Allosteric activation of metabotropic glutamate receptor 5

Abstract

Metabotropic glutamate receptor 5 (mGluR5) is a class C G protein-coupled receptor (GPCR) with both an extracellular ligand binding site and an allosteric intrahelical chamber located similarly to the orthosteric ligand binding site of Class A GPCRs. Ligands binding to this ancestral site of mGluR5 can act as positive (PAM), negative (NAM) or silent (SAM) allosteric modulators, and their medicinal chemistry optimization is notoriously difficult, as subtle structural changes may cause significant variation in activity and switch in the functional response. Here we present all atom molecular dynamics simulations of NAM, SAM and PAM complexes formed by closely related ligands and analyse the structural differences of the complexes. Several residues involved in the activation are identified and the formation of a continuous water channel in the active complex but not in the inactive ones is recognized. Our results suggest that the mechanism of mGluR5 activation is similar to that of class A GPCRs.

Communicated by Ramaswamy H. Sarma     

Allosteric activation of chymotrypsin-catalyzed hydrolysis of specific substrates

The rates of hydrolysis of three specific substrates of chymotrypsin, glutaryl-L-phenylalanine p-nitroanilide, acetyl-DL-tyrosine p-nitroanilide and acetyl-L-tyrosine anilide were enhanced by 2,2′-bis[α-(benzyldimethylammonium)methyl] azobenzene dibromide and less so by related compounds. Detailed studies with glutaryl-L-phenylalanine p-nitroanilide showed a 42-fold increase in k_cat with no change in Km. No acceleration (or inhibition) was noted with esters, hydroxamides or proteins as substrates. Tryptic hydrolysis of benzoyl-DL-arginine p-nitroanilide was unaffected. It was concluded that certain quaternary compounds can act as allosteric effectors of chymotrypsin.     

Allosteric interactions prime androgen receptor dimerization and activation

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Allosteric activation of PTEN phosphatase by phosphatidylinositol 4,5-bisphosphate

Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is a tumor suppressor that is lost in many human tumors and encodes a phosphatidylinositol phosphate phosphatase specific for the 3-position of the inositol ring. Here we report a novel mechanism of PTEN regulation. Binding of di-C8-phosphatidylinositol 4,5-P2 (PI(4,5)P2) to PTEN enhances phosphatase activity for monodispersed substrates, PI(3,4,5)P3 and PI(3,4)P2. PI(5)P also is an activator, but PI(4)P, PI(3,4)P2, and PI(3,5)P2 do not activate PTEN. Activation by exogenous PI(4,5)P2 is more apparent with PI(3,4)P2 as a substrate than with PI(3,4,5)P3, probably because hydrolysis of PI(3,4)P2 yields PI(4)P, which is not an activator. In contrast, hydrolysis of PI(3,4,5)P3 yields a potent activator, PI(4,5)P2, creating a positive feedback loop. In addition, neither di-C4-PI(4,5)P2 nor inositol trisphosphate-activated PTEN. Hence, the interaction between PI(4,5)P2 and PTEN requires specific, ionic interactions with the phosphate groups on the inositol ring as well as hydrophobic interactions with the fatty acid chains, likely mimicking the physiological interactions that PTEN has with the polar surface head groups and the hydrophobic core of phospholipid membranes. Mutations of the apparent PI(4,5)P2-binding motif in the PTEN N terminus severely reduced PTEN activity. In contrast, mutation of the C2 phospholipid-binding domain had little effect on PTEN activation. These results suggest a model in which a PI(4,5)P2 monomer binds to PTEN, initiates an allosteric conformational change and, thereby, activates PTEN independent of membrane binding.     

