Chemical Shifts in Amino Acids & Proteins
Chemical Shifts in Amino Acids & Proteins
HN Hα
Res. No. Median SD rc No. Median SD rc
A 1446 8.16 0.61 8.25 1429 4.18 0.50 4.35
C 882 8.44 0.66 8.31 942 4.72 0.63 4.69
D 975 8.34 0.62 8.41 936 4.59 0.32 4.76
E 1225 8.30 0.68 8.37 1167 4.17 0.45 4.29
F 668 8.40 0.76 8.23 694 4.61 0.61 4.66
G 1485 8.33 1.31 8.39 2295 3.92 0.68 3.97
H 421 8.27 0.96 8.41 450 4.61 1.02 4.63
I 789 8.24 0.68 8.19 807 4.15 0.62 4.23
K 1593 8.17 0.75 8.41 1500 4.20 0.48 4.36
L 1447 8.19 0.73 8.42 1426 4.24 0.51 4.38
M 326 8.30 0.63 8.42 325 4.29 0.49 4.52
N 862 8.33 0.84 8.42 827 4.67 0.46 4.75
P – – – – 683 4.42 0.40 4.44
Q 730 8.16 0.65 8.41 683 4.25 0.46 4.37
R 892 8.23 0.58 8.27 848 4.25 0.46 4.38
S 1113 8.27 1.43 8.38 1118 4.45 0.44 4.50
T 1082 8.16 0.82 8.24 1087 4.40 0.57 4.35
V 1157 8.21 0.82 8.44 1202 4.08 0.86 4.18
W 227 8.26 0.86 8.09 220 4.63 0.61 4.70
Y 685 8.26 0.81 8.18 717 4.58 0.61 4.60
N Cα C
Res. No. Median SD No. Median SD rc No. Median SD rc
A 335 122.8 8.7 118 52.1 2.1 50.8 40 177.8 2.4 175.8
C 62 117.8 3.7 35 55.0 3.1 53.9 40 172.2 2.0 173.9
D 216 120.3 4.1 77 53.0 2.1 52.7 31 176.9 1.4 174.2
E 258 120.9 3.2 112 56.7 2.6 55.4 42 177.2 2.1 173.7
F 136 121.3 4.4 79 56.2 2.6 56.2 38 174.7 2.5 172.9
G 277 109.1 4.0 171 44.0 1.9 43.9 52 172.7 2.1 171.8
H 59 119.5 3.5 30 53.8 5.7 53.6 6 175.8 1.8 172.2
I 169 123.6 4.6 59 60.0 3.0 59.6 22 175.8 1.9 174.2
K 364 120.7 4.0 153 56.0 2.1 54.6 30 175.7 2.2 174.5
L 289 122.0 4.4 115 53.7 1.9 53.8 26 176.5 1.8 174.7
M 79 120.9 4.8 42 54.7 2.2 54.0 19 177.4 1.8 173.4
N 172 118.9 5.1 65 52.7 1.9 53.8 26 173.7 1.9 173.1
P 34 137.7 3.8 61 62.3 1.6 61.9 19 175.0 2.1 174.1
Q 179 120.2 3.8 64 55.4 2.1 54.1 19 175.1 1.8 174.0
R 128 120.7 3.7 57 55.6 2.5 54.6 31 174.7 3.7 173.4
S 166 116.9 3.6 78 57.0 1.9 56.6 19 173.7 1.6 172.6
T 200 115.7 5.6 111 60.3 2.6 60.1 38 174.8 1.9 172.5
V 237 121.3 6.0 92 60.8 2.9 60.7 24 174.8 2.1 173.9
W 41 120.3 4.0 16 55.7 2.2 55.7 0 – – 173.4
Y 114 121.2 5.5 69 55.7 1.7 56.3 14 173.9 1.9 172.9
a Data extracted from version 1.0 of the BioMagResBank database.3 For each shift, the first three columns list the number of shifts, the median
value and the standard deviation SD about the mean Column labeled ‘rc’ gives peptide shifts for H-Gly-Gly-X-Ala-OH from Bundi and Wüthrich4
and Richarz and Wüthrich.5
3 CHEMICAL SHIFTS AND SECONDARY The same general trend is found for amide protons, whereas
STRUCTURE Hβ shifts move in the opposite direction by a smaller amount.
Amide protons at the N-terminus of helices tend to be shifted
Considerable attention has been paid to ways in which to high frequency compared with those at the C-terminus.
the Hα shift reflects local secondary structure. It has been These relationships are in many cases clear enough to drive
recognized for some time that β-sheet regions show high- secondary-structure assignments in proteins,13,14 and to gain
frequency shifts for this resonance, while helical regions show a qualitative idea of structural differences among homologous
low-frequency shifts. In the Wishart et al.12 survey, the mean systems. It has been shown that this dependence of Hα and
Hα positions in helices and sheets differ by nearly 0.8 ppm, and Hβ shifts on secondary structure can be explained in terms of
there is remarkably little overlap between the two distributions. peptide group contributions, as outlined below.15
These ideas may also be of use for linear peptides, where is conventional to incorporate in B those constants that would
conformational heterogeneity hampers quantitative NOE-based yield the expected contribution from a benzene ring, and to use
structure calculations. For example, amide proton shifts in i # (the ‘ring current intensity’ factor) to represent the ratio
model helical peptides are often periodic (with a 3–4 residue of the intensity expected for the ring in question to that of
repeat pattern);16,17 amphipathic helices show a periodic a benzene ring. There have been several attempts to estimate
behavior that appears to be related to curving of the helix these factors, based on both quantum mechanical and empirical
axis;18,19 and it may be possible to characterize helices calculations37,38
of marginal stability through an analysis of the solvent Two commonly used parameterizations of the geometric
dependence of backbone shifts.20 factors were proposed by Johnson and Bovey39 and by Haigh
The relationship of 15 N and 13 C shifts to secondary structure and Mallion.34 In the latter model, which is one of the simplest
is also of considerable current interest.9 – 12,21 Cα and carbonyl to implement, the geometric factor is
shifts exhibit a strong correlation with secondary structure,
both moving to higher frequency in helical conformations and 1 1
to lower frequency in β-strand or extended configurations. G(r) = sij + 3 (1)
As with Hα shifts, there is surprisingly little overlap between ij
ri3 rj
the distributions, which suggests that reliable conformational
conclusions may be drawn, and the Cα shift has been Here r i and r j are the distances from ring atoms i and j to the
used as a site-specific probe of the helix/coil transition in proton, and s ij is the area of the triangle formed by atoms i and
linear peptides.22 There are also indications from solid state j and the proton projected onto the plane of the aromatic ring.
