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Dynamics studies of a Malachite green-RNA complex revealing the origin of the red shift and energetic contributions of stacking interactions

Article Abstract:

In this study molecular dynamics simulation with explicit solvent to gain insight in to the nature of the remaining interactions on the red shift in the maximum absorption frequency and the binding affinity of the malachite green molecule is discussed. It is concluded that the charges of the RNA backbone and backbone and surrounding counterions play an influential role in redistributing the electronic structure of the MAG molecule while dispersive interactions with the RNA bases determine the binding strength, which correlates with ligand structural flatness, causing the observed red-shift in the MAG's visible spectrum.

RNA, Ligands, Ligands (Chemistry), Atomic properties

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Probing single-molecule T4 lysozyme conformational dynamics by intramolecular fluorescence energy transfer

Article Abstract:

The use of single-molecule spectroscopy to study enzyme conformational motions of T4 lysozyme under hydrolysis reaction of the polysaccharide walls of E. coli B cells is demonstrated. It is found that the time required for the enzyme to locate a binding site dominates the inhomogeneity in the overall reaction rate and that the subsequent steps have homogeneous rates among the individual enzymes examined.

All Other Basic Organic Chemical Manufacturing, Industrial organic chemicals, not elsewhere classified, Polysaccharides, Methods, Escherichia coli, Spectrum analysis, Spectroscopy, Hydrolysis, Lysozyme

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Single-molecule nanosecond anisotropy dynamics of tethered protein motions

Article Abstract:

The study was conducted on the nanosecond anisotropy dynamics of tethered protein motions. The study reveals the single-molecule rotational motion over wide time scale from subnanoseconds to seconds.

Analysis, Proteins, Anisotropy

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