Allosteric cooperativity between peptide and ATP binding sites on cAMP-dependent protein kinase catalytic subunit was studied kinetically for the reaction of phosphorylation of seven peptide substrates. The allosteric effect was quantified in terms of the interaction factor α by comparing binding effectiveness of a substrate molecule with the free enzyme and with the enzyme complex with another substrate. It was discovered that the magnitude of the allosteric feedback between these binding sites was governed by the effectiveness of substrate binding, which was varied by using different peptides, and the principle 'better binding: stronger allostery' was formulated. This interrelationship was further formalized in terms of a linear-free-energy relationship b p C p , S K α < at sub-millimolar b K values, changed into negative cooperativity with 1 α > at millimolar b K values. This means that inversion of the cooperative effect was induced by substrate structure, and allostery was used by this enzyme as an additional mechanism to discriminate between substrates, facilitating phosphorylation of good substrates and providing additional protection against phosphorylation of bad substrates. Some implications of this allosteric mechanism on substrate specificity of protein kinases were discussed.Abbreviations: Ala-kemptide -peptide inhibitor LRRAALG; AMPPNP -, -imidoadenosine β γ 5′-triphosphate; kemptidepeptide substrate LRRASLG; protein kinase A -catalytic subunit of cAMP dependent protein kinase.Enzyme: cAMP dependent protein kinase -EC 2.7.11.1.

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Among different approaches to control the COVID19 disease, there is clear interest to develop inhibitors which block the virus interaction with the host cells and through this simple mechanism could facilitate developing medication. In this report, interaction of the virus SARS CoV2 spike protein S1 binding site with potential antiviral peptide ligands is analysed computationally. The peptides are derived from the binding domain of the angiotensinconverting enzyme 2, which is the receptor site for this virus. These calculations reveal that although shortening of these peptides from the N terminus and C terminus reduces their docking energy on the S1 binding site, there is still a number of peptides which effectively bind to the binding site on the SARS CoV2 spike protein S1, and thus can be used as leads for further optimization of the inhibitory effect. Finally, this may open new perspectives for working out treatments against the virus infection.

Allosteric cooperativity in inhibition of protein kinase A was studied for the first time kinetically, by using the second-order rate constants of kemptide phosphorylation, measured in the absence and presence of inhibitors, and the effect of cooperativity was characterized in terms of the interaction factor . This kinetic method was evaluated for differently targeted inhibitors H89 and LRRAALG-NH 2 , and interaction of these compounds with the free enzyme and the enzyme-substrate complexes was quantified. The inhibitory effect of these compounds was asymmetric relatively ATP and kemptide, and allosteric enhancement of LRRAALG-NH 2 binding in the presence of ATP was revealed. This cooperative effect was compared with results of ligand binding studies and the principle "better binding -stronger allostery" was formulated and formalized in terms of a linear-free-energy relationship p( ) = C + S pK i , where p( ) stands for the negative logarithm of the interaction factor and pK i characterizes affinity of the free enzyme for the inhibitory peptide, C=-2.7 and S=0.9, r=0.92.

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aThe solvation effects observed in water-organic solutions were studied by combining data for reaction kinetics and dissolution equilibria by means of a linear free-energy (similarity) analysis. Kinetic data for the pH-independent hydrolysis of (4-methoxyphenyl)-2,2-dichloroacetate measured in this work and solubility data for naphthalene, and other substrates of low polarity, in aqueous binary mixtures of methanol, ethanol, acetonitrile, dimethyl sulfoxide (DMSO), and 1,4-dioxane were used. Linear similarity relationships were discovered for these data over the full range of solvent compositions studied. To gain insight into the similarities observed between these different phenomena, molecular dynamics simulations were carried out for naphthalene and an ester in water-acetonitrile solutions. The results revealed considerable preferential solvation of these substrates by the co-solvent. Linear relationships between the experimental data and the mole fractions of acetonitrile in the solvation shells of substrates were found. Surprisingly, a linear relationship was found between the mole fractions of acetonitrile in the solvation shells of the ester and naphthalene. This linearity indicated that a similar solvation mechanism governs even such different phenomena as dissolution and reaction kinetics. The relationships between the experimental data and the results of the molecular dynamics calculations found in this work explained the solvent effect observed in water-organic solutions on the molecular level.