studies of peptides that the carbonyl 13 C resonance moves to The sum is over the bonds in the ring. The Johnson–Bovey
higher frequency with decreasing CO· · · HN hydrogen-bond model sets up ‘rings’ of current above and below the plane of
length,23 – 27 a result that is in rough accord with quantum the atoms, and computes fields from this model. There appears
chemical calculations.26 Cβ shifts also show systematic to be very little difference between the two models, except at
differences between helices and sheets, but with much more very short distances.
overlap in the observed distributions. The heme group is an important special case for ring
The situation for amide 15 N shifts in proteins (as with amide current calculations, and a variety of empirical calculations
protons) is less clear. There are general differences between have been carried out.40 – 43 A simple model that gives good
shifts in helix and sheet structures of about 3 ppm, but the results treats the heme as five rings: four for the pyrroles,
overlap between the two distributions is often greater than and one ‘macrocycle’ that traverses the large conjugated ring
this, so that it is difficult to draw simple conclusions from a in the canonical valence-bond structure. Cross and Wright43
given set of shifts.12,28,29 There is a correlation between amide compared the results of this and other models with a dataset
proton and amide 15 N shifts, suggesting that similar physical composed of protein and model compound shifts, and Ösapay
effects are influencing both. There is some evidence that 15 N and Case38 used a larger heme protein database, including
shifts may be periodic in helices, reflecting the local structure, cytochromes c, b 5 , and c 551 and myoglobin. The empirical
but the relationship does not appear to be a simple one.16,30 formulas appear to reproduce the observed behavior quite well.
In both organic chemistry and biochemistry, empirical It has been recognized for some time that the magnetic
analyses of the effects of ‘distant’ substituents on chemical anisotropy of the peptide group is likely to contribute
shifts have played an important role for many years.31 There significantly to chemical shifts in proteins. McConnell35 has
are generally two such types of interaction: magnetic fields shown that when the observed proton and the ‘source’ of the
arising from anisotropies in the magnetic susceptibilities of magnetic anisotropy are far apart, the contribution to the local
distant functional groups, and electric fields created by distant shielding tensor depends upon the magnetic anisotropy of the
dipoles or charges. The former are strongest with conjugated distant group:
or partially delocalized electrons (such as in aromatic rings
or peptide groups) where there are significant anisotropies σm = (3L0 R 3 )−1 χii (1 − 3 cos2 θi ) (2)
in group magnetic susceptibilities.32 – 34 These groups then i=x,y,z
respond to an external spectrometer field B0 to create a
local magnetic field which can augment or oppose B0 .35 The Here L0 is the Avogadro constant, R is the distance from
electrostatic fields of distant groups influence chemical shifts the proton to the distant group, χ ii is a component of the
indirectly, by polarizing chemical bonds, and thus contributing magnetic susceptibility tensor, and θ i is the angle between
to shielding or deshielding of the nuclei.36 These mechanisms the i axis and the radius vector R. Since there is no direct
are considered in more detail in the following paragraphs. method for measuring the magnetic anisotropy of a peptide
group within a protein, all estimates of these effects are to
some extent empirical. Data for formamide44 suggest that the
4.1 Ring Current Calculations peptide group is nearly axially symmetric about the out-of-
plane axis, with an anisotropy χ of −5.1 ± 0.6 × 10−6
The general form of empirical theories is σ rc = iBG(r) where erg (G2 -mol)−1 . This value is in good agreement with the one
r is the vector from the observed proton to the aromatic ring, obtained using an empirical theoretical approach developed by
G(r) is a geometric factor, and i and B are constants.31,34 It Pauling:33 5.4 10−6 erg (G2 -mol)−1 .
18. N. E. Zhou, B. -Y. Zhu, B. D. Sykes, and R. S. Hodges, J. Am. 45. T. Asakura, Y. Niizawa, and M. P. Williamson, J. Magn. Reson.,
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This work was supported by NIH Grant GM45811. I thank Beverley
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Seavey and John Markley for providing access to the BioMagResBank
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Biographical Sketches
41. R. J. Abraham, G. R. Bedford, D. McNeillie, and B. Wright, Org.
Magn. Reson., 1980, 14, 418.
David A. Case, b 1948. B.S., 1970, Michigan State, A.M., 1972,
42. R. J. Abraham, J. Magn. Reson., 1981, 43, 491. Harvard, Ph.D., 1977, Harvard, USA. Approx. 90 publications.
43. K. J. Cross and P. E. Wright, J. Magn. Reson., 1985, 64, 220. Research interests include modeling of proteins and nucleic acids,
44. H. L. Tigelaar and W. H. Flygare, J. Am. Chem. Soc., 1972, 94, quantum mechanical studies of the active sites of metalloenzymes, and
343. computational aspects of NMR.