Kinetics and Regulation of Mammalian NADH-Ubiquinone Oxidoreductase (Complex I)

NADH-ubiquinone oxidoreductase (Complex I, European Commission No. 1.6.5.3) is one of the respiratory complexes that generate the proton-motive force required for the synthesis of ATP in mitochondria. The catalytic mechanism of Complex I has not been well understood, due to the complicated structure of this enzyme. Here, we develop a kinetic model for Complex I that accounts for electron transfer from NADH to ubiquinone through protein-bound prosthetic groups, which is coupled to the translocation of protons across the inner mitochondrial membrane. The model is derived based on the tri-bi enzyme mechanism combined with a simple model of the conformational changes associated with proton transport. To study the catalytic mechanism, parameter values are estimated by analyzing kinetic data. The model is further validated by independent data sets from additional experiments, effectively explaining the effect of pH on enzyme activity. Results imply that matrix pH significantly affects the enzyme turnover processes. The overall kinetic analysis demonstrates a hybrid ping-pong rapid-equilibrium random bi-bi mechanism, consolidating the characteristics from previously reported kinetic mechanisms and data.     

Single-shot phase contrast microscopy using polarisation-resolved differential phase contrast

We present a robust, low-cost single-shot implementation of differential phase microscopy utilising a polarisation-sensitive camera to simultaneously acquire four images from which phase contrast images can be calculated. This polarisation-resolved differential phase contrast (pDPC) microscopy technique can be easily integrated with fluorescence microscopy.     

Draft genome sequence of Lactobacillus plantarum strain DMR17 isolated from homemade cow dahi of Sikkim Himalayan region: an evaluation of lactate fermentation and secondary metabolism

Archives of Microbiology - Lactobacillus plantarum DMR17 was isolated from homemade cow dahi of Sikkim Himalayan region of India. Here, we report the draft genome sequence of this strain. A total...     

Metastable states of HYPK-UBA domain's seeds drive the dynamics of its own aggregation

Protein aggregation is a multi-step process that requires sequential structural transitions of monomers during their incorporation into oligomers. Such process involves the formation of various intermediate stages in protein structures. Seed-nucleation mediated oligomerization is observed in many aggregation-prone proteins. Understanding of the protein seed's structural features and mechanisms of its transition-state formation are important for knowing the details of post-nucleation aggregation process. We have identified the metastable states in the seeds of the Ubiquitin associated (UBA) domain of Huntingtin Interacting Protein K (HYPK). This is studied by monitoring the events of dynamic transitions of metastable seeds to aggregates or monomers through microscopy, biophysical and computational techniques. HYPK-UBA seeds can exist in specific metastable state(s) that show transition from closed to open conformations, thereby reorienting the helix associated hydrophobic patches to cause its self-aggregation. Metastable seeds show inter-seed exchange of monomers through simultaneous dissociation-association phenomenon. Monomer release from metastable seeds can cause the dissolution of the aggregates. Like metastable monomers, metastable seeds also show reduction in their secondary structure by altering the molecular contacts and solvent accessible hydrophobic surfaces. Induction of metastable seeds from the ground-state is a slow thermodynamic process and it results from excitable perturbations. Conclusively, we propose the concept that the thermodynamic induction of metastable states in HYPK-UBA seed potentiates the molecule to switch its conformations that increases the protein's self-aggregation by the mechanism of hydrophobic patch collapse, while also releasing the monomers from oligomeric seeds due to structural instability.     

Pyridine and other coal tar constituents as free radical-generating environmental neurotoxicants

Summary We have tested the hypothesis that chronic exposure to the principal constituents of the aqueous fraction of coal tar extracts can lead to the in vivo formation of substances which may produce neurological damage as the result of free radical generation and lipid peroxidation, these may be involved in the etiology of some neurological disorders. Artificial mixtures of the aqueous fraction of coal tar extracts were given in low concentrations to pigmented mice in their drinking water over a 3-month period. This resulted in significant increases in lipid peroxidation in the striatum, cerebellum and liver of the mice under test, the rank order being striatum > cerebellum > liver. These results are compatible with the possibility that coal tar emissions (as would be recovered or liberated in the burning, refining or beneficiation of coal) constitute a potential source of neurotoxicants with a predilection for damaging the nigrostriatal neuronal pathway. Our observations may thus have identified an important and hitherto unsuspected environmental source of neurotoxic chemicals, a possibility consistent with the proposed involvement of an environmental chemical factor in Parkinson's disease and perhaps in other neurological disorders.