GAPDH as a sensor of NO stress

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a classic glycolytic enzyme, and accumulating evidence has suggested that GAPDH is a multi-functional protein. In particular, its role as a mediator for cell death has been highlighted. For the last decade, many groups reported that a pool of GAPDH translocates to the nucleus under a variety of stressors, most of which are associated with oxidative stress. At the molecular level, sequential steps lead to nuclear translocation of GAPDH during cell death as follows: first, a catalytic cysteine in GAPDH (C150 in rat GAPDH) is S-nitrosylated by nitric oxide (NO) that is generated from inducible nitric oxide synthase (iNOS) and/or neuronal NOS (nNOS); second, the modified GAPDH becomes capable of binding with Siah1, an E3 ubiquitin ligase, and stabilizes it; third, the GAPDH-Siah protein complex translocates to the nucleus, dependent on Siah1's nuclear localization signal, and degrades Siah1's substrates in the nucleus, which results in cytotoxicity. A recent report suggests that GAPDH may be genetically associated with late-onset of Alzheimer's disease. (-)-deprenyl, which has originally been used as a monoamine oxidase inhibitor for Parkinson's disease, binds to GAPDH and displays neuroprotective actions, but its molecular mechanism is still unclear. The NO/GAPDH/Siah1 death cascade will contribute to the molecular understanding of a role of GAPDH in neurodegenerative disorders and help to establish novel therapeutic strategies.     

Allosteric activation of aspartate transcarbamylase with a fluorescent nucleotide analogue: linear-benzo-ATP.

The interaction of Escherichia coli aspartate transcarbamylase with linear-benzo-ATP has been investigated by means of fluorescence spectroscopy. The fluorescent nucleotide analogue activates the enzyme to the same extent as ATP. Fluorescence polarization has been used to determine the association constant of lin-benzo-ATP with aspartate transcarbamylase (ATCase) which is 5 X 10(-3) M-1 at pH 8.7, at 4 degrees C, assuming six binding sites. This association constant is similar to those previously obtained for ATP at a variety of temperatures, buffers, and pH. The fluorescence emission of lin-benzo-ATP is not quenched when bound to ATCase, which indicates absence of pi interactions between the activator and tyrosyl residues in the protein. These residues have been implicated in the stereochemical mechanism of allosteric interactions in ATCase. Furthermore, this fluorescence behavior implicates hydrogen bond formation between the amino group of lin-benzo-ATP and a nucleophilic center at the enzyme binding site. The fact that lin-benzo-ATP activates ATCase is consistent with a previously published model for nucleotide regulation of the enzyme.     

Protein kinase C as a stress sensor

While there are many reviews which examine the group of proteins known as protein kinase C (PKC), the focus of this article is to examine the cellular roles of two PKCs that are important for stress responses in neurological tissues (PKC gamma and epsilon) and in cardiac tissues (PKC epsilon). These two kinases, in particular, seem to have overlapping functions and interact with an identical target, connexin 43 (Cx43), a gap junction protein which is central to proper control of signals in both tissues. While PKC gamma and PKC epsilon both help protect neural tissue from ischemia, PKC epsilon is the primary PKC isoform responsible for responding to decreased oxygen, or ischemia, in the heart. Both do this through Cx43. It is clear that both PKC gamma and PKC epsilon are necessary for protection from ischemia. However, the importance of these kinases has been inferred from preconditioning experiments which demonstrate that brief periods of hypoxia protect neurological and cardiac tissues from future insults, and that this depends on the activation, translocation, or ability for PKC gamma and/or PKC epsilon to interact with distinct cellular targets, especially Cx43. This review summarizes the recent findings which define the roles of PKC gamma and PKC epsilon in cardiac and neurological functions and their relationships to ischemia/reperfusion injury. In addition, a biochemical comparison of PKC gamma and PKC epsilon and a proposed argument for why both forms are present in neurological tissue while only PKC epsilon is present in heart, are discussed. Finally, the biochemistry of PKCs and future directions for the field are discussed, in light of this new information.     

Allosteric activation and competitive inhibition of yeast phosphofructokinase by d-fructose

Purified phosphofructokinase from bakers yeast is activated by d-fructose in low concentrations (up to 1 mM) and inhibited by high concentrations. The stimulatory effect of d-fructose is similar, but smaller than that of AMP. In the presence of AMP (0.4 mM or higher) d-fructose does no longer stimulate, but its inhibitory effect persists (K _I =8 mM). Its dualistic action on phosphofructokinase activity indicates that d-fructose might induce low frequency in glycolytic oscillations by direct interaction with the enzyme.     

