Folding of the Apolipoprotein A1 Driven by the Salt Concentration as a Possible Mechanism to Improve Cholesterol Trapping
The folding of the cholesterol—trapping apolipoprotein A1 in aqueous solution at increasing ionic strength—is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the conformation of the protein, such as the radius of gyration, the radial distribution function and the end-to-end distance. Additionally we report information using tools specifically tailored for the characterization of proteins, such as the mean smallest distance matrix and the Ramachandran plot. We find that two qualitatively different configurations of this protein are preferred: one where the protein is extended, and one where it forms loops or closed structures. It is argued that the latter promote the association of the protein with cholesterol and other fatty acids.
KeywordsRadial Distribution Function Ramachandran Plot Open Conformation Closed Conformation Beta Sheet
This project was financed by CONACYT, grant 132056. We would like to acknowledge many educational conversations on this topic with A. López–Vallejo López. The authors thank also J. Limón (IFUASLP) for technical support with GPU installation. MABA and AGG thank the UASLP for its hospitality.
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