Random coil chemical shifts

Schwarzinger, S., G.J.A. Kroon, T.R. Foss, P.E. Wright, and HJ. Dyson. 2000. Random coil chemical shifts in acidic 8M urea Implementation of random coil shift data in NMR view. J. Biomol. NMR 18 43-48. 

After the assignment process is complete, various types of NMR data can be used to build up a picture of the secondary structure of the peptide (based on coupling constants, chemical shifts, and NOEs) and then, if required, a full 3D structure can be determined. Figure 6 shows some of this information for Vcl.l. As noted earlier, deviations from random coil chemical shifts provide an indication of secondary structure, and in the case of Vcl.l. a region of negative aH secondary shifts provides a first indication that the helix typically present in a-conotoxins is indeed present in Vcl.l (Fig. 6A). This conclusion is supported by the CSI, coupling, and NOE data in Fig. 6B. Finally, the 3D structure is shown in various representations in the lower panels of the figure (58). 

Figure 12.9 displays graphically the proton chemical shifts of all 20 amino acids in an unstructured peptide context. These are called random coil chemical shifts because they are not influenced by the through-space effects observed in specifically folded proteins. In this environment, there is not much chemical-shift dispersion Hn falls between 8 and 9 ppm, Ha between 4 ppm and the water resonance ( 4.8 ppm), and the side-chain Hn resonances... 

The random-coil chemical shifts shown in Figure 12.9 have very little variation in Hn or Hq, chemical shifts among the 20 amino acids. Furthermore, if we have more than one of a particular amino acid in an unstructured protein, they will be indistinguishable by chemical shift. Sometimes proteins are observed in an unfolded state, and this can be clearly seen... 

The isotropic chemical shift, such as those of the Ca and CP sites, can be a strong indicator of local molecular conformation. Emprrical °° ° and theoretical results can be used to define an average ( random coil ) chemical shift for each amino acid residue type. It has been found that deviations from these reference values can be interpreted in terms of the local backbone conformation. In particular, the quantity AS, defined as... 

Braun D, Wider G, Wiithrich K (1994) Sequence-corrected N random coil chemical shifts. J Am Chem Soc 116 8466-8469... 

The deviations of chemical shifts from random coil values, especially for 13C , and H , provide a valuable probe of secondary struc-... 

Figure 25 Schematic representation of the distinction of BC chemical shifts between the a-helix and loops for Ala Cp (A) and Val C=0 (B) carbons of bR. The random coil peaks for both are located at the boundary between the BC NMR peaks of the a-helix and loops. From Ref. 25 with permission.

Chemical shifts are very sensitive probes of the molecular environment of a spin. However, in many cases their dependence on the structure is complicated and either not fully understood or too intricate to allow the derivation of reliable conformational constraints [37, 38]. An exception in this respect are the deviations of 13C (and, to some extent, 1 xf) chemical shifts from their random coil values that are correlated with the local... 

Furthermore, in flexible linear peptides the chemical shifts are typical of random structures similar to nonfolded proteins. Deviation from these random shifts sometimes identifies specific conformational preferences. NH-proton chemical shifts depend strongly on external influences (solvent, temperature, concentration, specific sequence). Random coil shifts for these protons correlate less well than chemical shifts of the a-protons or a-carbonsJ19-261 Not only are the shift differences of different heterotopic protons similar, but also those of diastereotopic P-protons. A preferred side-chain conformation is normally only found when there is also a preferred backbone conformation. 

Table 5.24. 13C Chemical Shifts (6C in ppm) of Randomly Coiled Poly(8-bromoadenylic Acid), Polyadenylic Acid and Corresponding 5 -Mononucleotides Temperature 70 °C Solvent D2Q, pD 7.0-7.3 [781],...

Figure 10.1 -NMR spectrum of thioredoxin, reducedform. Labels show chemical-shift values typical of various hydrogen types in protein chains having random coil conformation. Some signals lie outside these ranges because of specific interactions not present in random coils. Atom labels are as found in PDB coordinate files. Spectrum generously provided by Professor John M. Louis.

Advances in NMR instrumentation and methodology have now made it possible to determine site-specific proton chemical shift assignments for a large number of proteins and nucleic acids (1,2). It has been known for some time that in proteins the "structural" chemical shifts (the differences between the resonance positions in a protein and in a "random coil" polypeptide (3-5),) carry useful structural information. We have previously used a database of protein structures to compare shifts calculated from simple empirical models to those observed in solution (6). Here we demonstrate that a similar analysis appears promising for nucleic acids as well. Our conclusions are similar to those recently reported by Wijmenga et al (7),... 

Fig. 3. Range of chemical shifts for aH in amino acids. The bars are centered at the average shift value for the respective amino acid (BioMagResBank [http //www. bmrb.wisc.edu/] (54)). The dark grey bars represent the 68% and the light grey bars the 95% confidence interval. The values for diamagnetic proteins were taken from the BioMagResBank in mid-February 2007. The vertical black lines highlight the random coil shift. The x marks the random coil shift for oxidized cysteine.

C-CP-MAS NMR produces a broad resonance with a chemical shift of 31.2 ppm,129 a characteristic of mid-chain methylene carbons of fatty acids in the V-amylose complex. The results showed that up to 43% of amylose in non-waxy rice starch, 33% in oat starch, and 22% in normal maize and wheat starch granules are complexed with lipids at a single helical conformation, and the remaining amylose is free of lipids and is in a random coil conformation.212 Up to 60% of apparent amylose in waxy barley starch is complexed with lipids.212... 

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