Structure, Mutagenesis, and QM:MM Modeling of 3-Ketosteroid Δ1-Dehydrogenase from Sterolibacterium denitrificans─The Role of a New Putative Membrane-Associated Domain and Proton-Relay System in Catalysis.

3-Ketosteroid Δ1-dehydrogenases (KstD) are important microbial flavin enzymes that initiate the metabolism of steroid ring A and find application in the synthesis of steroid drugs. We present a structure of the KstD from Sterolibacterium denitrificans (AcmB), which contains a previously uncharacterized putative membrane-associated domain and extended proton-relay system. The experimental and theoretical studies show that the steroid Δ1-dehydrogenation proceeds according to the Ping-Pong bi-bi kinetics and a two-step base-assisted elimination (E2cB) mechanism. The mechanism is validated by evaluating the experimental and theoretical kinetic isotope effect for deuterium-substituted substrates. The role of the active-site residues is quantitatively assessed by point mutations, experimental activity assays, and QM/MM MD modeling of the reductive half-reaction (RHR). The pre-steady-state kinetics also reveals that the low pH (6.5) optimum of AcmB is dictated by the oxidative half-reaction (OHR), while the RHR exhibits a slight optimum at the pH usual for the KstD family of 8.5. The modeling confirms the origin of the enantioselectivity of C2-H activation and substrate specificity for Δ4-3-ketosteroids. Finally, the cholest-4-en-3-one turns out to be the best substrate of AcmB in terms of ΔG of binding and predicted rate of dehydrogenation.

1,2-Hydrogenation and Transhydrogenation Catalyzed by 3-Ketosteroid Δ1-Dehydrogenase from Sterolibacterium denitrificans-Kinetics, Isotope Labelling and QM:MM Modelling Studies.

Bacteria and fungi that are able to metabolize steroids express 3-ketosteroid-Δ1-dehydrogenases (KstDs). KstDs such as AcmB form Sterolibacterium denitrificans Chol-1 catalyze the enantioselective 1α,2ß-dehydrogenation of steroids to their desaturated analogues, e.g., the formation of 1,4-androstadiene-3,17-dione (ADD) from 4-androsten-3,17-dione (AD). The reaction catalyzed by KstD can be reversed if the appropriate electron donor, such as benzyl viologen radical cation, is present. Furthermore, KstDs can also catalyze transhydrogenation, which is the transfer of H atoms between 3-ketosteroids and 1-dehydrosteroids. In this paper, we showed that AcmB exhibits lower pH optima for hydrogenation and dehydrogenation by 3.5-4 pH units than those observed for KstD from Nocardia corallina. We confirmed the enantiospecificity of 1α,2ß-hydrogenation and 1α,2ß-transhydrogenation catalyzed by AcmB and showed that, under acidic pH conditions, deuterons are introduced not only at 2ß but also at the 1α position. We observed a higher degree of H/D exchange at Y363, which activates the C2-H bond, compared to that at FAD, which is responsible for redox at the C1 position. Furthermore, for the first time, we observed the introduction of the third deuteron into the steroid core. This effect was explained through a combination of LC-MS experiments and QM:MM modelling, and we attribute it to a decrease in the enantioselectivity of C2-H activation upon the deuteration of the 2ß position. The increase in the activation barrier resulting from isotopic substitution increases the chance of the formation of d3-substituted 3-ketosteroids. Finally, we demonstrate a method for the synthesis of 3-ketosteroids chirally deuterated at 1α,2ß positions, obtaining 1α,2ß-d2-4-androsten-3,17-dione with a 51% yield (8.61 mg).

Mining anion-aromatic interactions in the Protein Data Bank.

Mutual positioning and non-covalent interactions in anion-aromatic motifs are crucial for functional performance of biological systems. In this context, regular, comprehensive Protein Data Bank (PDB) screening that involves various scientific points of view and individual critical analysis is of utmost importance. Analysis of anions in spheres with radii of 5 Å around all 5- and 6-membered aromatic rings allowed us to distinguish 555 259 unique anion-aromatic motifs, including 92 660 structures out of the 171 588 structural files in the PDB. The use of a scarcely exploited (x, h) coordinate system led to (i) identification of three separate areas of motif accumulation: A - over the ring, B - over the ring-substituent bonds, and C - roughly in the plane of the aromatic ring, and (ii) unprecedented simultaneous comparative description of various anion-aromatic motifs located in these areas. Of the various residues considered, i.e. aminoacids, nucleotides, and ligands, the latter two exhibited a considerable tendency to locate in region Avia archetypal anion-π contacts. The applied model not only enabled statistical quantitative analysis of space around the ring, but also enabled discussion of local intermolecular arrangements, as well as detailed sequence and secondary structure analysis, e.g. anion-π interactions in the GNRA tetraloop in RNA and protein helical structures. As a purely practical issue of this work, the new code source for the PDB research was produced, tested and made freely available at https://github.com/chemiczny/PDB_supramolecular_search.

