Abstract: Methods are disclosed for preparing biologically active protein conjugates using negatively charged polymers that protect the protein within the conjugate so that it retains a substantial amount of its biological activity following conjugation (e.g., procedure in which a protein is conjugated to a pharmaceutical agent, a solid support, a reporter molecule, a group carrying a reporter molecule, an acylating agent, a chelating agent, a cross-linking agent, a targeting group, and a ligand and binding group). The invention also includes novel protein conjugates prepared by those methods.