphosphates

“…There are several models available to explain substrate inhibition (44), but one attractive model for Ugd K-12 invokes the possibility that multiple molecules of NAD enter the active site. The structure of Ugd Kp (which shares 93% sequence similarity with Ugd K-12 ) has been solved from a cocrystal of the enzyme with NAD, revealing that the binding pocket for NAD is relatively open (11).…”

Systems Biology of Phenotypic Robustness and Plasticity

“…Barkai and Leibler (1997) showed how feedback in simple metabolic networks can lead to robustness of enzyme activity around a setpoint, and that the setpoint can be altered by changing the parameters of the system. Parallel pathways are thought to convey robustness in gene regulatory and biochemical networks (Wagner 2000), as are substrate inhibition mechanisms (Reed et al 2010). In development, lateral inhibition and Turing-style reaction-diffusion mechanisms (Turing 1952;Meinhardt 1982;Meir et al 2002;De Joussineau et al 2003;Salazar-Ciudad et al 2003) with short range autocatalysis and long range inhibition produce bistable spatial patterns of high and low activator biosynthesis.…”

“…A large number of enzymes are activated or inhibited by metabolites from elsewhere in the network. A surprisingly large number of enzymes exhibit substrate inhibition (Reed et al 2010), which adds to the nonlinearity. Transporters import and recycle metabolites within and between cells, and the circulatory system shuttles metabolites between tissues and organs.…”