Model Setup and Procedures for Prediction of Enzyme Reaction Kinetics with QM-Only and QM:MM Approaches.

The enzyme-catalyzed reactions are traditionally studied with experimental kinetic assays. The modern theoretical modeling techniques provide a complementary way to investigate these catalytic reactions. Experimental assay frequently does not allow an unequivocal answer to the factors controlling the reaction mechanism. On the other hand, the theoretical experiments provide a precise understanding of the molecular-level steps involved in catalytic reactions. However, modeling requires at least structural data on the enzyme and reactant, and the complexity of the enzyme systems can still be a challenge.In this chapter, we are going to describe how to apply theoretical modeling methods, such as MD simulation, QM-only cluster models of enzyme active site, or QM:MM multiscale modeling to study enzyme kinetics and even to predict kinetic isotope effect (KIE). We present a full protocol that starts from the PDB structure of the enzyme, through MD simulation of enzyme: substrate complex and statistical analysis of MD trajectory, selection of a model of the active site, and study of reaction pathways. We show how theoretical predictions basing on QM-only cluster models, QM:MM model, or multiple QM:MM models derived from QM:MM:MD simulations can be correlated with experimental kinetic results. Finally, we show how one can calculate intrinsic KIE associated with an individual molecular step.

Universal capability of 3-ketosteroid Δ1-dehydrogenases to catalyze Δ1-dehydrogenation of C17-substituted steroids.

BACKGROUND: 3-Ketosteroid Δ1-dehydrogenases (KSTDs) are the enzymes involved in microbial cholesterol degradation and modification of steroids. They catalyze dehydrogenation between C1 and C2 atoms in ring A of the polycyclic structure of 3-ketosteroids. KSTDs substrate spectrum is broad, even though most of them prefer steroids with small substituents at the C17 atom. The investigation of the KSTD's substrate specificity is hindered by the poor solubility of the hydrophobic steroids in aqueous solutions. In this paper, we used 2-hydroxpropyl-ß-cyclodextrin (HBC) as a solubilizing agent in a study of the KSTDs steady-state kinetics and demonstrated that substrate bioavailability has a pivotal impact on enzyme specificity. RESULTS: Molecular dynamics simulations on KSTD1 from Rhodococcus erythropolis indicated no difference in ΔGbind between the native substrate, androst-4-en-3,17-dione (AD; - 8.02 kcal/mol), and more complex steroids such as cholest-4-en-3-one (- 8.40 kcal/mol) or diosgenone (- 6.17 kcal/mol). No structural obstacle for binding of the extended substrates was also observed. Following this observation, our kinetic studies conducted in the presence of HBC confirmed KSTD1 activity towards both types of steroids. We have compared the substrate specificity of KSTD1 to the other enzyme known for its activity with cholest-4-en-3-one, KSTD from Sterolibacterium denitrificans (AcmB). The addition of solubilizing agent caused AcmB to exhibit a higher affinity to cholest-4-en-3-one (Ping-Pong bi bi KmA = 23.7 µM) than to AD (KmA = 529.2 µM), a supposedly native substrate of the enzyme. Moreover, we have isolated AcmB isoenzyme (AcmB2) and showed that conversion of AD and cholest-4-en-3-one proceeds at a similar rate. We demonstrated also that the apparent specificity constant of AcmB for cholest-4-en-3-one (kcat/KmA = 9.25∙106 M-1 s-1) is almost 20 times higher than measured for KSTD1 (kcat/KmA = 4.71∙105 M-1 s-1). CONCLUSIONS: We confirmed the existence of AcmB preference for a substrate with an undegraded isooctyl chain. However, we showed that KSTD1 which was reported to be inactive with such substrates can catalyze the reaction if the solubility problem is addressed.

