NMR studies of the non-haem Fe(II) and 2-oxoglutarate-dependent oxygenases

Performance, kinetics, and mechanism of 1,2,3-trimethylbenzene biodegradation by a newly isolated marine microalga

Recently, marine pollution by the accidental spills of C9 aromatics has raised public concerns, especially for 1,2,3-trimethylbenzene (1,2,3-TMB) because it is high-toxic and refractory. However, insufficient understanding of molecular mechanism underlying the biodegradation of 1,2,3-TMB hindered research on its bioremediation. In addition, microalgae-mediated bioremediation is popular due to its eco-friendliness and carbon sequestration. In this study, a marine diatom with degradation capability of 1,2,3-TMB, Chaetoceros sp. QG-1, was isolated from coastal area of Quangang, China. According to kinetics, the degradation efficiency of 1,2,3-TMB was the highest at 5 mg/L (K = 0.237/d) compared with other concentrations. Furthermore, the degradation mechanism of 1,2,3-TMB by Chaetoceros sp. QG-1 was revealed through analysis of degradation products and omics. 1,2,3-TMB was converted into 2,3-dimethylbenzoic acid and 2-hydroxypropionic acid by enzymes including non-heme Fe (II) and 2-oxoglutarate-dependent (2OG Fe (II)) oxygenase, UDP-glucose-6-dehydrogenase, aldehyde dehydrogenase, and other short-chain dehydrogenases, wherein, 2OG Fe (II) oxygenase was identified as the key enzyme to oxidize 1,2,3-TMB. This study provided species and theoretical supports for the bioremediation of marine environments contaminated with 1,2,3-TMB.

Protein Flexibility of the α-Ketoglutarate-Dependent Oxygenase Factor-Inhibiting HIF-1: Implications for Substrate Binding, Catalysis, and Regulation

Protein dynamics are crucial for the mechanistically ordered enzymes to bind to their substrate in the correct sequence and perform catalysis. Factor-inhibiting HIF-1 (FIH) is a nonheme Fe(II) α-ketoglutarate-dependent oxygenase that is a key hypoxia (low p_O2) sensor in humans. As these hypoxia-sensing enzymes follow a multistep chemical mechanism consuming α-ketoglutarate, a protein substrate that is hydroxylated, and O₂, understanding protein flexibility and the order of substrate binding may aid in the development of strategies for selective targeting. The primary substrate of FIH is the C-terminal transactivation domain (CTAD) of hypoxia-inducible factor 1α (HIF) that is hydroxylated on the side chain of Asn803. We assessed changes in protein flexibility connected to metal and αKG binding, finding that (M+αKG) binding significantly stabilized the cupin barrel core of FIH as evidenced by enhanced thermal stability and decreased protein dynamics as assessed by global amide hydrogen/deuterium exchange mass spectrometry and limited proteolysis. Confirming predictions of the consensus mechanism, (M+αKG) increased the affinity of FIH for CTAD as measured by titrations monitoring intrinsic tryptophan fluorescence. The decreased protein dynamics caused by (M+αKG) enforces a sequentially ordered substrate binding sequence in which αKG binds before CTAD, suggesting that selective inhibition may require inhibitors that target the binding sites of both αKG and the prime substrate. A consequence of the correlation between dynamics and αKG binding is that all relevant ligands must be included in binding-based inhibitor screens, as shown by testing permutations of M, αKG, and inhibitor.

2-Oxoglutarate regulates binding of hydroxylated hypoxia-inducible factor to prolyl hydroxylase domain 2

The binding of prolyl-hydroxylated HIF-α to PHD2 is hindered by prior 2OG binding; likely, leading to the inhibition of HIF-α degradation under limiting 2OG conditions.

Prolyl hydroxylation of hypoxia inducible factor (HIF)-α, as catalysed by the Fe(ii)/2-oxoglutarate (2OG)-dependent prolyl hydroxylase domain (PHD) enzymes, has a hypoxia sensing role in animals. We report that binding of prolyl-hydroxylated HIF-α to PHD2 is ∼50 fold hindered by prior 2OG binding; thus, when 2OG is limiting, HIF-α degradation might be inhibited by PHD binding.

Development of NMR and thermal shift assays for the evaluation of Mycobacterium tuberculosis isocitrate lyase inhibitors

The enzymes isocitrate lyase (ICL) isoforms 1 and 2 are essential for Mycobacterium tuberculosis survival within macrophages during latent tuberculosis (TB). As such, ICLs are attractive therapeutic targets for the treatment of tuberculosis. However, there are few biophysical assays that are available for accurate kinetic and inhibition studies of ICL in vitro. Herein we report the development of a combined NMR spectroscopy and thermal shift assay to study ICL inhibitors for both screening and inhibition constant (IC50) measurement. Operating this new assay in tandem with virtual high-throughput screening has led to the discovery of several new ICL1 inhibitors.