PLoS ONE · 2015 · 17 citations · 47 references
Life SciencesBiochemistryPhysiologyGlycobiologyStructural BioinformaticsStructural BiologyCalcium SignalingCalcium-binding ProteinsGlycan-protein InteractionsProtein GlycoengineeringProtein GlycosylationProtein StructureCalcium Binding DomainsCalcium-binding Site StructureCalcium-dependent Conformational ChangeComputational Biology ModelsGlycosylation MechanismsGlycosylation SitesPhospholipase A2 PathwayProtein Dynamics Analysis
The major cat allergen, Fel d 1, is a structurally complex protein with two N-glycosylation sites that may be filled by different glycoforms. In addition, the protein contains three putative Ca2+ binding sites. Since the impact of these Fel d 1 structure modifications on the protein dynamics, physiology and pathology are not well established, the present work employed computational biology techniques to tackle these issues. While conformational effects brought upon by glycosylation were identified, potentially involved in cavity volume regulation, our results indicate that only the central Ca2+ ion remains coordinated to Fel d 1 in biological solutions, impairing its proposed role in modulating phospholipase A2 activity. As these results increase our understanding of Fel d 1 structural biology, they may offer new support for understanding its physiological role and impact into cat-promoted allergy.
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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
Canonical sampling through velocity rescaling
Giovanni Bussi, Davide Donadio, Michele Parrinello · The Journal of Chemical Physics · 2007 · 18.4K citations · Full text
Natural Sciences, Chemistry, Physics +17