Side-chain assignments

Figure 4 Sequential assignment of the backbone atoms for the segment Pro-109 to Val-113 of inhibited sfSTR by 4-D HCANNH and 4-D HCA(CO)NNH. Four planes are shown from each spectrum. The assigned backbone atoms are indicated in (A). In (B) the upper four planes in solid lines are from the 4-D HCANNH and the lower four planes in dashed lines are from the 4-D HCA(CO)NNH. The chemical shifts for the four correlated nuclei in each case are shown. The correlations continue for the segment Pro-109 to Pro-129. As Pro lacks a protonated N, this residue serves as a "stop" signal. The correlation of 19 residues with Pro at the N- and C-terminal ends is unique for this segment in the sequence of sfSTR, therefore these backbone atoms are specifically assigned without having to further assign side chain atoms. (From Ref. 5.)...

If the same alkyl group occurs more than once as a side chain, this is indicated by the prefixes di-, tri-, tetra-, etc. Side chains are cited in alphabetical order (before insertion of any multiplying prefix). The name of a complex radical (side chain) is considered to begin with the first letter of its complete name. Where names of complex radicals are composed of identical words, priority for citation is given to that radical which contains the lowest-numbered locant at the first cited point of difference in the radical. If two or more side chains are in equivalent positions, the one to be assigned the lowest-numbered locant is that cited first in the name. The complete expression for the side chain may be enclosed in parentheses for clarity or the carbon atoms in side chains may be indicated by primed locants. 

Because each side chain can be identifiably assigned to a particular component, the mixture coefficients and the normal distribution parameters can be detennined separately. 

Quaternary salts have been prepared from a number of these bases. 7-(Dialkylaminoalkyl)amino-l,2,3a,4-tetraazaindenes (132) were prepared and converted into mono-quaternary salts, but no structures were assigned to the salts and the quaternary center may well be in the side-chain. When this ring system carries 3-methyl and 5-alkyl or... 

One form of the polyatomic ion I, has an unusual V-shaped structure one I atom lies at the point of the V, with a linear chain of two I atoms extending on each side. The bond angles are 88° at the central atom and 180° at the two atoms in the side chains. Draw a Lewis structure for L that explains its shape and indicate the hybridization you would assign to each nonterminal atom. 

Terwilliger TC. Automated side-chain model building and sequence assignment by template matching. Acta Cryst 2003 D59 45-9. 

C13-0078. Assign each amino acid in Problem as possessing hydrophobic or hydrophilic side chains. Explain... 

D-NOESY- H- C-HMQC/HSQC Sequential assignment of the spin systems, in particular, identification of nOes between side chains... 

In the M. trichosporium OB3b system, a third intermediate, T, with kmax at 325 nm (e = 6000 M-1cm 1) was observed in the presence of the substrate nitrobenzene (70). This species was assigned as the product, 4-nitrophenol, bound to the dinuclear iron site, and its absorption was attributed primarily to the 4-nitrophenol moiety. No analogous intermediate was found with the M. capsulatus (Bath) system in the presence of nitrobenzene. For both systems, addition of methane accelerated the rate of disappearance of the optical spectrum of Q (k > 0.065 s-1) without appreciatively affecting its formation rate constant (51, 70). In the absence of substrate, Q decayed slowly (k 0.065 s-1). This decay may be accompanied by oxidation of a protein side chain. 

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