Allosteric regulation | EPFL Graph Search

In biochemistry, allosteric regulation (or allosteric control) is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site. The site to which the effector binds is termed the allosteric site or regulatory site. Allosteric sites allow effectors to bind to the protein, often resulting in a conformational change and/or a change in protein dynamics. Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are called allosteric inhibitors. Allosteric regulations are a natural example of control loops, such as feedback from downstream products or feedforward from upstream substrates. Long-range allostery is especially important in cell signaling. Allosteric regulation is also particularly important in the cell's ability to adjust enzyme activity. The term allostery comes from the Ancient Greek allos (), "other", and stereos (), "solid (object)". This is in r

Allosteric regulation and targeting of Bruton's tyrosine kinase (Btk) in B-cell lymphoma

Daniel Pereira Duarte

Bruton's tyrosine kinase (Btk) is a key component of BCR signaling required for B-cell maturation and activation. Loss-of-function mutations throughout the Btk protein cause human X-linked agammaglobulinemia (XLA), a heritable genetic disorder characterized by the absence of mature B-cells and lack of adaptive immune response. In contrast, Btk signaling sustains the growth of several B-cell neoplasms, which may be treated with small-molecule tyrosine kinase inhibitors (TKIs) targeting the ATP-site of the kinase. No alternative targeted therapy is available for patients who acquire resistance to current Btk inhibitors. Whereas a number of intramolecular interactions amongst the PH, SH3, SH2, and kinase domain (KD) are well resolved and stabilize a compact autoinhibited conformation, the molecular mechanisms governing Btk activation are not fully understood. Using a combination of in silico, structural, cellular, and molecular approaches, we discovered an allosteric interface between the SH2 and the N-lobe of the KD that is critical for kinase activation in vitro and cells. In contrast to the low Btk activity of the KD alone, the presence of the SH2 domain is sufficient to increase Btk phosphorylation at Y551 and multiple other sites. This provides the structural mechanism by which a subset of XLA mutations mapped to the SH2 domain near the interface region strongly perturbs Btk activation, even though the SH2 canonical function is preserved. Furthermore, we demonstrated that the active Btk SH2-kinase adopts an elongated conformation with a dynamic contact interface structurally distinct than to the ones observed for other tyrosine kinases, such as Abl, Fes, and Csk. As allosteric interactions provide unique targeting opportunities far from the ATP-site, we developed an engineered repebody protein binding to the human Btk SH2 domain. The crystal structure of the SH2-repebody complex combined with other structural approaches demonstrated that the repebody disrupts the SH2-kinase interaction. The repebody prevented activation of wild-type and TKI-resistant Btk in vitro and cells seen by a significant decrease in Btk phosphorylation. In parallel, sole allosteric targeting inhibited Btk-dependent signaling and reduced proliferation of malignant B-cells dependent on the BCR signaling. Therefore, the SH2-kinase interface is critical for Btk activation and is the first targetable site able to trigger allosteric inhibition. As Btk targeted therapy has a great impact on several conditions, including B-cell malignancies and autoimmune diseases, this study provides a rationale to support the development of alternative Btk inhibitors. This approach for targeted inhibition could particularly benefit patients with current therapy-resistant Btk variants.

