Allosteric crosstalk in modular proteins: Function fine-tuning and drug design

Abstract

Modular proteins are regulatory proteins that carry out more than one function. These proteins upregulate or downregulate a biochemical cascade to establish homeostasis in cells. To switch the function or alter the efficiency (based on cellular needs), these proteins require different facilitators that bind to a site different from the catalytic (active/orthosteric) site, aka 'allosteric site', and fine-tune their function. These facilitators (or effectors) are allosteric modulators. In this Review, we have discussed the allostery, characterized them based on their mechanisms, and discussed how allostery plays an important role in the activity modulation and function fine-tuning of proteins. Recently there is an emergence in the discovery of allosteric drugs. We have also emphasized the role, significance, and future of allostery in therapeutic applications.

Keywords: Allostery; Drug design; Enzyme kinetics; Multi-domain proteins; Protein function regulation; Therapeutics.

Graphical abstract

Fig. 1

(A) Proximity of allosteric and orthosteric sites in proteins. (B) Effect of different allosteric effectors (PAM: Positive allosteric modulator; NAM: Negative allosteric modulator) on enzyme activity.

Fig. 2

Effect of allosteric regulators on the functional outcome of proteins. (A) Signal (DNA damage)-induced PARP1 recruits repair proteins to initiate the DNA repair pathway. Schematic representation of allosteric regulation of PARP1 by DNA (agonist) and PAR (both partial agonist and partial antagonist). (B) Schematic representation of RNA degradation cascade by type III CRISPR-Cas system, where Cas10 and Csm6 are allosterically regulated by RNA and cOAs, respectively. The operon system and the genes associated with the type III CRISPR-Cas system is shown at the bottom of the panel. The left side of the panel represents the recognition of the viral RNA by the type III CRISPR-Cas system. (C) Schematic representation of DNA-induced allosteric activation of cGAS protein in cGAS-STING pathway.

Fig. 3

(A) Representative GPCR with ligands bound at different experimentally validated allosteric sites. Schematic representation of allosteric regulation of different GPCRs - (B) GABA_A receptor, (C) mGlu receptor, (D) ghrelin and cannabinoid 1 receptors. The effect of agonist, antagonist, and inverse agonist on the ghrelin receptor is shown by a representative kinetic plot. The effect of PAM and BAM on the cannabinoid receptor is shown by a representative histogram.

Fig. 4

Mechanism of regulation of different proteins by different types of allosteric effectors. (A) Schematic representation of forward and reverse allostery in PARP1 (panel-i) and bidirectional allostery in phosphofructokinase (PFK) (panel-ii). (B) Schematic representation of active and inactive states of KRAS GTPase with G12C mutation, and its allosteric inhibition by suicidal (covalent) inhibitor.

Fig. 5

Allosteric regulation by end-products. (A) Allosteric regulation of PKF by substrate (ATP) and end by-product (ADP). (B) Allosteric regulation of RNR enzymes by their end-products, where the end-products provide substrate specificity to RNR, whereas the last end-product (dATP) acts as an inhibitor of RNR. Schematic representation of allosteric regulation of active (S-dimer) and inactive (I-dimer) states of RNR by ATP and dATP. The panel on the right shows the mechanism of allosteric activation and inhibition of RNR, through a conformational change in loop 2, by different effectors and substrates. (C) Crosstalk-mediated allosteric regulation of SUVH and CMT proteins by their respective end-products for maintenance of epigenetic marks in the genome.

Fig. 6

(A) Schematic representation of inhibition by ‘allosteric competition’. (B) Approaches to determine the effect of the allosteric modulator on substrate binding and catalytic activity of proteins.