Tryptophan structure determination

Goda, Y., Suzuki, J., Maitani, T., Yoshihira, K., Takeda, M., and Uchiyama, M., 3-anilino-L-alanine, structural determination of UV-5, a contaminant in EMS-associated L-tryptophan samples, Chem. Pharm. Bull., 40, 2236, 1992. 

Figure 22 Schematic description of a structure determination of a denatured protein by combining pulse labelling with NOE. In the denatured state U, hyperpolarization (CIDNP) is generated in a tryptophan residue by the reaction with a sensitizer PS, transferred to nearby amino acids by cross-relaxation (NOE), and then transferred to the native protein N by fast refolding, where it is observed. Further explanation, see text. Reproduced from Ref. 232 with permission copyright...

Tertiary Structure - Attempts to predict tertiary structure of proteins have not been as successful as those for predicting secondary structure. Folding of sequences depends critically on specific side chain interactions, often far removed from one another in the amino acid sequence. Attempts to predict tertiary structure include efforts to recognize overall patterns in tertiary folding combined with the prediction of secondary structure. These efforts have led to the successful prediction of an ot//f-barrel structure for tryptophan synthase, which is in excellent agreement with the structure determined by x-ray diffraction. 

Structural determination of the ComX pheromone synthesis studies on ComXRO-E-2 pheromone and ComXRO-E-2 peptides containing modified tryptophan residue with a geranyl group 07Y608. 

Both enzymes belong to the family of a,p-hydrolases." The active site of MeHNL is located inside the protein and connected to the outside through a small channel, which is covered by the bulky amino acid tryptophane 128." It was possible to obtain the crystal structure of the complex with the natural substrate acetone cyanohydrin with the mutant SerSOAla of MeHNL. This complex allowed the determination of the mode of substrate binding in the active site." A summary of 3D structures of known HNLs was published recently." " ... 

The crystal structure of the extracellular domain of P0 has also been determined [41]. The arrangement of molecules in the crystal indicates that P0 may exist on the membrane surface as a tetramer (Fig. 7-7) that can link to other tetramers from the opposing membrane to form an adhesive lattice, like a molecular Velcro . The structure also suggests that P0 mediates adhesion through the direct interaction of apically directed tryptophan side chains with the opposing membrane [42], in addition to homo-philic protein-protein interaction. 

The reference 28 authors continue to detail experimental observations that place voltage sensor helices in positions within the membrane. Miller and coworkers conducted site-directed mutagenesis for all residues of helices Sl-S3. ° In these experiments, tryptophan (trp) residues were substituted for each amino acid in turn to determine which residues would be trp-tolerant. These experiments confirmed a-helical conformations for SI and S2 and showed that K+ channel function was altered when trp residues were placed in some (labeled non-trp-tolerant), but not all, positions. The same treatment for helix S3 yielded complex results. At S3 s N-terminal end the distribution of trp-tolerant positions were consistent with an a-helical structure, however, this was not the case at S3 s C-terminal end. Other tests indicated that S3 might be helical for its entire length and that the N-terminal end interfaces with both lipid and protein while the C-terminal end interfaces with water. Comparisons of trp-tolerant or trp-intolerant residues over several different Kv channel... 

---