Protein engineering relationships

Much of protein engineering concerns attempts to explore the relationship between protein stmcture and function. Proteins are polymers of amino acids (qv), which have general stmcture +H3N—CHR—COO , where R, the amino acid side chain, determines the unique identity and hence the stmcture and reactivity of the amino acid (Fig. 1, Table 1). Formation of a polypeptide or protein from the constituent amino acids involves the condensation of the amino-nitrogen of one residue to the carboxylate-carbon of another residue to form an amide, also called peptide, bond and water. The linear order in which amino acids are linked in the protein is called the primary stmcture of the protein or, more commonly, the amino acid sequence. Only 20 amino acid stmctures are used commonly in the cellular biosynthesis of proteins (qv). 

Chimeragenesis and SDM are powerful techniques that can be used to investigate the complex relationships between protein structure and function. The methods detailed here are relatively simple to perform and can be carried out in a short period of time. They are applicable to any protein type for which the cDNA is available and can be modified for many different purposes in protein engineering. 

Ward WHJ, Timms D, Fersht AR. 1990. Protein engineering and the study of structure-function relationships. Trends Pharmacol Sci 11 280... 

The important contribution of protein engineering to the study of protein stability is that defined structural changes can be made in a protein and the change in stability measured. In this way, the relationship between structure and stability can be established experimentally. Fortunately, it is easier to measure changes in stability accurately than it is absolute values of stability. 

Linear free-energy relationships 58, 62-65,86,87,599 protein engineering of enzymes and 442-444... 

Biological information is stored in the nucleotide base structure of DNA. By manipulating the structure of DNA it is possible to improve and understand the structure and functional relationships of catalysts (termed protein engineering). Considerable improvements have been made to products derived from enzyme systems, both in the quality and amount of metabolites, enzymes and proteins produced by organisms (often termed genetic engineering). 

With the considerable evolution achieved in recent years in the elucidation of structure-function relationship of proteins, as well as in the areas of protein engineering and bioinformatics, many new developments are expected in the field of new-generation biopharmaceuticals. These will have significant advantages for patients, including lower immunogenicity, lower frequency of injections, and enhanced stability in serum. 

A.R. Fersht, Linear Free Energy Relationships are Valid, Protein Engineering, 1987,1, 442. 

Relevant applications from our laboratory, regarding protein engineering with noncoded amino acids as a tool in the study of protein folding and function, will be presented. In particular, we will discuss the use of noncoded amino acids in structure-activity relationship (SAR) studies of hirudin binding to thrombin, as well as the incorporation of noncoded analogs of tryptophan and tyrosine (i.e., 7-azatryptophan and 3-nitrotyrosine) as spectroscopic probes for studying the hirudin-thrombin interaction. 

One of the most pretentious approaches for future biochemical engineering would consist of tailoring proteins to desired fvmctions by protein engineering. Pioneering work has for example been done in the area of biocatalysis, but it is commonplace that rational exploitation of protein engineering will require an enormous amount of additional knowledge on the primary - tertiary structure - function relationships. These again emphasize the importance of thermodynamics in the area of protein stability. 

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