Thermodynamic analysis of protein kinase A Iα activation |
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Authors: | O N Rogacheva A V Popov E V Savvateeva-Popova V E Stefanov B F Shchegolev |
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Institution: | (1) Department of Biomedical Engineering, Surgery, and Cellular and Integrative Physiology, IUPUI, Indianapolis, IN, USA |
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Abstract: | Thermodynamic analysis of protein kinase A (PKA) Iα activation was performed using Quantum 3.3.0 docking software and a Gaussian
03W quantum mechanical computational package. Expected stacking interactions between adenine of 3′:5′-AMP and aromatic moieties
of amino acids were taken into account by means of MP2/6-31G(d) IPCM (iso-density polarizable continuum model) computations
(ɛ = 4.0). It is demonstrated that thermodynamically favorable agonist-induced PKA Iα activation is mediated by two processes.
First, 3′:5′-AMP binding is accompanied by structural changes leading to a thermodynamically favorable regulatory subunit
conformation, which is hardly realized in the absence of the ligand (ΔGRo = −23.9 ± 8.2 kJ/mol). Second, 3′:5′-AMP affinity to the regulatory subunit conformation observed after agonist-induced PKA
Iα activation is higher than that to inactive holoenzyme complex (ΔG3′:5′−AMPo = −28.1 ± 9.7 kJ/mol). ATP is capable of docking into the 3′:5′-AMP-binding site B of the regulatory subunit complexed with
the catalytic one, resulting in inhibition of kinase activation. True constants of 3′:5′-AMP binding to PKA Iα holoenzyme
were found to be 60 and 57 μM for the regulatory subunit domains A and B, respectively. These constants, unlike the binding
equilibrium constant determined using established experimental techniques and ranging from 15 nM to 2.9 μM, are proved to
be direct measures of 3′:5′-AMP-PKA Iα binding affinity. Their values are in a reasonable agreement with the changes in 3′:5′-AMP
concentration in the cell (2-55 μM) and account for PKA Iα activation in response to adequate stimuli. |
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