Chemical shifts and structure - PowerPoint PPT Presentation

1 / 6
About This Presentation

Chemical shifts and structure


in other words, chemical shifts depend upon the structural environment and thus ... observation of relationships between chemical shifts and protein secondary ... – PowerPoint PPT presentation

Number of Views:98
Avg rating:3.0/5.0
Slides: 7
Provided by: mattc5


Transcript and Presenter's Notes

Title: Chemical shifts and structure

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

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

Wishart, Sykes Richards J Mol Biol (1991) 222,
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.
Chemical shift indices
  • 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
  • a dense grouping means at least 70 nonzero
  • 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

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
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.
Write a Comment
User Comments (0)