Hydrothermal processes are provided for preparing hybrid proteins containing altered SS/SH bonds, thereby yielding hybrid proteins having enhanced functional properties. The processes involve steam treatment of an aqueous protein-containing slurry containing at least two different proteins in a jet cooker (16) or similar device in order to heat shock and thereby alter the conformation of some of the proteins, followed by relatively rapid cooling to cause formation of the desired hybrids. Plant and animal proteins may be processed, and the starting slurry can be pH-modified and/or supplemented with one or more additional ingredients (e.g., salts, phosphates, fatty acids, polysaccharides, alcohols, aromatic compounds). The hybrid proteins are useful as food ingredients (e.g., solubility, wetability, dispersibility, foaming, emulsification, viscosity, gelation or thickening agents).