The Journal of Physical Chemistry B · 2014 · 32 citations · 45 references
Life SciencesBiochemistryMolecular BiologyEnzymologyProtein BiochemistryStructural BiologyActive Site ArchitectureCatalytic MechanismsEnzyme Active SitesProtein BindingProtein DesignProtein StructureActive Site ChemistryActive Site DesignActive Site MechanismsActive Site ResiduesComputational Active Site DesignEnzyme Active-site GeometryEsterase ActivityEsterase-mediated Activation
Human serum albumin (HSA) is a critical transport plasma protein accounting for ∼60% of the total protein content in blood. Remarkably, this protein is also found to display esterase activity. In this study, we apply theoretical studies to elucidate the origin of the esterase-like activity arising from the Sudlow site I. Using MD and QM/MM calculations, we investigate which active site residues are involved in the reaction, and the precise mechanistic sequence of events. Our results suggest Lys199, His242, and Arg257 help give rise to the esterase activity and that the most catalytically efficient active site configuration requires that both Lys199 and Aspirin are in their neutral forms. The abundance of HSA in the body suggests the protein might be a suitable target for the computational guided design of acetyl based pro-drugs of acidic molecules that often displayed limited oral exposure due to their unmasked ionizable substituent.
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Molecular dynamics with coupling to an external bath
Herman J. C. Berendsen, Johan P. M. Postma, Wilfred F. van Gunsteren et al. · The Journal of Chemical Physics · 1984 · 31K citations · Full text
Natural Sciences, Chemistry, Physics +17
Yan Zhao, Donald G. Truhlar · Theoretical Chemistry Accounts · 2007 · 30K citations · Full text
Natural Sciences, Chemistry, Physics +17
LINCS: A linear constraint solver for molecular simulations
Berk Hess, Henk Bekker, Herman J. C. Berendsen et al. · Journal of Computational Chemistry · 1997 · 17.1K citations
Natural Sciences, Chemistry, Physics +14