Disclosed is a method for identification of key amino acids in plant proteins critical in generating allergenic activity through mapping the epitope(s) harboring human IgE binding activity. The identified epitope (s) are then modified by amino acid substitution preferably by alanine substitution, for reduced or negative IgE-binding activity. A plant gene expression system comprising a DNA construct placed operably under the control of a promoter sequence that confers seed-specific expression is also disclosed for the expression of the modified proteins. The Brazil nut 2S sulfur-rich protein was exemplified. The method disclosed herein is particularly useful for the production of dietary proteins with improved nutritional quality and reduced or negative allergenicity for human and animal consumption through genetic engineering.