Kinetic, thermodynamic, and structural properties of the aminoglycoside
Emtricitabine (FTC) and lamivudine (3TC), containing an oxathiolane ring with unnatural (−)-stereochemistry, are widely used nucleoside reverse transcriptase inhibitors (NRTIs) in anti-HIV therapy. Treatment with FTC or 3TC primarily selects for the HIV-1 RT M184V/I resistance mutations. Here we provide a comprehensive kinetic and structural basis for inhibiting HIV-1 RT by (−)-FTC-TP and (−)-3TC-TP and drug resistance by M184V. (−)-FTC-TP and (−)-3TC-TP have higher binding affinities (1/
- Award ID(s):
- 1856617
- PAR ID:
- 10154174
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Communications Biology
- Volume:
- 2
- Issue:
- 1
- ISSN:
- 2399-3642
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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ABSTRACT N3‐ acetyltransferase‐VIa (AAC‐VIa) are determined. Among the aminoglycosideN3 ‐acetyltransferases, AAC‐VIa has one of the most limited substrate profiles. Kinetic studies showed that only five aminoglycosides are substrates for this enzyme with a range of fourfold difference ink catvalues. Larger differences inK M(∼40‐fold) resulted in ∼30‐fold variation ink cat/K M. Binding of aminoglycosides to AAC‐VIa was enthalpically favored and entropically disfavored with a net result of favorable Gibbs energy (ΔG < 0). A net deprotonation of the enzyme, ligand, or both accompanied the formation of binary and ternary complexes. This is opposite of what was observed with several other aminoglycosideN3 ‐acetyltransferases, where ligand binding causes more protonation. The change in heat capacity (ΔCp) was different in H2O and D2O for the binary enzyme–sisomicin complex but remained the same in both solvents for the ternary enzyme–CoASH–sisomicin complex. Unlike, most other aminoglycoside‐modifying enzymes, the values of ΔCp were within the expected range of protein‐carbohydrate interactions. Solution behavior of AAC‐VIa was also different from the more promiscuous aminoglycosideN3 ‐acetyltransferases and showed a monomer‐dimer equilibrium as detected by analytical ultracentrifugation (AUC). Binding of ligands shifted the enzyme to monomeric state. Data also showed that polar interactions were the most dominant factor in dimer formation. Overall, thermodynamics of ligand‐protein interactions and differences in protein behavior in solution provide few clues on the limited substrate profile of this enzyme despite its >55% sequence similarity to the highly promiscuous aminoglycosideN3 ‐acetyltransferase. Proteins 2017; 85:1258–1265. © 2017 Wiley Periodicals, Inc. -
Abstract Cupin dioxygenases such as salicylate 1,2‐dioxygense (SDO) perform aromatic C−C bond scission via a 3‐His motif tethered iron cofactor. Here, transient kinetics measurements are used to monitor the catalytic cycle of SDO by using a nitro‐substituted substrate analog, 3‐nitrogentisate. Compared to the natural substrate, the nitro group reduces the enzymatic
k catby 500‐fold, thereby facilitating the detection and kinetic characterization of reaction intermediates. Sums and products of reciprocal relaxation times derived from kinetic measurements were found to be linearly dependent on O2concentration, suggesting reversible formation of two distinct intermediates. Dioxygen binding to the metal cofactor takes place with a forward rate of 5.9×103 M−1 s−1: two orders of magnitude slower than other comparable ring‐cleaving dioxygenses. Optical chromophore of the first intermediate is distinct from thein situ generated SDO Fe(III)−O2⋅−complex but closer to the enzyme‐substrate precursor. -
Hydrolysis of ionic liquid–treated substrate with an Iocasia fonsfrigidae strain SP3-1 endoglucanase
Abstract Recently, we reported the discovery of a novel endoglucanase of the glycoside hydrolase family 12 (GH12), designated IfCelS12A, from the haloalkaliphilic anaerobic bacterium
Iocasia fonsfrigidae strain SP3-1, which was isolated from a hypersaline pond in the Samut Sakhon province of Thailand (ca. 2017). IfCelS12A exhibits high substrate specificity on carboxymethyl cellulose and amorphous cellulose but low substrate specificity on b-1,3;1,4-glucan. Unlike some endoglucanases of the GH12 family, IfCelS12A does not exhibit hydrolytic activity on crystalline cellulose (i.e., Avicel™). High-Pressure Liquid Chromatography (HPLC) and Thin Layer Chromatography (TLC) analyses of products resulting from IfCelS12-mediated hydrolysis indicate mode of action for this enzyme. Notably, IfCelS12A preferentially hydrolyzes cellotetraoses, cellopentaoses, and cellohexaoses with negligible activity on cellobiose or cellotriose. Kinetic analysis with cellopentaose and barely b-d -glucan as cellulosic substrates were conducted. On cellopentaose, IfCelS12A demonstrates a 16-fold increase in activity (K M = 0.27 mM;k cat = 0.36 s−1;k cat /K M = 1.34 mM−1s−1) compared to the enzymatic hydrolysis of barley b-d -glucan (K M : 0.04 mM,k cat : 0.51 s−1,k cat /K M = 0.08 mM−1s−1). Moreover, IfCelS12A enzymatic efficacy is stable in hypersaline sodium chlorids (NaCl) solutions (up to 10% NaCl). Specifically, IfCel12A retains notable activity after 24 h at 2M NaCl (10% saline solution). IfCelS12A used as a cocktail component with other cellulolytic enzymes and in conjunction with mobile sequestration platform technology offers additional options for deconstruction of ionic liquid–pretreated cellulosic feedstock.Key points •
IfCelS12A from an anaerobic alkaliphile Iocasia fronsfrigidae shows salt tolerance •
IfCelS12A in cocktails with other enzymes efficiently degrades cellulosic biomass •
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meta ‐nitrophenylacetic acid as the release mechanism. Isothermal titration calorimetry (ITC) was used an alternative to usual approaches to measure the Zn2+binding affinities of these new compounds owing to unsuccessful measurement by competitive titration with 4‐(2‐pyridylazo)resorcinol (PAR). MorphDeCage forms a 1 : 1 ligand‐metal complex with a 106 μM Kdvalue. PyrDeCage forms both a 1 : 1 and 1 : 2 metal: ligand complexes with 3.2 and 21.7 μM Kdvalues respectively. To further demonstrate the efficacy of the ITC methodology and provide a comparison to direct UV‐vis titrations data, two photocages based on Sanger's reagent (SRPs) were prepared. The Kdvalues of the SRPs measured by UV‐vis titration and ITC were internally consistent and support the retraction of the original report (J. Am. Chem. Soc .2020 ,142 , 3806–3813), which was withdrawn due to errors in binding affinity measurements. -
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