hncaco.m

Protein-specific HN(CA)CO experiment (Figure 7.41 of "Protein NMR Spectroscopy", 2nd edition) using pre-set values of J-couplings used in the magnetisation transfer stages. The simulation uses the bidirectional propagation method described in (http://dx.doi.org/10.1016/j.jmr.2014.04.002).

Syntax

fid=hncaco(spin_system,parameters,H,R,K)

Arguments

parameters.npoints - a vector of three integers giving the

                            number of points in the three temporal
                            dimensions, ordered as [t1 t2 t3].

   parameters.sweep       - a vector of three real numbers giving
                            the sweep widths in the three frequen-
                            cy dimensions, ordered as [f1 f2 f3].

   parameters.J_nh        - 1H-15N J-coupling in Hz to be used for
                            magnetisation transfer.

   parameters.T           - evolution delay in the indirect 15N
                            dimension, in seconds.

   parameters.delta2      - coherence transfer delay in seconds.

   H   - Hamiltonian matrix, received from context function

   R   - relaxation superoperator, received from context function

   K   - kinetics superoperator, received from context function

Outputs

fid - three-dimensional free induction decay

Note: spin labels must be set to PDB atom IDs ('CA', 'HA', etc.) in
      sys.labels for this sequence to work properly.

TODO: whoever understands how phase cycles and quadratures work in
      3D NMR is welcome to add a phase-sensitive version.

m.walker@soton.ac.uk
ilya.kuprov@weizmann.ac.il

Examples

Below is the output (3D spectrum and three projections) of the HN(CA)CO pulse sequence for the GB1 protein (examples/nmr_proteins/hncano_gb1.m).

Notes

1. The sequence is hard-wired to work on 1H,13C,15N proteins and uses PDB labels to select spins that will be affected by otherwise ideal pulses.
2. Channels: F1 is 15N, F2 is 13C, F3 is 1H.
3. Spin labels must be set to PDB atom IDs ('CA', 'HA', etc.) in sys.labels for this sequence to work properly

See also

Protein pulse sequences

Version 2.5, authors: Matt Walker, Ilya Kuprov