Engineering of Macromolecules: Basic Outline
During the last quarter of the 20th century, following two major developments made it possible to change the structure of macro­molecules in a pre-determined way leading to their desired functional role.
First is the possibility of site-directed mutagenesis permitting changes in genes at known sites leading to modification of function in a predetermined way; and second is the availability of computational and graphical tools which allowed, on the screen, the display and exploration of the three dimensional structures of macromolecules.

These two developments allow us to decide about the three dimensional structure of protein/drug needed for a desired purpose, before using recombinant DNA technology (for proteins), or organic synthesis (for drugs) for the production of the desired macromolecule.
The different steps generally involved in protein engineering are shown in diagram, and include the following: (i) The protein sample is prepared from an organism and it is characterized with a ligand (e.g. enzyme-substrate, receptor-hormone or antibody-antigen interaction). (ii) The three dimensional (3-D) structure is studied through NMR (nuclear magnetic resonance) and X-ray diffraction patterns of crystals. (iii) 3-D structure is displayed with interactive computer graphics and the available information is used to suggest a novel design suiting the needs. (iv) The desired DNA sequence that is expected to give the novel designed protein is then either synthesized or obtained by site directed mutagenesis of an available gene. (v) The novel gene is introduced into a suitable expression system and the gene product is extracted, purified and characterized biochemically. (vi) If biochemical characterization does not satisfy the earlier predicted structure, the cycle may be repeated again, till the desired structure is available.
It should be noted that the above steps of protein engineering share steps used for designing of drugs, insecticides, herbicides, and peptide vaccines that will be partly discussed in the next, although there are other additional approaches that are used for drug discovery.

The only difference is that the drug designing concerns only the ligand, which can be modified more effectively by chemical synthesis, while in protein engineering, generally the recombinant DNA technology is used.
The three dimensional structures for a few proteins that are related to the novel protein of interest will normally be available to a protein engineer, while planning production of a novel protein for the desired needs.
Therefore, as discussed above, a procedure is needed for generating the three dimensional structure of the macromolecule (protein) of interest.
This may be achieved de novo through modelling from homologous or analogous proteins, if they are available.
This is described as knowledge based modelling and designing through the use of computer software including computer graphics, computer simulations and databases (computer software includes the entire set of procedures and programmes to be used on the computer to solve problems along with the operating aids).
The computational aspects of knowledge based approaches in designing of macromolecules including proteins and enzymes are shown in diagram.