Tryptophan, structure

Transition state theory, 46,208 Transmission factor, 42,44-46,45 Triosephosphate isomerase, 210 Trypsin, 170. See also Trypsin enzyme family active site of, 181 activity of, steric effects on, 210 potential surfaces for, 180 Ser 195-His 57 proton transfer in, 146, 147 specificity of, 171 transition state of, 226 Trypsin enzyme family, catalysis of amide hydrolysis, 170-171. See also Chymotrypsin Elastase Thrombin Trypsin Plasmin Tryptophan, structure of, 110... 

NMR results for gramicidin A incorporated into oriented DMPC bilayers produced results that were interpreted as being consistent with the structure of gramicidin A incorporated into SDS micelles (i.e. no tryptophan 9/15 stacking). The results of a Raman spectroscopy study of water accessibility to the tryptophan indole NH sites of gramicidin A incorporated into a hposome (dilauroyl-L-a-phosphatidylchoUne) aqueous suspension were interpreted as being consistent with the stacked tryptophan structure. Obviously, the... 

Studies of the E. coli lac operon defined the promoter as a distinct genetic element [152] located before the operator [151,152] and serving as the site for initiation of transcriptions [165]. This conclusion was based on the occurrence of presumed promoter mutations [151,181] which limited the expression of the operon. The existence of such mutant versions of natural promoters as well as the above described natural low-efficiency promoters such as P2 makes it evident that the site for initiation of transcription can exist in more than one form and with different efficiencies. In the following sections are examples of various promoters created by mutation within the tryptophan structural genes. Since at least some of these are also transcribed and translated into a protein product, there exists the hope that eventual analysis of amino acid sequences will disclose the nucleotide sequences of the various forms of the promoter. 

Hu, X.H., Spiro, T.G. Tyrosine and tryptophan structure markers in hemoglobin ultraviolet resonance Raman spectra mode assignments via subunit-specific isotope labeling of recombinant protein. Biochemistry 36, 15701-15712 (1997)... 

Ruan, C., Yang, Z., Hallowita, N. and Rodgers, M.T. (2005) Cation/jr interactions with a model for the side chain of tryptophan structures and absolute binding energies of alkali metal cation-indole complexes. J. Phys. Chem. A, 109,11539-11550. 

Figure 3.2. Crystal structures of (upper left) Cu(L-tryptophan)(2,2 bipyridine) CIO 4 (upper right) Cu(L-Tryptophan)(1, l()-phenanthroline)ClO4 . 5H2O and (lower) Cu(L-...

Figure 4.7 Two of the enzymatic activities involved in the biosynthesis of tryptophan in E. coli, phosphoribosyl anthranilate (PRA) isomerase and indoleglycerol phosphate (IGP) synthase, are performed by two separate domains in the polypeptide chain of a bifunctional enzyme. Both these domains are a/p-barrel structures, oriented such that their active sites are on opposite sides of the molecule. The two catalytic reactions are therefore independent of each other. The diagram shows the IGP-synthase domain (residues 48-254) with dark colors and the PRA-isomerase domain with light colors. The a helices are sequentially labeled a-h in both barrel domains. Residue 255 (arrow) is the first residue of the second domain. (Adapted from J.P. Priestle et al., Proc.

Hyde, C.C., et al. Three-dimensional structure of the tryptophan synthase az pz multienzyme complex from Salmonella typhimurium. J. Biol. Chem. 263 17857-17871, 1988. 

The elegant genetic studies by the group of Charles Yanofsky at Stanford University, conducted before the crystal structure was known, confirm this mechanism. The side chain of Ala 77, which is in the loop region of the helix-turn-helix motif, faces the cavity where tryptophan binds. When this side chain is replaced by the bulkier side chain of Val, the mutant repressor does not require tryptophan to be able to bind specifically to the operator DNA. The presence of a bulkier valine side chain at position 77 maintains the heads in an active conformation even in the absence of bound tryptophan. The crystal structure of this mutant repressor, in the absence of tryptophan, is basically the same as that of the wild-type repressor with tryptophan. This is an excellent example of how ligand-induced conformational changes can be mimicked by amino acid substitutions in the protein. 

Figure 8.20 Schematic diagrams of docking the trp repressor to DNA in its inactive (a) and active (b) forms. When L-tryptophan, which is a corepressor, hinds to the repressor, the "heads" change their positions relative to the core to produce the active form of the repressor, which hinds to DNA. The structures of DNA and the trp repressor are outlined.

Zhang, R.-G., et al. The crystal structure of trp aporepressor at 1.8 A shows how binding tryptophan enhances DNA affinity. Nature 327 591-S97, 1987. 

The nonpolar amino acids (Figure 4.3a) include all those with alkyl chain R groups (alanine, valine, leucine, and isoleucine), as well as proline (with its unusual cyclic structure), methionine (one of the two sulfur-containing amino acids), and two aromatic amino acids, phenylalanine and tryptophan. Tryptophan is sometimes considered a borderline member of this group because it can interact favorably with water via the N-H moiety of the indole ring. Proline, strictly speaking, is not an amino acid but rather an a-imino acid. 

Conversely, when A-alkyl tryptophan methyl esters were condensed with aldehydes, the trans diastereomers were observed as the major products." X-ray-crystal structures of 1,2,3-trisubstituted tetrahydro-P-carbolines revealed that the Cl substituent preferentially adopted a pseudo-axial position, forcing the C3 substituent into a pseudo-equatorial orientation to give the kinetically and thermodynamically preferred trans isomer." As the steric size of the Cl and N2 substituents increased, the selectivity for the trans isomer became greater. A-alkyl-L-tryptophan methyl ester 42 was condensed with various aliphatic aldehydes in the presence of trifluoroacetic acid to give predominantly the trans isomers. ... 

The structure of the complex of (S)-tryptophan-derived oxazaborolidine 4 and methacrolein has been investigated in detail by use of H, B and NMR [6b. The proximity of the coordinated aldehyde and indole subunit in the complex is suggested by the appearance of a bright orange color at 210 K, caused by formation of a charge-transfer complex between the 7t-donor indole ring and the acceptor aldehyde. The intermediate is thought to be as shown in Fig. 1.2, in which the s-cis conformer is the reactive one. 

Pewnim T, Seifert J. 1993. Structural requirements for altering the L-tryptophan metabolism in mice by organophosphorous and methylcarbamate insecticides. Eur J Pharmacol 248 237-241. 

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