Polypeptides absolute configuration

Polypeptides. These are a string of a-amino acids usually with the natural 5(L) [L-cysteine is an exception and has the R absolute configuration] or sometimes "unnatural" 7f(D) configuration at the a-carbon atom. They generally have less than -100 amino acid residues. They can be naturally occurring or, because of their small size, can be synthesised chemically from the desired amino acids. Their properties can be very similar to those of small proteins. Many are commercially available, can be custom made commercially or locally with a peptide synthesiser. They are purified by HPLC and can be used without further purification. Their purity can be checked as described under proteins. 

Absolute Configuration of Natural Amino Acids and Polypeptides... 

Absolutely no excimer has been detected when 1-naphthyl groups are linked to a helical polypeptide in a similar manner [49, 50]. The stabilization energy of naphthyl excimers may be too small to hold excimer configurations. 

An interesting aspect in the structures of iron-sulfur proteins are some amino acid sequences which are approximately the same in a number of proteins. Thus, as observed in Fig. 5.6, there are also some sequences, e.g. Cys-X-X-Cys or Cys-X-X-Cys-X-X-Cys, in which the relative positions of the cysteine residues which are known to directly bind the Fe-S are absolutely conserved in proteins from different species. Since the coordinative environment of iron sulfur cluster in different species are practically the same, the specificity of sites in a given protein are fundamentally determined by the configuration of the rest of the polypeptidic chain. This feature, besides the wide distribution of ferredoxins in numerous different species, permits us to establish philogenetic relationships as that illustrated in Fig. 5.7. 

The term protein is employed for compounds exhibiting molar mass > 10 g mol, and the term polypeptide is reserved for the shorter chains. The C-marked carbon atom is unsymmetrical (except for A = H) and always has absolute [S] configuration (indicated as L by biochemists). 

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