Protein GB1, ¹³C and ¹⁵N (I=1/2)

¹³C/¹⁵N (I=1/2) spinning sideband simulation.

The following is the spinning sideband simulation of a macromolecule, protein GB1. The \(^{13}\text{C}\) and \(^{15}\text{N}\) CSA tensor parameters were obtained from Hung et al. [1], which consists of 42 \(^{13}\text{C}\alpha\), 44 \(^{13}\text{CO}\), and 44 \(^{15}\text{NH}\) tensors. In the following example, instead of creating 130 spin systems, we download the spin systems from a remote file and load it directly to the Simulator object.

import matplotlib.pyplot as plt

from mrsimulator import Simulator
from mrsimulator.method.lib import BlochDecaySpectrum
from mrsimulator.method import SpectralDimension
from mrsimulator import signal_processor as sp

Create the Simulator object and load the spin systems from an external file.

sim = Simulator()

host = "https://ssnmr.org/sites/default/files/mrsimulator/"
filename = "protein_GB1_15N_13CA_13CO.mrsys"
sim.load_spin_systems(host + filename)  # load the spin systems.
print(f"number of spin systems = {len(sim.spin_systems)}")

Out:

number of spin systems = 130
all_sites = sim.sites().to_pd()
all_sites.head()
isotope isotropic_chemical_shift shielding_symmetric.zeta shielding_symmetric.eta
0 15N 123.33333333333333 ppm -118.66666666666667 ppm 0.101124
1 15N 121.66666666666667 ppm -115.33333333333333 ppm 0.225434
2 15N 125.33333333333333 ppm -110.66666666666667 ppm 0.000000
3 15N 125.33333333333333 ppm -110.66666666666667 ppm 0.126506
4 15N 126.0 ppm -114.0 ppm 0.192982


Create a \(^{13}\text{C}\) Bloch decay spectrum method.

method_13C = BlochDecaySpectrum(
    channels=["13C"],
    magnetic_flux_density=11.74,  # in T
    rotor_frequency=3000,  # in Hz
    spectral_dimensions=[
        SpectralDimension(
            count=8192,
            spectral_width=5e4,  # in Hz
            reference_offset=2e4,  # in Hz
            label=r"$^{13}$C resonances",
        )
    ],
)

Since the spin systems contain both \(^{13}\text{C}\) and \(^{15}\text{N}\) sites, let’s also create a \(^{15}\text{N}\) Bloch decay spectrum method.

method_15N = BlochDecaySpectrum(
    channels=["15N"],
    magnetic_flux_density=11.74,  # in T
    rotor_frequency=3000,  # in Hz
    spectral_dimensions=[
        SpectralDimension(
            count=8192,
            spectral_width=4e4,  # in Hz
            reference_offset=7e3,  # in Hz
            label=r"$^{15}$N resonances",
        )
    ],
)

Add the methods to the Simulator object and run the simulation

# Add the methods.
sim.methods = [method_13C, method_15N]

# Run the simulation.
sim.run()

# Get the simulation dataset from the respective methods.
dataset_13C = sim.methods[0].simulation  # method at index 0 is 13C Bloch decay method.
dataset_15N = sim.methods[1].simulation  # method at index 1 is 15N Bloch decay method.

Add post-simulation signal processing.

processor = sp.SignalProcessor(
    operations=[sp.IFFT(), sp.apodization.Exponential(FWHM="10 Hz"), sp.FFT()]
)
# apply post-simulation processing to dataset_13C
processed_dataset_13C = processor.apply_operations(dataset=dataset_13C).real

# apply post-simulation processing to dataset_15N
processed_dataset_15N = processor.apply_operations(dataset=dataset_15N).real

The plot of the simulation after signal processing.

fig, ax = plt.subplots(
    1, 2, subplot_kw={"projection": "csdm"}, sharey=True, figsize=(9, 4)
)

ax[0].plot(processed_dataset_13C, color="black", linewidth=0.5)
ax[0].invert_xaxis()

ax[1].plot(processed_dataset_15N, color="black", linewidth=0.5)
ax[1].set_ylabel(None)
ax[1].invert_xaxis()

plt.tight_layout()
plt.show()
plot 0 protein GB1

Total running time of the script: ( 0 minutes 1.943 seconds)

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