EPFL2020

Investigation of physiological roles of AMPK-activated protein kinase y3

Philipp Jurijvic Rhein

Clinical trials have shown that direct activators of an evolutionary-conserved metabolic sensor, AMP-activated protein kinase (AMPK), are beneficial in preventing/treating a range of metabolic disorders, including type 2 diabetes. These activators, including 991/MK-8722, bind at regulatory site, termed the allosteric drug and metabolite (ADaM-site) at the interface between the catalytic alpha subunit and regulatory beta subunit. In addition, another approach for direct activation of AMPK is through mimicking its natural ligands, AMP/ADP, by binding to the nucleotide site in the y3 subunit, e.g. 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR). Interestingly, their ability to influence glucose homeostasis is reported to be through activation of AMPK complexes found within the skeletal muscle. The AMPKy3 is unique as an AMPK subunit isoform since it is selectively expressed in glycolytic skeletal muscle fibres. To gain more insight into the y3 isoform-specific regulation of glucose metabolism, we used a y3 knock-out (y3-/-) mouse model to investigate the effects of the AICAR and 991/MK-8722. We confirm that y3 isoform expression and activity is high glycolytic muscles, including extensor digitorum longus (EDL), whereas there is very little detected in oxidative soleus (SOL) muscle. We show that AICAR and 991/MK-8722 stimulated glucose uptake in both EDL and SOL muscles. Interestingly, only the ability of AICAR to induce glucose uptake was blunted in EDL muscle taken from y3-/- mice. Consistent with this, whole-body glucose clearance was also impaired in y3-/- mice in response to an AICAR, whilst MK-8722 lowered blood glucose similarly between WT and y3-/- mice. Despite the presence of y1-containing complexes, which are the most predominant complexes in both EDL and SOL muscles, this suggests that different AMPKy isoforms play different roles in glucose homeostasis in response to AICAR. We further looked at de novo glycogen synthesis and glucose utilisation in skeletal muscle. Despite similar basal glucose uptake between muscles from WT and y3-/-, y3-deficiency results in lower basal glycogen content only in glycolytic muscles. We show that this is not due to an inability to synthesise glycogen de novo, since MK-8722 was able to increase glycogen levels in EDL. Instead, we show that the decrease in basal glycogen in y3-/- EDL, may be linked lower expression of UDP-glucose pyrophosphorylase 2 (UGP2). This suggests that AMPKy3 may play a role in steering the molecular fate of glucose inside the cell. Taken together, whilst we show that AMPKy3 is dispensable for ex vivo glucose transport and in vivo glucose homeostasis in response to ADaM-site AMPK activators, nucleotide-mediated activation of y3 by AICAR is impaired. Further research is required to understand the nucleotide regulation of different y-containing AMPK complexes. This differential activation mechanism could be exploited to specifically target AMPKy3 complexes in the muscle, and potentially avoid deleterious effects of activation of AMPK complexes in other tissues.

EPFL2021

Reprogramming G Protein-Coupled Receptor Structure, Function And Signaling By Computational Design

Dániel Kéri

G protein-coupled receptors (GPCRs) are 7-transmembrane alpha-helical integral membrane proteins on which cells heavily rely to receive information regarding their external environment. These receptors are able to transfer information to intracellular downstream effectors upon stimulation from their cognate ligands, which can be considerably diverse. They can include light, small molecules, peptides, protons; Due to its evolutionary success, over millions of years of evolution, this protein family has expanded to include over 800 members. Despite the large size of the family and the diverse inputs they accept, the structure and the mechanism for relaying signals to their downstream partners, G proteins and B-arrestins, remains largely the same. As these receptors are involved in a great deal of biological processes such as sight (rhodopsin), cognition (dopamine, serotonin, opioid receptors), immunity (chemokine receptors), heart function (adrenergic, angiotensin receptors), etc.; a great deal of effort has gone into understanding their structure and function. Our efforts have gone into understanding their signaling properties and rationally modifying them. Most proteins are fairly flexible entities and their structures tend to oscillate and move around, sampling a number of conformations. Nature has taken advantage of these natural motions to regulate protein function from distant binding sites, in a phenomenon called allostery. GPCRs are unique in the sense that their primary function relies on allostery. By tweaking the allosteric signaling of GPCRs, we hope to have a better understand allostery, use the principles we learn to create designer GPCR biosensors with the desired sensitivity, and to eventually create de novo allosteric proteins. In this work, I present our progress in this effort, which has been significant. We have created a highly accurate in silico method to allosterically alter relative stabilities of the active and inactive states of the GPCR dopamine D2 receptor, but also to independently control its allosteric signaling strength. With our methodology we have been able to create receptors which have high basal activities by selectively stabilizing the active state of the receptor. This has already facilitated the structure determination of the active, G protein-bound dopamine D2 receptor; a first for this GPCR. Additionally, we have created a number of dopamine D2 variants with roughly 100 times higher sensitivity to dopamine than the WT receptor. These efforts continue to characterize the functional effects of these allosteric mutations. Furthermore, we are also working on a collaboration to rewire the signaling pathway of the adenosine A2A receptor. Adenosine is a common immunosuppresant in solid tumor micro-environments (TMEs). By rewiring the downstream signaling of the A2A receptor, we hope to reverse the response of T-cells in these TMEs to activate and attack the solid tumor.

EPFL2021

Reprogramming G Protein-Coupled Receptor Structure, Function And Signaling By Computational Design

Dániel Kéri

EPFL2021

Allosteric regulation and targeting of Bruton's tyrosine kinase (Btk) in B-cell lymphoma

Daniel Pereira Duarte

EPFL2020

Investigation of physiological roles of AMPK-activated protein kinase y3

Philipp Jurijvic Rhein

EPFL2021