Atrial contractility and fibrotic biomarkers are associated with atrial fibrillation after elective coronary artery bypass grafting.

OBJECTIVE: New-onset postoperative atrial fibrillation is common after cardiac surgery. Less has been reported about the relationship among fibrosis, inflammation, calcium-induced left atrial and right atrial contractile forces, and postoperative atrial fibrillation. We sought to identify predictors of postoperative atrial fibrillation. METHODS: From August 2016 to February 2018, we evaluated 229 patients who had preoperative sinus rhythm before elective primary coronary artery bypass grafting. Of 229 patients, 191 maintained sinus rhythm postoperatively, whereas 38 patients developed atrial fibrillation. Preoperative tissue inhibitor of metalloproteinase-1, pentraxin-3, matrix metallopeptidase-9, galectin-3, high-sensitivity C-reactive protein, growth differentiation factor 15, and transforming growth factor-ß were measured. Clinical and echocardiographic findings (tricuspid annular plane systolic excursion for right heart function) and calcium-induced force measurements from left atrial and right atrial-derived skinned myocardial fibers were recorded. RESULTS: Patients with atrial fibrillation were older (P = .001), had enlarged left atrial (P = .0001) and right atrial areas (P = .0001), and had decreased tricuspid annular plane systolic excursion (P = .001). Levels of matrix metallopeptidase-9 and pentraxin-3 were decreased (P < .05), whereas growth differentiation factor 15 was increased (P = .001). We detected lower left atrial force values at calcium-induced force measurements 5.5 (P < .05), 5.4 (P < .01), and 5.3 to 4.52 (P = .0001) and right atrial force values at calcium-induced force measurements 5.0 to 4.52 (P < .05) in patients with postoperative atrial fibrillation. Multivariable analysis showed that advanced age (P = .033), decreased left atrial force value at calcium-induced force measurement of 5.5 (P = .033), enlarged left atrial (P = .013) and right atrial (P = .081) areas, and reduced tricuspid annular plane systolic excursion (P = .010) independently predicted postoperative atrial fibrillation. CONCLUSIONS: Advanced age, decreased left atrial force value at calcium-induced force measurement of 5.5, enlarged left atrial and right atrial areas, and reduced tricuspid annular plane systolic excursion were identified as independent predictors for postoperative atrial fibrillation.

Ankle-brachial pressure index estimated by laser Doppler in patients suffering from peripheral arterial obstructive disease.

Ankle-brachial index (ABI) measurements are widely used for evaluating the functional state of circulation in the lower limbs. However, there is some evidence that the value of ABI does not accurately reflect the degree of walking impairment in symptomatic patients with peripheral arterial obstructive disease (PAOD). We investigated the diagnostic value of ABI estimated by means of laser Doppler flowmetry (IT) for evaluating limb ischemia. We wanted to know whether laser Doppler could be more sensitive than the Doppler method in predicting walking capacity in patients with stable intermittent claudication. We analyzed a group of 30 patients with intermittent claudication (Fontain II, II/III) who were admitted for reconstructive treatment. There were 21 men and 9 women, aged 46-74 (mean 61) years. All patients underwent the treadmill test, and pain-free walking distances were measured. In each patient, we measured ABI using the two different methods: Doppler ultrasound device (ABI-Doppler) and laser Doppler (ABI-laser Doppler). The claudication distances were 25-200 m (mean 73 +/- 50.2 m). ABI-Doppler was 0.2-0.7 (0.582 +/- 0.195). ABI-laser Doppler measurements were 0.581 (+/-0.218). A correlation was found between ABI-Doppler and claudication distance (r = 0.46, P = 0.009). Also, ABI-laser Doppler values significantly correlated with claudication distances (r = 0.536, P = 0.002). The ABI evaluated by laser Doppler correlated well with claudication distances in patients with PAOD. Comparison of Doppler and laser Doppler measurements used for determining ABI showed that both methods have similar predictive power for walking capacity; however, higher correlation was observed between claudication distances and ABI measured by laser Doppler flowmetry. ABI-laser Doppler measurements are easier, are quicker, and seem to be better suited for noncompliant patients. Further investigation should be undertaken to determine whether laser Doppler is superior to the Doppler method in advanced occlusive arterial disease.