Chemical shift index

The original CSI method makes use of the fact that 1Hα chemical shifts of amino acid residues in helices tends to be shifted upfield (i.e. towards the right side of an NMR spectrum) relative to their random coil values and downfield (i.e. towards the left side of an NMR spectrum) in beta strands.

The CSI is a graph-based technique that essentially employs an amino acid-specific digital filter to convert every assigned backbone chemical shift value into a simple three-state (-1, 0, +1) index.

This approach generates a more easily understood and much more visually pleasing graph of protein chemical shift values.

A list of the amino acid-specific random coil chemical shifts for CSI calculations is given in Table 1.

[2][3][4][5] This performance depends partly on the quality of the NMR data set as well as the technique (manual or programmatic) used to identify the protein secondary structures.

These include: 1) a prediction method that employs statistically derived chemical shift/structure potentials (PECAN);[11] 2) a probabilistic approach to secondary structure identification (PSSI);[12] 3) a method that combines secondary structure predictions from sequence data and chemical shift data (PsiCSI),[13] 4) a secondary structure identification approach that uses pre-specified chemical shift patterns (PLATON)[14] and 5) a two-dimensional cluster analysis method known as 2DCSi.