Ligand structure controlled allostery in cAMP-dependent protein kinase catalytic subunit

Abstract

Protein kinase A (cAMP dependent protein kinase catalytic subunit, EC 2.7.11.11) binds simultaneously ATP and a phosphorylatable peptide. These structurally dissimilar allosteric ligands influence the binding effectiveness of each other. The same situation is observed with substrate congeners, which reversibly inhibit the enzyme. In this review these allosteric effects are quantified using the interaction factor, which compares binding effectiveness of ligands with the free enzyme and the pre-loaded enzyme complex containing another ligand. This analysis revealed that the allosteric effect depends upon structure of the interacting ligands, and the principle "better binding: stronger allostery" observed can be formalized in terms of linear free-energy relationships, which point to similar mechanism of the allosteric interaction between the enzyme-bound substrates and/or inhibitor molecules. On the other hand, the type of effect is governed by ligand binding effectiveness and can be inverted from positive allostery to negative allostery if we move from effectively binding ligands to badly binding compounds. Thus the outcome of the allostery in this monomeric enzyme is the same as defined by classical theories for multimeric enzymes: making the enzyme response more efficient if appropriate ligands bind.

Allosteric Effect of Adenosine Triphosphate on Peptide Recognition by 3′5′-Cyclic Adenosine Monophosphate Dependent Protein Kinase Catalytic Subunits

“…Most interestingly, this increase was again correlated with the binding effectiveness of the nucleotide and its analogues [21]. This means that both binding sites involved in the interactions with peptides and ATP (or its analogues), are involved in allosteric regulation, as was described in [21].…”

“…Most interestingly, this increase was again correlated with the binding effectiveness of the nucleotide and its analogues [21]. This means that both binding sites involved in the interactions with peptides and ATP (or its analogues), are involved in allosteric regulation, as was described in [21]. Therefore the pa value is correlated with pK values for both ligands and even a weakly binding ligand could cause a relatively large allosteric effect, if its partner ligand is a strong binder.…”

“…4 Similarity plot for the binding effectiveness of peptides I-VI (from Table 1) with the free enzyme (pK L ) and its complex with ATP (pK i ). Data for PKI and PKI (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24) were obtained from the literature (PKI: pK i = 9.5 [13] and pK L = 5.6 [14]; PKI(5-24): pKi = 9.7 [15] and pK L = 5.7 [16]) allosteric effect and ligand binding affinity was previously observed in the case of peptide substrates (points 1-7 in Fig. 5) with PKAc which led to the formulation of the principle ''better binding-stronger allostery'' [10].…”

Computational modeling of cAMP­-dependent protein kinase allostery

“…Direct evidence that allosteric interaction between ATP and the peptide substrate binding sites manifests in the catalytic subunit of cAMPdepen dent protein kinase (PKAc) was presented by Masterson et al (2008). Thereafter, the idea of allosteric regulation in PKAc was expanded by Kuznetsov and Järv (2009),…”

“…who presented a comprehensive survey of the available ex perimental data about allosteric interactions in this enzyme. This analysis revealed that the interaction of peptide sub strates or inhibitors with PKAc is influenced by the sim ultaneous binding of ATP or its analogs and, conversely, the binding effectiveness of ATP is governed by the pres ence of peptides (Kuznetsov and Järv 2009).…”