Allosteric activation of antithrombin critically depends upon hinge region extension

Antithrombin (AT) inhibits most of the serine proteases generated in the blood coagulation cascade, but its principal targets are factors IXa, Xa, and thrombin. Heparin binding to AT, via a specific pentasaccharide sequence, alters the conformation of AT in a way that promotes efficient inhibition of factors IXa and Xa, but not of thrombin. The conformational change most likely to be relevant to protease recognition is the expulsion of the N-terminal portion of the reactive center loop (hinge region) from the main beta-sheet A. Here we investigate the hypothesis that the exosites on the surface of AT are accessible for interaction with a protease only when the hinge region is fully extended, as seen in the related Michaelis complex between heparin cofactor II and thrombin. We engineered a disulfide bond between residues 222 on strand 3A and 381 in the reactive center loop to prevent the extension of the hinge region upon pentasaccharide binding. The disulfide bond did not significantly alter the ability of the variant to bind to heparin or to inhibit thrombin. Although the basal rate of factor Xa inhibition was not affected, that of factor IXa inhibition was reduced to the limit of detection. In addition, the disulfide bond completely abrogated the pentasaccharide accelerated inhibition of factors Xa and IXa. We conclude that AT hinge region extension is the activating conformational change for inhibition of factors IXa and Xa, and propose models for the progressive and activated AT Michaelis complexes with thrombin, factor Xa, and factor IXa.     

Allosteric activation of plasma membrane receptors--physiological implications and structural origins

Allosteric modulation of receptors has physiological not just pharmacological significance. Thus, the chemical context in which an agonist signal is received can have a major impact on the nature of the physiological response by modifying receptor sensitivity and/or maximal activity-even the nature of the signalling response. In addition, recognising that an endogenous activator is the allosteric modulator of a known receptor, rather than the agonist of a novel receptor, has the potential to solve, in dramatic fashion, key physiological questions. What is an allosteric modulator and why are allosteric effects on receptors so diverse and frequently complex? What is the scope of allosteric effects? Can the existence of endogenous modulators be predicted from a receptor's amino acid sequence? How should screening for endogenous allosteric modulators be undertaken? These questions form the framework of this mini-review on physiological and structural aspects of receptor allostery.     

Allosteric activation of coagulation factor VIIa visualized by hydrogen exchange

Coagulation factor VIIa (FVIIa) is a serine protease that, after binding to tissue factor (TF), plays a pivotal role in the initiation of blood coagulation. We used hydrogen exchange monitored by mass spectrometry to visualize the details of FVIIa activation by comparing the exchange kinetics of distinct molecular states, namely zymogen FVII, endoproteolytically cleaved FVIIa, TF-bound zymogen FVII, TF-bound FVIIa, and FVIIa in complex with an active site inhibitor. The hydrogen exchange kinetics of zymogen FVII and FVIIa are identical indicating highly similar solution structures. However, upon tissue factor binding, FVIIa undergoes dramatic structural stabilization as indicated by decreased exchange rates localized throughout the protease domain and in distant parts of the light chain, spanning across 50A and revealing a concerted interplay between functional sites in FVIIa. The results provide novel insights into the cofactor-induced activation of this important protease and reveal the potential for allosteric regulation in the trypsin family of proteases.     

Allosteric activation via kinetic control: potassium accelerates a conformational change in IMP dehydrogenase

Allosteric activators are generally believed to shift the equilibrium distribution of enzyme conformations to favor a catalytically productive structure; the kinetics of conformational exchange is seldom addressed. Several observations suggested that the usual allosteric mechanism might not apply to the activation of IMP dehydrogenase (IMPDH) by monovalent cations. Therefore, we investigated the mechanism of K(+) activation in IMPDH by delineating the kinetic mechanism in the absence of monovalent cations. Surprisingly, the K(+) dependence of k(cat) derives from the rate of flap closure, which increases by ≥65-fold in the presence of K(+). We performed both alchemical free energy simulations and potential of mean force calculations using the orthogonal space random walk strategy to computationally analyze how K(+) accelerates this conformational change. The simulations recapitulate the preference of IMPDH for K(+), validating the computational models. When K(+) is replaced with a dummy ion, the residues of the K(+) binding site relax into ordered secondary structure, creating a barrier to conformational exchange. K(+) mobilizes these residues by providing alternate interactions for the main chain carbonyls. Potential of mean force calculations indicate that K(+) changes the shape of the energy well, shrinking the reaction coordinate by shifting the closed conformation toward the open state. This work suggests that allosteric regulation can be under kinetic as well as thermodynamic control.     

Danger perception and stress response through an olfactory sensor for the bacterial metabolite hydrogen sulfide

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