Proteins aromatic side-chains

Hu, G., Gershon, P. D., Hodel, A. E. Quiocho, F. A. mRNA cap recognition dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains. Proceedings of the National Academy of Science USA 96, 7149-7154 (1999). 

Absorption of proteins in the 230-300 nm range is determined by the aromatic side chains of tyrosine (Xmax = 274 am), tryptophan (Xmax = 280 nm), and phenylalanine (Xmax = 257 nm). Because the difference in the absorption spectra of native and unfolded protein molecules is generally small, difference spectra can... 

The near-UV CD of bovine o -lactalbumin is shown in Figure 35b. The strong CD of the native protein contrasts with the weak CD of the molten globule, which is comparable to that of the heat- and Gdm-HCl-denatured protein. The weakness of the aromatic CD bands in the molten globule is attributable to the absence of a well-defined conformation and environment for the aromatic side chains, which leads to averaging of the aromatic CD contributions over many conformations and thus to extensive cancellation. 

Aromatic side chains of amino acids such as phenylalanine, tryptophan, and tyrosine are found in general in the interior of proteins, in hydrophobic regions. In some proteins they mediate helix-helix contacts. It is to be expected that agents containing aromatic groups could interact with proteins via aromatic-aromatic interactions, as for instance, proven by X-ray studies of biphenyl compounds which inhibit sickle-cell hemoglobin gelation. 

Phenylalanine and tryptophan contain aromatic side chains that, like the aliphatic amino acids, are also relatively non-polar and hydrophobic (Figure 1.4). Phenylalanine is unreactive toward common derivatizing reagents, whereas the indolyl ring of tryptophan is quite reactive, if accessible. The presence of tryptophan in a protein contributes more to its total absorption at 275-280nm on a mole-per-mole basis than any other amino acid. The phenylalanine content, however, adds very little to the overall absorbance in this range. 

For quantitative analysis of protein concentration the colorimetric Bradford-assay [147] is most commonly used. Here another Coomassie dye, Brilliant Blue G-250, binds in acidic solutions to basic and aromatic side chains of proteins. Binding is detected via a shift in the absorption maximum of the dye from 465 nm to 595 nm. Mostly calibration is performed with standard proteins like bovine serum albumin (BSA). Due to the varying contents of basic and aromatic side chains in proteins, systematic errors in the quantification of proteins may occur. 

C. R. Coan, L. M. Hinman, and D. A. Deranleau, Charge-transfer studies of the availability of aromatic side chains of proteins in guanidine hydrochloride, Biochemistry 14, 4421 4427... 

Fig. 5. The aromatic cluster of the hydrophobic core of GTD-43, a helrx-loop-helrx dimer, and some of the assigned long-range NOEs that demonstrate the interactions of the aromatic side chains in the folded motif The formation of aromatic clusters has been observed in several designed proteins. Reproduced with permission from J Am Chem Soc (1997) 119 8598. ( 1997 ACS)...

The results of kinetic and X-ray crystallographic experiments on mutant carbonic anhydrases II, in which side-chain alterations have been made at the residue comprising the base of the hydrophobic pocket (Val-143), illuminate the role of this pocket in enzyme-substrate association. Site-specific mutants in which smaller hydrophobic amino acids such as glycine, or slightly larger hydrophobic residues such as leucine or isoleucine, are substituted for Val-143 do not exhibit an appreciable change in CO2 hydrase activity relative to the wild-type enzyme however, a substitution to the bulky aromatic side chain of phenylalanine diminishes activity by a factor of about 10 , and a substitution to tyrosine results in a protein which displays activity diminished by a factor of about 10 (Fierke et o/., 1991). 

In addition to the specificity-determining P, aromatic side chain, the amide groups of this substrate can form specific hydrogen bonds to the protein (Fig. 12-10). These hydrogen bonds presumably help the enzyme to recognize the compound, which is bound with Km of 0.03 M and is hydrolyzed (with liberation of NH3)288 289 with /c at -0.17 s"1. 

As well as providing a means of measuring 1 H/2H-exchange in proteins, NMR is a most powerful technique for studying the mobility of individual amino acids. For example, the rotational freedom of the aromatic side chains of tyrosine and phenylalanine about the C 3—Cy bond is readily studied by various NMR methods. ]H NMR can detect whether or not the aromatic ring is constrained in an anisotropic environment. In an isotropic environment or where there is rapid rotation on the NMR time scale, the 3 and 5 protons of phenylalanine and tyrosine are symmetrically related, as are the 2 and 6 (structures 1.12). The resultant spectrum is of the AA BB type, containing two pairs of closely separated doublets. But if there is slow rotation in an anisotropic environment, the symmetry breaks down to give four separate resonances (an ABCD spectrum), since the 5 and 6 protons are in different states from the 2 and 3. At an intermediate time... 

Trypsin, chymotrypsin, and elastase—three members of the serine protease family—catalyze the hydrolysis of proteins at internal peptide bonds adjacent to different types of amino acids. Trypsin prefers lysine or arginine residues chymotrypsin, aromatic side chains and elastase, small, nonpolar residues. Carboxypeptidases A and B, which are not serine proteases, cut the peptide bond at the carboxyl-terminal end of the chain. Carboxypeptidase A preferentially removes aromatic residues carboxypeptidase B, basic residues. (Illustration copyright by Irving Geis. Reprinted by permission.)... 

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