Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method

These ligands form hydrogen bond interactions with R170 from one chain and S183, H185 of the other chain and various water molecules. However, no inhibitor was found in the interface of L-LDH when co-crystallized with oxaloacetate and NADH. Instead, sulfate ions were present in the same location interacting with R170, H185 of one chain and H185 of the other (Fig. 3a). Identifying enzymes subject to feedback inhibition can reveal key regulatory nodes in metabolic networks. These nodes are crucial for controlling the flow of metabolites through the network. By targeting these nodes, researchers can manipulate metabolic pathways for biotechnological or therapeutic purposes.

Achieving Optimal Growth through Product Feedback Inhibition in Metabolism

This prevents the wasteful breakdown of glucose when sufficient ATP is already available. This cooperativity is often observed in enzymes with multiple subunits, where each subunit contains an active site. Activators typically stabilize a conformation of the enzyme that has a higher affinity for the substrate, thereby increasing catalytic activity. Conversely, inhibitors stabilize a conformation with a lower affinity for the substrate, reducing or even abolishing enzyme activity. In experiments, it has been shown that the ATP-independent GDH pathway is preferred under glucose-limited growth 32, 33, which is also consistent with the optimal FBA behavior that we find in our nutrient-integration module. Furthermore, when both carbon and nitrogen are available in excess, the ATP-independent GDH pathway is largely inactive, corresponding to 34.

Allosteric Inhibition and Activation

In feedback inhibition, the end product binds to an allosteric site on the enzyme, causing a conformational change that reduces the enzyme's activity. The concept of feedback inhibition was first proposed in the 1950s and 1960s, when researchers began to study the regulation of metabolic pathways. The discovery of feedback inhibition was a major breakthrough in understanding how cells regulate their metabolic processes. Feedback inhibition is defined as a regulatory mechanism where the final product of a metabolic pathway inhibits an enzyme involved in an earlier step of the pathway. This mechanism is significant because it allows cells to conserve resources, prevent waste, and maintain a stable internal environment.

Defining the Rate-Limiting Step

This confuses many students as bonds between atoms lower the energy compared to when the atoms are not bonded. The hydrolysis of the molecules below is exergonic because more energy is released during bond formation in the new products than was required to break the bonds in the reactants. In addition, other effects, such as preferential hydration of the products, lower charge density, and fewer competing resonances in the products, all contribute to the thermodynamically favorable hydrolysis of the reactants. By identifying key regulatory nodes in metabolic pathways, researchers can develop targeted therapies to modulate pathway activity for disease treatment.

As metabolites can inhibit multiple enzymes, the number of inhibitory interactions is substantially different to the number of inhibitors per metabolite class. The dominance of ‘Nucleosides, Nucleotides, and Analogues’ is also reflected on the level of the most potent single inhibitors, adenylate and nicotinamide nucleotides (Fig. 1e, Supplementary Data 1). Importantly, the chemical identity of the inhibitors was found to reveal the enzyme class they most likely inhibit (Fig. 1f, Supplementary Tables 3–5). Despite the inhibition network includes also weak inhibitors as stored in BRENDA, and its underlying data are subject to literature bias, the network reveals highly distinct topology that is dependent on the chemical class of the metabolites. Feedback inhibition is a crucial regulatory mechanism in cellular metabolism that ensures the efficient use of resources and maintains cellular homeostasis.

3. Regulation and negative feedback

In the purine biosynthesis pathway, the accumulation of ATP and GTP acts as feedback inhibitors for the enzyme amidophosphoribosyltransferase. This ensures a balanced supply of nucleotides, which are essential for DNA and RNA synthesis. By modulating enzyme activity, feedback inhibition prevents imbalances that could disrupt cellular replication and transcription processes. These examples underscore the role of feedback inhibition in cellular processes, illustrating its capacity to maintain metabolic equilibrium and support cellular function. Allosteric regulation modulates enzyme activity through the binding of effector molecules feedback inhibition in metabolic pathways at sites distinct from the active site. This interaction induces conformational changes in the enzyme, either enhancing or inhibiting its function.

• Histidine binding alongside AMP causes conformational changes in ATP-PRT structure where active site of enzyme is closed and amino acid residues involved in binding of PRPP also disrupt that hindered catalytic activity 50.
• This prevents the wasteful breakdown of glucose when sufficient ATP is already available.
• However, data in the absence of theory are limited as was clearly pointed out by Pigliucci 91.
• Three superclasses including (1) Aromatic Heteropolycyclic Compounds, (2) Aromatic Heteromonocyclic Compounds and (3) Aromatic Homomonocyclic Compounds were merged to one group named (i) Aromatic Cyclic Compounds.
• Given the steady-state concentrations and flux for the closed loop pathway, let us break the negative feedback loop.

