Aromatic sidechains

The motions of sidechains in proteins play an important role in their dynamics. The time scales involved range from picoseconds for local oscillations in a single potential well to milliseconds or longer for some barrier crossings, such as the 180° rotations (ring flips ) of aromatic sidechains. This range of motions makes it necessary to use a variety of theoretical approaches in the analysis of sidechain dynamics they include molecular dynamics, activated dynamics, and stochastic dynamics (see Chapt. IV.). There are a number of well-characterized examples where sidechain motions have been shown to play a specific role in protein function. 

The comparison in Fig. 23a and b of the dynamics of Tyr-21 in the protein and in an isolated peptide shows that the latter behaves much more like an unhindered oscillator than the former. In the protein the aromatic ring un- 

To clarify the dynamic character of the ring fluctuations, it is useful to introduce time correlation functions.210 211 The time correlation function CA(t) = 4(s + t)A(s)) for a dynamical variable j4 is obtained by multiplying. 4(,s), the value of A at times, byA(s + t), the value taken by A after the system has evolved for an additional time, t, and averaging over the initial time s. If the averaging is done over a sufficiently long dynamical simulation of an equilibrated system, CA(t) will be independent of the initial time, s, used in the calculation it is then customary to write CA(t) = /4(r)v4(0) . If A is the fluctuation of a variable from its mean value, y4(0) 2 is the mean-square fluctuation of the variable for an equilibrated system, while the time correlation function, CA(t), describes the average way in which the fluctuation decays. 

The torsional potential of mean force (Fig. 24) and the correlation function for the torsional motions of the Tyr-21 ring in BPTI suggest that the time dependence of A t can be described by the Langevin equation for a damped harmonic oscillator (see Chapt. IV.C and D). 

Here I = 7.5 X 1015 g-cm2/mol is the moment of inertia of the ring about the torsional axis, 7/3 is the friction constant, k is the harmonic restoring force constant, and/(f) represents the random torques acting on the ring due to fluctuations in its environment. In using the Langevin equation, we implicitly assume that variations in/(f) occur on a much shorter time scale than do 

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Fig. 1.6 A comparison of the CD spectra of oligopeptoids with achiral Npm side chains (1) and with a-chiral, aromatic sidechains of S and R chirality (2 and 6, respectively). Sample concentration was 60 j,M in acetonitrile. Spectra were acquired at room temperature. Npm = (N-[l-phenylmethyljglycine) Nspe= (S)-N-(l -phenylethyl)glycine Nrpe= (R)-N-(l -phenylethyl)glycine...

In the mid to late 1980s, many research groups focused on methods and processes to prepare L-phenylalanine (Chapter 3). This was a direct result of the demand for the synthetic, artificial sweetener aspartame. One of the many routes studied was the use of phenylalanine dH (Scheme 19.4, R = C6H5CH2) with phenylpyruvate (PPA) as substrate.57-58 This enzyme from Bacillus sphaericus shows a broad substrate specificity and, thus, has been used to prepare a number of derivatives of L-phenylalanine.59 A phenylalanine dH isolated from a Rhodococcus strain M4 has been used to make L-homophenylalanine (.S )-2-amino-4-pheny I butanoic acid], a key, chiral component in many angiotensin-converting enzyme (ACE) inhibitors.40 More recently, that same phenylalanine dH has been used to synthesize a number of other unnatural amino acids (UAAs) that do not contain an aromatic sidechain.43... 

Figure 1. Typical Tj and T2 relaxation measurements of TGF-a. Relaxation data for the aromatic sidechain protons of residue Y38 are shown for TGF-a in the absence (panels C+D) and presence (panels A+B E+F) of EGFR-ED. Panels A, C and E depict Tj experimental data and panels B, D and F depict T2 data. In panels A B are plots of typical curve-fit data.

