title: Binding dynamics and energetic insight into the molecular forces driving nucleotide binding by guanylate kinase.
abstract: Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unique substrate specificities. We investigated the energetic contribution to guanylate kinase substrate binding and the forces underlying ligand recognition. In the range from 20 to 35°C, the thermodynamic profiles displayed marked decrease in binding enthalpy, while the free energy of binding showed little changes. GMP produced a large binding heat capacity change of -356 cal mol(-1) K(-1), indicating considerable conformational changes upon ligand binding. Interestingly, the calculated ΔCp was -32 cal mol(-1) K(-1), indicating that the accessible surface area is not the central change in substrate binding, and that other entropic forces, including conformational changes, are more predominant. The thermodynamic signature for GMP is inconsistent with rigid-body association, while dGMP showed more or less rigid-body association. These binding profiles explain the poor catalytic efficiency and low affinity for dGMP compared with GMP. At low temperature, the ligands bind to the receptor site under the effect of hydrophobic forces. Interestingly, by increasing the temperature, the entropic forces gradually vanish and proceed to a nonfavorable contribution, and the interaction occurs mainly through bonding, electrostatic forces, and van der Waals interactions.
authors.affiliation: Department of Pharmacology, Faculty of Veterinary Medicine, Kafr El-Shikh University, Kafr El-Shikh 33516, Egypt. mahmoud.kandeal@vet.kfs.edu.eg
authors.forename: Mahmoud
authors.initials: M
authors.lastname: Kandeel
authors.forename: Yukio
authors.initials: Y
authors.lastname: Kitade
mesh_terms: D001665:Binding Sites; D002151:Calorimetry; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003848:Deoxyguanine Nucleotides / Q000378:metabolism; D019277:Entropy; D006157:Guanosine Monophosphate / Q000378:metabolism; D051528:Guanylate Kinases / Q000378:metabolism*; D006860:Hydrogen Bonding; D007700:Kinetics; D009711:Nucleotides / Q000378:metabolism*; D010963:Plasmodium falciparum / Q000737:chemistry / Q000201:enzymology*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D055672:Static Electricity; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D003848:Deoxyguanine Nucleotides; D009711:Nucleotides; C007257:2'-deoxyguanosine 5'-phosphate; D006157:Guanosine Monophosphate; D051528:Guanylate Kinases