Chemical shifts and structure

1
Chemical shifts and structure

• chemical shifts depend upon local electron
  distributions, bond hybridization states,
  proximity to polar groups, nearby aromatic rings,
  local magnetic anisotropies.
• in other words, chemical shifts depend upon the
  structural environment and thus can provide
  information about structure
• observation of relationships between chemical
  shifts and protein secondary structure has led to
  the development of some useful empirical rules

2
Ha chemical shifts and secondary structure

• Ha chemical shifts are generally lower for
  a-helices than for b-sheets
• the figure at right shows distributions of Ha
  chemical shifts observed in sheets (lighter bars)
  and helices (darker bars). The black bar in each
  distribution is the median.
• Ha chemical shifts in a-helices are on average
  0.39 ppm below random coil values, while
  b-sheet values are 0.37 ppm above random coil
  values.

Wishart, Sykes Richards J Mol Biol (1991) 222,
311.
3
Chemical shift index (CSI)

• trends like these led to the development of the
  concept of the chemical shift index as a tool
  for assigning secondary structure using chemical
  shift values.
• one starts with a table of reference values for
  each amino-acid type, which is essentially a
  table of random coil Ha values
• CSIs are then assigned as follows
• exptl Ha shift rel. to reference assigned CSI
• within 0.1 ppm 0
• gt0.1 ppm lower -1
• gt0.1 ppm higher 1

Wishart, Sykes Richards Biochemistry (1992)
31, 1647-51.
4
Chemical shift indices
CSI
residue

• one can then plot CSI vs. sequence and assign
  2ndary str. as follows
• any dense grouping of four or more -1s,
  uninterrupted by 1s is assigned as a helix,
  while any dense grouping of three or more
  1s, uninterrupted by -1s, is assigned as a
  sheet.
• a dense grouping means at least 70 nonzero
  CSIs.
• other regions are assigned as coil
• this simple technique assigns 2ndary structure
  w/90-95 accuracy
• similar useful relationships exist for 13Ca, 13Cb
  13CCO shifts

5
heres a figure showing deviations of Ca and Cb
chemical shifts from random coil values when in
either a-helix or b-sheet conformation
for a-helices, Ca shifts are higher than normal,
whereas Cb shifts are lower than normal. Note in
your reading of the apo-calmodulin paper that Ca
shifts are used in characterizing the structure
of the interdomain linker
6
Chemical shifts and structural restraints

• so CSI is a useful technique for identifying
  secondary structures from chemical shift data
• explicit restraints on structure are also
  derivable from chemical shifts, analogous to our
  nOe-derived distance restraints, our
  coupling-constant-derived dihedral angle
  restraints and our hydrogen-exchange derived
  hydrogen bond restraints. However, these are not
  in very wide use yet.