Identification and structural characterization of proteins and peptides


  1. You are working in modern laboratory of structural biology having the state-of-the-art equipment for identification and characterization of proteins and peptides on molecular and chemical bond level. Your project partner has purified a small protein and according to chromatographic and SDS-PAGE analyses, the molecular mass of the unknown protein is about 4 kDa. You have got 1 ml of that sample in buffered water solution, where the protein concentration is about 1 mM. How would you identify and analyse the structure of the unknown small protein? (8 points)
    • Why purity of protein is important prior structural characterization? (2 points)
    • How could you check the protein concentration? (2 points)
  2. Your project partner has also a short pentapeptide, LTFKD, as marked with one letter symbol. Before NMR analyses
    • Draw the structure of the peptide (2 point)
    • Explain the properties of various amino acid side-chains (2 points)
    • Explain the polymerization of individual amino acids (2 points)
  3. In the initial stage of NMR studies of each resonance must be associated with a specific nucleus present in the molecule. This process is called assignment. The strategies used for the assignment procedure depend on whether homonuclear 2D spectra (unlabelled proteins), 15N heteronuclear spectra (15N labelled proteins), or triple resonance spectra (15N/13C doubly labelled proteins) are available. LTFKD peptide is unlabelled. Thus, explain the basic principal for the process of homonuclear sequential assignment of the pentapeptide. (6 points)