Thermodynamics and Kinetics of Association of Antibiotics with the Aminoglycoside Acetyltransferase (3)-IIIb, a Resistance-Causing Enzyme

2010-05-18
Norris, Adrianne L.
Özen, Can
Serpersu, Engin H.
The thermodynamic and kinetic properties of interactions of antibiotics with the aminoglycoside acetyltransferase (3)-IIIb (AAC) are determined with several experimental methods. These data represent the first such characterization of an enzyme that modifies the 2-deoxystreptamine ring common to all aminoglycoside antibiotics. Antibiotic substrates For AAC include kanamycin A, kanamycin B, tobramycin, sisomicin, neomycin B, paromomycin, lividomycin A, and ribostamycin. Kinetic studies show that kanamycin group aminoglycosides have higher k(cat) values than members of the neomycin group. Only small aminoglycosides without intraring constraints show substrate inhibition. Isothermal titration calorimetry (ITC) and fluorescence measurements are consistent with a molecular size-dependent stoichiometry where binding stoichiometries are 1.5-2.0 for small antibiotics and 1.0 for larger. Antibiotic-enzyme interaction occurs with a favorable enthalpy (Delta H < 0) and a compensating unfavorable entropy (T Delta S < 0). The presence of coenzyme A significantly increases the affinity of the antibiotic for AAC. However, the thermodynamic properties of its ternary complexes distinguish this enzyme from other aminoglycoside-modifying enzymes (AGMEs). Unlike other AGMEs, the enthalpy of binding becomes more favored by 1.7-10.0-fold in the presence of the cosubstrate CoASH, while the entropy becomes 2.0-22.5-fold less favored. The overall free energy change is still only 1.0-1.9 kcal/mol from binary to ternary for all antibiotics tested, which is similar to those for other aminoglycoside-modifying enzymes. A computationally derived homology model provides structural support for these conclusions and further indicates that AAC is likely a member of the GCN5-related acetyltransferase family of proteins.
BIOCHEMISTRY

Suggestions

Electro-chemo-mechanical induced fracture modeling in proton exchange membrane water electrolysis for sustainable hydrogen production
Aldakheel, Fadi; Kandekar, Chaitanya; Bensmann, Boris; Dal, Hüsnü; Hanke-Rauschenbach, Richard (2022-10-01)
This work provides a framework for predicting fracture of catalyst coated membrane (CCM) due to coupled electro-chemo-mechanical degradation processes in proton exchange membrane water electrolysis (PEMWE) cells. Electrolysis in the catalyst layer (CL) bulk, diffusion of Hydrogen proton through the membrane (MEM), and mechanical compression at the interface with the porous transport layer (PTL) generate micro-cracks that influence the catalyst degradation. Based on our experimental observations, we propose ...
Molecular recognition of poly(A) by small ligands: an alternative method of analysis reveals nanomolar, cooperative and shape-selective binding
Persil Çetinkol, Özgül (Oxford University Press (OUP), 2009-02-01)
A few drug-like molecules have recently been found to bind poly(A) and induce a stable secondary structure (T(m)approximate to 60 degrees C), even though this RNA homopolymer is single-stranded in the absence of a ligand. Here, we report results from experiments specifically designed to explore the association of small molecules with poly(A). We demonstrate that coralyne, the first small molecule discovered to bind poly(dA), binds with unexpectedly high affinity (K(a) >10(7) M(-1)), and that the crescent sh...
Thermodynamic properties of simple liquid metals calculated using an analytic pair potential
Khajil, T. M. A.; Tomak, Mehmet (American Physical Society (APS), 1988-11-1)
An analytic pair potential proposed by Pettifor and Ward is used to calculate the thermodynamic properties of Na, Mg, and Al. The energy, pressure, and bulk-modulus values calculated using the Pettifor-Ward pair potential are in qualitative accord with calculations based on other models.
Investigation of biologically important small molecules: quantum chemical and molecular dynamics calculations
Tekin, Emine Deniz; Erkoç, Şakir; Department of Physics (2010)
In this thesis, six small molecules (S-allylcysteine, S-allyl mercaptocysteine, allicin, methyl propyl disulfide, allyl methyl sulfide and dipropylsulfide) that are found in garlic and onion, and are known to be beneficial for human health were studied using molecular mechanics, semi-empirical methods, ab-initio (Restricted Hartree Fock), and density functional theory. Using the same methods, a synthetic pyrethroid pesticide molecule, called cyfluthrin, was also studied. Structural, vibrational and electron...
Enantioselective synthesis of new chiral 2-aziridinyl phosphonates and studies of their biological activities
Doğan, Özdemir; Beksultanova, Nurzhan; ALTANLAR, NURTEN; Simsek, Duygu; KARABIYIK, HASAN (2017-02-15)
A new series of chiral aziridinyl phosphonates has been synthesized and evaluated for antibacterial and antifungal activities. For the synthesis, a Gabriel-Cromwell reaction was used to form aziridinyl phosphonates in 52-83% yield. In order to evaluate antibacterial and antifungal activities, MIC values were measured. Although most of the compounds showed insignificant activity, two of them provided low to moderate antifungal activity.
Citation Formats
A. L. Norris, C. Özen, and E. H. Serpersu, “Thermodynamics and Kinetics of Association of Antibiotics with the Aminoglycoside Acetyltransferase (3)-IIIb, a Resistance-Causing Enzyme,” BIOCHEMISTRY, pp. 4027–4035, 2010, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/30731.