Proteins design examples

The determination of quantity in complex mixtures is also vital in health care and medicine. We are all familiar with the medical examinations in which a sample of blood or urine is sent to a laboratory for analysis. The procedures used have been developed by chemists, and are performed by trained chemical technicians. The high level of automation achieved by the chemists who designed these analytical procedures has greatly reduced the costs of such analyses. Clinical analysis continues to be driven by a need for better methods to detect and measure important proteins, for example, that while present in tiny amounts are relevant to our health and well-being. 

Based on our current understanding of ribosomal protein synthesis, several strategies have been developed to incorporate amino acids other than the 20 standard proteinogenic amino acids into a peptide using the ribosomal machinery . This allows for the design of peptides with novel properties. On the one hand, such a system can be used to synthesize nonstandard peptides that are important pharmaceuticals. In nature, such peptides are produced by nonribosomal peptide synthetases, which operate in complex pathways. On the other hand, non-natural residues are a useful tool in biochemistry and biophysics to study proteins. For example, incorporation of non-natural residues by the ribosome allows for site-specific labeling of proteins with spin labels for electron paramagnetic resonance spectroscopy, with... 

FIGURE 5-1 Heme. The heme group is present in myoglobin, hemoglobin, and many other proteins, designated heme proteins. Heme consists of a complex organic ring structure, protoporphyrin IX, to which is bound an iron atom in its ferrous (Fe2+) state, (a) Porphyrins, of which protoporphyrin IX is only one example, consist of four pyr-... 

An interesting approach to the treatment of autoimmune diseases is design of peptide mimics that bind into the antigen-binding groove of specific MHC proteins. For example, a protease-resistant pyrrolinone-peptide hybrid has been designed to bind to the rheumatoid-arthritis-associated HLA-DR1.326... 

The lipase-catalysed access to enantiomerically pure compounds remains a versatile method for the separation of enantiomers. The selected examples shown in this survey demonstrate the broad applicability of lipases in terms of substrate structures and enantioselectivity. More recently, modem molecular biology methods such as rational protein design and especially directed evolution103 will further boost the development of tailor-made lipases for future applications in the synthesis of optically pure compounds. It has been already shown that a virtually non-enantioselective lipase (E=l.l in the resolution of 2-methyldecanoate) could be evolved to become an effective biocatalyst (E>50). Furthermore, variants were identified which showed opposite enantiopreference. 

All these approaches have been used to alter protein function, to increase the activity or solubility of proteins, or to adapt enzymes for industrial applications. The goal of artificial man-made proteins with tailor-made activities is, however, still far away and none of the currently existing approaches provides the ultimate solution to the directed evolution of proteins. Nevertheless, numerous examples of successfully altered and improved proteins clearly show the power of directed evolution for protein design. 

---