custom made matlab software  (MathWorks Inc)

Journal: Nature Communications

Article Title: Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome

doi: 10.1038/s41467-023-40416-5

Figure Lengend Snippet: a Simplified representation of the 70S ribosome with the AMK binding site indicated with the blue star. b The unbiased ( F o – F c ) difference electron density map of AMK bound near the decoding center is contoured at 2.3σ. c AMK binds within helix h44 of the decoding center where the AHB moiety forms three unique interactions. d Time courses of f[ 3 H]Met-Phe-Phe tripeptide formation with EF-Tu ternary complex (TC) (5 μM) and EF-G (5 µM) in the absence (black) and presence of 20 μM AMK (red). Solid lines represent the double exponential fit of the data with SEM from n = 3 independent experiments. e Time evolution of fluorescence traces obtained for the EF-G (5 μM) catalyzed movement of pyrene-labeled mRNA on 70S ribosomes (0.5 μM) in the presence of various concentrations (0-5 µM) of AMK. The inhibition of mRNA movement by AMK was estimated from amplitudes of the slow phase of fluorescence traces relative to the total transition (normalized to 1) indicative of inhibited fraction of the ribosomes. f The fraction of AMK-inhibited pre-TC plotted against AMK concentration. Data were fitted with hyperbolic function (solid line) and half-inhibitory concentration ( K I ) of AMK on the inhibition of translocation was estimated from mid-point of transition. Experiments were conducted in triplicates and error bars indicate the SEM of data.

Article Snippet: Experiments were conducted in triplicates, data were fitted in Origin(Pro), Version 2016 (OriginLab Corp.), and error bars indicate the SEM of data.

Techniques: Binding Assay, Fluorescence, Labeling, Inhibition, Concentration Assay, Translocation Assay

Journal: Nature Communications

Article Title: Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome

doi: 10.1038/s41467-023-40416-5

Figure Lengend Snippet: a Time courses of BOP-Met-Phe-Leu release from the P site of the ribosomes in pre-TC (0.1 μM) upon mixing with RF2 (1 μM) in the presence of various concentrations of AMK (0-1 μM). The near monophasic curves are fitted with double exponential function (solid lines) and the rates and amplitudes of the predominant fast phase (> 99%) were determined. The fraction inhibited was estimated from the fractional loss in fluorescence amplitude for a given AMK concentration considering the total amplitude of fluorescence transition (without AMK) as 1. b Fraction inhibition of RF2-mediated peptide release as the function of increasing concentrations of AMK. Solid line is the hyperbolic fit of data from which half-maximal inhibitory concentration ( K I ) of AMK for peptide release was estimated. c Time tra c es for Rayleigh light scattering upon splitting of post-TC ribosomes (0.5 μM) into subunits by the concerted action of RRF (20 μM) and EF-G (10 μM) in the presence of various concentrations of AMK (0–20 μM). The scattering traces were fitted with double exponential function and the rates and amplitudes of both the fast and slow phases were determined. d Fraction inhibition of RRF and EF-G-mediated ribosome splitting was estimated from the fractional loss of the amplitude of the fast phase considering amplitude of the entire transition without AMK as 1. The solid line represents the hyperbolic fit of the fraction inhibition plotted against AMK concentration from which the half-maximal concentration ( K I ) of AMK to inhibit ribosome recycling was estimated. Experiments were conducted in triplicates, data were fitted in Origin(Pro), Version 2016 (OriginLab Corp.), and error bars indicate the SEM of data.

Article Snippet: Experiments were conducted in triplicates, data were fitted in Origin(Pro), Version 2016 (OriginLab Corp.), and error bars indicate the SEM of data.

Techniques: Fluorescence, Concentration Assay, Inhibition