Neighboring amino

Eor a macromolecule such as a large protein, the steps in characterization involve, first, identification of the spin systems present, using correlated spectroscopy, and identification of neighboring amino acids. The long range noes are then assigned, and three bond coupling constants ate deterrnined. 

Secondary structure (Section 27.19) The conformation with respect to nearest neighbor amino acids in a peptide or protein. The a helix and the pleated (3 sheet are examples of protein secondary structures. 

SH2 and SH3 domains refer to src homology 2 and 3, a non-receptor tyrosine kinase where these domains were identified originally. They bind to phos-phorylated tyrosine and pro line rich epitopes, respectively, with specificities each in respect to the neighboring amino acids. Grb2 is an adapter molecule par excellence having both SH2 and SH3 domains (see also the respective article in this volume). 

Independent proof of these assignments is obtained from chemical studies. In the g/Mco-derivative (54), the hydroxyl groups at C-2 and C-4 can be inverted stereospecifically via oxazolidine derivatives with the neighboring amino group, thus unequivocally proving the stereochemical relationships between C-2, C-3 and C-4 in compounds (54)— (56) 10). 

The crystal structures of the SH2 domains of Src tyrosine kinase and Lck tyrosine kinase in complex with Tyr phosphorylated peptides have enabled important insight to be obtained into recognition of the phosphotyrosine residue and the neighboring amino acids in class lA of SH2 domains. The phosphate residue is boimd in a deep pocket of the SH2 domain, at the end of which an invariant Arg residue (Arg PB5) is located which contacts the negatively charged phosphate by a two-pronged interaction. It can be estimated that a phosphoserine or phosphothreonine residue would be too short to enter into a similar interaction with the Arg residue. 

PROTEIN STRUCTURE IS DETERMINED BY ATTRACTIONS BETWEEN NEIGHBORING AMINO ACIDS... 

Steric constraints introduced by the /V-alkyl group. 12,17 The steric hindrance of the /V-alkyl group is experienced both by the peptide backbone and the side chains of neighboring amino acids. 18 ... 

Also, upon binding of a ligand to a protein, Trp observables (intensity, polarization, and lifetime) can be altered, and so one can follow this binding with Trp fluorescence. In proteins, tryptophan fluorescence dominates. Zero or weak tyrosine and phenylalanine fluorescence results from energy transfer to tryptophan and/or neighboring amino acids. 

The tertiary structure of the protein induces a high energy transfer between the Trp residue and the neighboring amino acids. This induces low values in the fluorescence parameters of the Trp residue in the native state in comparison to those measured when the protein is denatured, and so the energy transfer is weak. 

Any polymer of amino acids linked by amide bonds between the amino group of each amino acid and the carboxyl group of the neighboring amino acid. The terms dipeptide, tripeptide, etc. may specify the number of amino acids in the peptide, (p. 1174)... 

The problem of N-terminal variants in recombinant proteins is not uncommon. E. coli synthesizes proteins with a formylated methionine at the N terminus. In vivo, E. coli often removes N-formyl methionine with the action of a deformylase followed by methionine amino peptidase. This removal is not always exact and neighboring amino acids in the peptide chain influence the removal.130 This can yield recombinant products lacking a number of encoded amino acids at the N terminus. For smaller proteins, these product-related impurities generally are detected and quantitated by RP-HPLC. However, large proteins differing by only one or two N-terminal amino acids may be difficult to resolve by RP-HPLC. In these instances, peptide mapping by RP-HPLC is a valuable tool. 

Sharpless oxidation of the oxazole 52 provides an intermediate epoxide, which is attacked by the neighboring amino group, eventually leading to the pyrrolo[2,3-r/ isoxazole 53 (Equation 12). Variation of the aryl substituent provided access to a set of related derivatives in excellent yields <2006TL4957>. 

Bruice s contention that there is very little stabilization of the TS by CM, rather it is a favorable binding of the NAC that accounts for its catalytic activity, has been met with much skepticism. An early study by Wiest and Houk" looked at chorismate models with coordinated waters and aminidium cations in positions that matched interacting groups found in the crystal structure of CM with a coordinated substrate. These model computations suggested that the neighboring amino acid residues could be stabilizing the TS. 

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