At the transcriptional level, multiple promoter binding sites along with other cooperative mechanisms like DNA looping yield ultrasensitive responses 49 (Fig. 4A). The response time for transcriptional feedback is limited by protein degradation (and dilution), which in microorganisms is typically of the order of tens of minutes to hours. Metabolite-pool sizes, on the other hand, may change in just few seconds, e.g. the glutamine pool increased by over 10-fold in seconds in the nutrient-switching experiment described above. The fast dynamics of metabolite-pool sizes suggests the need for fast feedback mechanisms. Fast regulation can be realized through various post-translational mechanisms – allosteric regulation of protein aggregates, e.g. ATP molecules bind cooperatively to a homodimer of pantothenate kinase 50, competition, e.g.

Deregulation of amino acids feedback inhibition

Metabolic feedback inhibition for instance can be a direct consequence of the catalytic mechanisms itself10. In other instances, distally produced metabolites act as inhibitors by having strong structural similarity with the enzymatic substrates. For instance, phosphoenolpyruvate inhibits triosephosphate isomerase (TPI) due to extensive structural similarity with dihydroxyacetone phosphate, which constrains the activity of glycolysis when cells respire5,11.

Engineering of regulatory domain is key contributor to accomplish deregulation of feedback inhibition, (b). Blocking entry of inhibitor into binding domain by modifying the key amino acid residues positioned at the entrance of feedback inhibitor binding site, steric hindrance and charge modification is of paramount importance for deregulation, (c). In case of dimer, tetramer or hexameric structures, mutations at interface or junction of two monomeric units may disrupt signal transfer and ultimately destroy enzyme activity. Eliminate metastability of protein due to inhibitor binding As histidine binding introduces compactness in trimeric, or multimeric structure of ATP-PRT enzyme.

This behaviour is the basis for the supply/demand metabolic architecture put forward by Hofmeyr and co-workers 68–70. This control pattern ensures that the pathway flux is determined by demand (which has the higher flux control coefficient) rather than by supply (figure 8). Now that we have looked at the distribution of flux control in a unbranched pathway we can now turn our attention to pathways that include negative feedback loops. On the face of it, negative feedback is a simple process that involves subtracting a portion of the output from the input (figure 4).

• The structural characteristics of ATP-phosphoribosyl transferase (ATP-PRT) enzyme (feedback inhibited by end product histidine) revealed two forms i.e. homo-hexamer or hetero-octamer.
• In the second module, representing a bidirectional pathway, metabolites are interconverted, albeit at a cost, with the consequent risk of running a futile cycle (e.g., interconversion of fructose-6-phosphate and fructose-1,6-bisphosphate (FBP)).
• The side chain of tyrosine 185 in the unphosphorylated form is shown in CPK-colored sticks and labeled.
• Understanding the role of feedback inhibition in cellular regulation has significant implications for the development of novel therapeutic strategies.
• This function was obtained as the growth rate of a heteropolymer made from equal stoichiometries of monomers with pool sizes 29.

The analysis on the two-step pathway can be extended to larger pathways with negative feedback and the conclusions from the two step study apply equally. There are standard methods for deriving the control expressions 34,71 which will not be described here, but tools such as Mathematica or open source specialized tools such as SymCA 72 can be used. Where is the control coefficient for the unregulated but equivalent system and is the elasticity of the feedback loop. The control coefficient for the unregulated equivalent system can be easily determined by simply setting the negative feedback elasticity to zero in the control coefficient for the regulated pathway.

For example, consider the dynamics of -ketoglutarate and glutamine, the carbon skeleton and the most nitrogen-rich product of central nitrogen metabolism. -ketoglutarate is part of the TCA cycle, and many TCA cycle metabolites show similar patterns to its temporal response during nitrogen limitation and re-addition 25. Accordingly, we consider the -ketoglutarate level as an indicator of available carbon (specifically, carbon in the TCA cycle).

For example, the biosynthesis of histidine is regulated by feedback inhibition, where the end product histidine inhibits the first enzyme in the pathway, ATP phosphoribosyltransferase. Feedback inhibition is a crucial regulatory mechanism in cellular metabolism, allowing cells to maintain homeostasis and respond to changes in their environment. This process involves the inhibition of an enzyme or a series of enzymes in a metabolic pathway by the end product of that pathway. By controlling the activity of key enzymes, feedback inhibition ensures that the cell produces the necessary metabolites in the required quantities, avoiding waste and conserving energy.

In the context of feedback inhibition, the end product of a metabolic pathway acts as a negative allosteric modulator. Yet, metabolic control should occur on the production of acetylglutamate, regardless of its origin. Therefore, feedback inhibition on both the synthase and the kinase is believed to be general for organisms using cyclic ornithine synthesis. In contrast, NAG synthetase would appear to be a less suitable target, because in those organisms that recycle the acetyl group in the route of ornithine synthesis it only plays a purely anaplerotic role 90.