Sequence in polypeptides

P. Edman, Method for determination of the amino acid sequence in polypeptides, Acta Chem. Scand. 4 283-293 (1930)... 

Ziemer et. al. C3623 utilized the KNN-method for the identification of amino acid sequences in polypeptides. A multicategory classification was applied to identify separately the N- and C-terminal amino acids in dipeptides. 40 structural classes were defined representing the 20 commonly occurring amino acids in both the N- and C-terrainal position. 

Genetic code the rules for translation of base sequences in nucleic acids into amino acid sequences in polypeptides (see Protein synthesis). The nucleic acid bases are read off as triplets. There are four bases, and thus 64 (43) different permutations ( words ). As there are only 20 amino acids specified by the code, many triplets can be, and are, redundant. The table lists the amino acids by triplet, or codon. 

Tsujii and Tokiwa [148] concluded from the shift in the melting point of calf thymus DMA that lauroylprolylprolylglycine has a larger influence on the tertiary structure of the DNA than does SDS. The results showed that the amino acid sequence in polypeptide surfactants could play an important role in the interaction with the DNA. They concluded that the primary factor governing the interaction with DNA is the molecular structure of surfactants, rather than their surface activity or ionic nature. 

Over 20 different methods have been proposed for predictions of secondary stmcture they can be categorized in two broad classes. The empirical statistical methods use parameters obtained from analyses of known sequences and tertiary stmctures. All such methods are based on the assumption that the local sequence in a short region of the polypeptide chain determines local stmcture as we have seen, this is not a universally valid assumption. The second group of methods is based on stereochemical criteria, such as compactness of form with a tightly packed hydrophobic core and a polar surface. Three frequently used methods are the empirical approaches of P.Y. Chou and G.D. Fasman and of J. Gamier, D.J. Osguthorpe and B. Robson (the GOR method), and third, the stereochemical method of V.l. him. 

Later we return to an analysis of the 1° structure of proteins and the methodology used in determining the amino acid sequence of polypeptide chains, but let s first consider the extraordinary variety and functional diversity of these most interesting macromolecules. 

Edman degradation A method of amino acid sequencing in proteins in which successive V-terminal amino acids are removed from the polypeptide chain and identified. 

Many naturally occurring hormones and antibiotics are polypeptides and investigation into both the amino acid constituents and their sequence in the polypeptide chain are important areas of research. These investigations may reveal information regarding the biologically active part of the molecule, a fact that may then be used in the commercial production of a synthetic peptide... 

Primary structure (amino acid sequence in a polypeptide chain)... 

The relationship between the base sequence in DNA and the amino acid sequence in the protein is known as the genetic code. With four bases (A, C, G and T) 64 three-base combinations are possible to provide the code for the amino acids (e.g. GTA, CCG). All but three of these are used to code for the polymerisation of the 20 different amino acids (in fact, 21, see Chapter 8) to form a polypeptide chain that can then form a protein. Most amino acids are, therefore, coded for by more than one three-base combination (Appendix 20.2). The link between the three-base... 

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