Structural Analysis of a Dipeptide

Chapter 2, Section A Chapter 3, Sections A, B, G Chapter 4, Section B. 

The primary structure of a peptide or protein is defined by the sequence of amino acids. In this experiment the procedures that are in common use to determine protein primary structure are applied to an unknown dipeptide. Amino acid composition of the peptide will be determined by acid hydrolysis followed by HPLC, CE, or paper chromatography. The identity of the NH2-terminal amino acid will be achieved by the dansyl method followed by thin-layer chromatography. 

Structural elucidation of natural macromolecules is an important step in understanding the relationships between the chemical properties of a biomolecule and its biological function. The techniques used in organic structure determination (NMR, IR, UV, and MS) are quite useful when applied to biomolecules, but the unique nature of natural molecules also requires the application of specialized chemical techniques. Proteins, polysaccharides, and nucleic acids are polymeric materials, each composed of hundreds or sometimes thousands of monomeric units (amino acids, monosaccharides, and nucleotides, respectively). But there is only a limited number of these types of units from which the biomolecules are synthesized. For example, only 20 different amino acids are found in proteins but these different amino acids may appear several times in the same protein molecule. Therefore, the structure of 

The general structure of the zwitterionic form of an L-amino acid. R represents the side chain. COO H3N - C - H R 

Abbreviations of the 20 Common Amino Acids Found in Proteins 

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Mattos, C., Giammona, D. A., Petsko, G. A. and Ringe, D. (1995) Structural analysis of the active site of porcine pancreatic elastase based on the X-ray crystal structures of complexes with trifluoroacetyl-dipeptide-anilide inhibitors. Biochemistry, 34, 3193-3203. 

The combined use of the simulated and experimental Vhh couplings and H ROESY spectra has been made by Peter et who performed a conformational analysis of the dipeptide Val-Phe isomers. Possible problems and pitfalls, when deriving structural properties of such small and extremely flexible molecules from the NMR data only, have been discussed by them. 

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