The Proteomic Code: a molecular recognition code for proteins

The 25-year-old history of this concept is reviewed from the first independent suggestions by Biro and Mekler, through the works of Blalock, Root-Bernstein, Siemion, Miller and others, followed by the discovery of a Common Periodic Table of Codons and Nucleic Acids in 2003 and culminating in the recent conceptualization of partial complementary coding of interacting amino acids as well as the theory of the nucleic acid-assisted protein folding.A novel cloning method for the design and production of specific, high-affinity-reacting proteins (SHARP) is presented. This method is based on the concept of proteomic codes and is suitable for large-scale, industrial production of specifically interacting peptides.Nucleic acids and proteins are the carriers of most (if not all) biological information. This information is complex, well organized in space and time. These two kinds of macromolecules have polymer structures. Nucleic acids are built from four nucleotides and proteins are built from 20 amino acids (as basic units). Both nucleic acids and proteins can interact with each other and in many cases these interactions are extremely strong (Kd ~ 10-9-10-12 M) and extremely specific. The nature and origin of this specificity is well understood in the case of nucleic acid-nucleic acid (NA-NA) interactions (DNA-DNA, DNA-RNA, RNA-RNA), as is the complementarity of the Watson-Crick (W-C) base pairs. The specificity of NA-NA interactions is undoubtedly determined at the basic unit level where the individual bases have a prominent role.Our most established view on the specificity of protein-protein (P-P) interactions is completely different [1]. In this case the amino acids in a particular protein together establish a large 3D structure. This structure has protrusions and cavities, charged and uncharged areas, hydrophobic and hydrophilic patches on its surface, which altogether form a complex 3D pattern of spatial and physico-chemical properties. Two proteins will specifically i