Multiscale modeling of protein transport in silicon membrane nanochannels. Part 1. Derivation of molecular parameters from computer simulations

Wed, 06/29/2022 - 05:51 By Anonymous

Titolo: Multiscale modeling of protein transport in silicon membrane nanochannels. Part 1. Derivation of molecular parameters from computer simulations

Mallard Blue binding to heparin, its SDS micelle-driven de-complexation, and interaction with human serum albumin: A combined experimental/modeling investigation

Wed, 06/29/2022 - 05:51 By Anonymous

Titolo: Mallard Blue binding to heparin, its SDS micelle-driven de-complexation, and interaction with human serum albumin: A combined experimental/modeling investigation
Abstract: Heparin is a sulfated glycan widely used as anticoagulant in medicine. Mallard Blue (MalB), a small cationic dye developed in our laboratories, is able to detect heparin in serum and plasma in a doseresponse manner, with performance superior to its direct competitors. However, many aspects of MalB/heparin binding still remain to be explored which, once solved, may foster the clinical use of MalB.
Among these, the characterization of the energetics that drives the MalB/heparin binding process, the competition for MalB binding by other polyanions (e.g., negatively-charged surfactant micelles), and the interaction of MalB with serum proteins are of particular interest. This work fills this gap by means of a combination of experimental investigations (UV-visible spectroscopy and isothermal titration calorimetry), and computational approaches based on molecular dynamics (MD) simulation techniques. In
combination, the results obtained show that MalB efficiently binds to both heparin and SDS, with the binding being enthalpic in nature; yet, SDS is able to extract MalB from its complex with heparin when the surfactant is in its self-assembled form, the driving force underlying SDS-induced MalB/heparin decomplexation being entropic in nature as the two enthalpies of binding effectively cancel each other out.
Once bound to SDS, the dye remains electrostatically bound to the micellar surface and does not penetrate the micelle palisade layer, as verified by steered molecular dynamics/umbrella sampling simulations. Finally, the affinity of MalB for human serum albumin (HSA), the most abundant plasma protein, is found to be lower than that for heparin, confirming the ability of the dye to work in complex physiological environments.

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