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August 2022

Energy minimization for tertiary structure prediction of homologous proteins: Purothionin and viscotoxin A3 models from crambin

Journal/Book: J. Biomol. Structure Dynamics 2 (4), 831-848. 1985;

Abstract: Homologous proteins may fold into similar three-dimensional structures.Spectroscopic evidence suggests this is true for the cereal grainthionins, the mistletoe toxins, and for crambin, three classes of plantproteins. We have combined primary sequence homology and energyminimization to predict the structures alpha 1-purothionin (from Durumwheat) and viscotoxin A3 (from Viscum album, European mistletoe) fromthe high resolution (0.945 A) crystal structure of crambin (from Crambeabyssinica). Our predictions will be verifiable because we havediffraction-quality crystals of alpha 1-purothionin whose structure weare have predicted. The potential energy minimizations for each proteinwere performed both with and without harmonic constraints to its initialbackbone to explore the existence of local minima for the predictedproteins. Crambin was run as a control to examine the effects of thepotential energy minimization on a protein with a well-known structure.Only alpha 1-purothionin which has one fewer residue in a turn regionshows a significant difference for the two minimization paths. Theresults of these predictions suggest that alpha 1-purothionin andviscotoxin are amphipathic proteins, and this character may relate tothe mechanism of action for these proteins. Both are mildlymembrane-active and their amphipatic character is well suited forinteraction with a lipid bilayer. Author.


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