Figure 2. Transferred NOESY and NOESY spectra of desmopressin. The aromatic-sidechain region of the transferred NOESY spectrum of desmopressin in the presence of 0.1 mole equivalent NP-II (panel A) and the same spectral region of the NOESY spectrum of desmopressin in absence of NP-II (panel B).

Certain members of the heptaene subgroup, e.g. candicidin, ascosin and hamycin, contain an aromatic amine sidechain p-aminoacetophenone (3), which is alkali-labile [33-36]. In other heptaenes, e.g. candimycin and perimycin, the aromatic sidechain is A -methylated (4) [34]. 

The presence of mycosamine or perosamine confers a basic character on the polyene molecule. Many of the polyene antibiotics, e.g. nystatin, amphotericin B and candicidin are amphoteric, possessing an equal number of basic (hexo-samine or aromatic sidechain) and acidic (carboxyl) groups. Other polyenes, e.g. filipin and fungichromin, possess no ionizable groups at all, i.e. they are nonpolar. 

This group contains over 30 described members, including two of clinical impor tance, amphotericin B and candicidin. Heptaenes can be divided into three subgroups on the basis of the presence or absence of an aromatic sidechain. 

The heptaenes of the candicidin group [61 ], candicidin, hamycin and ascosin, contain an aromatic sidechain (3) derived fromp-aminoacetophenone [9,34,35]. 

The third group, which includes perimycin and candimycin, also possesses an aromatic sidechain but in this-case it is A -methylated as in formula (4) [63]. Perimycin also contains a unique amino sugar, perosamine (2) [31]. 

Another noteworthy finding of the binding of maltose to domain II in the open structure is the considerable number of unpaired buried sugar OHs making contacts with the aromatic sidechains. This finding indicates that a significant fraction of the binding interface in the open structure is non-complementary. More importantly, it further implies a smaller actual contact surface involved in purely hydrophobic interaction between domain II and maltose. 

Figure 6 Illustration of a five-structure conformational ensemble for the protein BUSI. Only the backbone and aromatic sidechains are shown. This was the first complete protein structure to be determined in solution from NMR data ...

Figure 8 Illustration of the ensemble of 10 E. coli Flavodoxin structures obtained from homology modeling using distance geometry, superimposed on the crystal structure (heavy line) so as to minimize the coordinate differences to the alpha carbons in residues 4-170. Only the heavy backbone and aromatic sidechain atoms are shown, together with those of the flavin mononucleotide cofactor (lower left)...

The Aromatic Hypothesis. In addition to the specifically conserved tryptophan residues, we had previously noted that the squalene-hopene cyclase and the oxidosqualene-lanosterol cyclase are generally rich in both tprptophan and tyrosine, amino acid residues with electron-rich aromatic sidechains (42), The squ ene-hopene cyclase contains 3.2% tryptophan and 4.0% tyrosine. The median values for representation of these amino acids in E, coli proteins are 1.2% and 2.7%, respectively (43). The levels of tryptophan and tyrosine found in the B. acidocaldarius enzyme exceed those found in > 95% and 85% of E, coli proteins, respectively. The oxidosqualene-lanosterol cyclase contains 3.0% ti tophan and 6.3% tyrosine. When compared to proteins from the yeast S. cerevisiae (for which the me an values for representation of tryptophan and tyrosine are 0.9% and 3.3%, respectively), the C. albicans enzyme i ssesses these amino acids at levels greater than those found in 99% of all S. cerevisiae proteins. 

Support for the aromatic h> othesis comes from model studies and protein crystal structure analysis. In biomimetic model studies, Dougherty has shown that cation-x interactions can stabilize both ground and transition states (44), and has used these results to predict the involvement of aromatic sidechains in receptors and enzymes that operate on cationic species (45,46). In the structural realm, the widespread occurrence of amino-aromatic interactions have been noted (47). In addition, a cocrystal structure shows that the myeloma protein McPC603 interacts with tile quaternary ammonium ion of its ligand phosphorylcholine through the... 

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