The present invention relates to protein conjugates comprising an aprotinin-derived polypeptide, which facilitates transport of the conjugate across the blood-brain barrier, and an antibody moiety that selectively binds a target within the CNS. The protein conjugates are further defined by the inclusion of a linker; by the number of polypeptides conjugated to each antibody moiety; by the positions at which the antibody moiety and the polypeptides are conjugated; and by the larger configuration of the conjugate (in which every polypeptide is linked only to the antibody moiety). Modified aprotinin-derived polypeptides, linker-bound antibody moieties, pharmaceutical compositions, kits, and methods of making and using the protein conjugates are also features of the invention.