Dec 18, 2024

Public workspaceC_CACO_IPAP.nan

DOI
dx.doi.org/10.17504/protocols.io.kxygxy3bkl8j/v1
  • NAN KB1,
  • Alex Eletsky2,
  • John Glushka2
  • 1Network for Advanced NMR ( NAN);
  • 2University of Georgia
NAN-KB UGA
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DOI: dx.doi.org/10.17504/protocols.io.kxygxy3bkl8j/v1
Protocol Citation: NAN KB, Alex Eletsky, John Glushka 2024. C_CACO_IPAP.nan. protocols.io https://dx.doi.org/10.17504/protocols.io.kxygxy3bkl8j/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: May 27, 2024
Last Modified: December 18, 2024
Protocol Integer ID: 100680
Keywords: protein nmr, assignment, backbone, amides, 15N, hsqc
Funders Acknowledgements:
NSF
Grant ID: 1946970
Disclaimer
This protocol is part of the knowledge base content of NAN: The Network for Advanced NMR ( https://usnan.nmrhub.org/ )
Specific filenames, paths, and parameter values apply to spectrometers in the NMR facility of the Complex Carbohydrate Research Center (CCRC) at the University of Georgia.
Abstract
This protocol describes running a 2D carbon detected CACO_IPAP pulse sequence which correlates CA(i) carbons with CO(i) carbons.
It yields two 2D sub-spectra, so use 'splitcomb ipap 2' to process in Topspin.

15N and 13C labeling are required.

It uses the Topspin library pulseprogram 'c_caco_ia'.


Attachments
Icon for biotop.pdf
biotop.pdf
2.5MB
Icon for NUS_poisson_gap_files.zip
NUS_poisson_gap_file...
12KB
Guidelines
NUS sampling is usually not required for 2D experiments, since time savings are small, unless running multiple 2D experiments. If using NUS keep sampling amount ~30-50%.

For processing in TopSpin use 'splitcomb ipap 2' command to extract individual sub-spectra.
Before start
A sample must be inserted in the magnet either locally by the user after training, or by facility staff if running remotely.

This protocol requires a sample is locked, tuned/matched on 1H, 13C and 15N channels, and shimmed. At a minimum, 1H 90° pulse width and offset O1 should be calibrated and a 1D proton spectrum with water suppression has been collected according to the protocol PRESAT_bio.nan. Prior acquisition of a 2D 13C- HSQC and 3D HNCO are also recommended, according to protocols HSQC_13C.nan and HNCO_3D.nan.

General aspects of the use of the bioTop module are described in more detail in the protocols listed below.

It is recommended to calibrate 1H carrier offset, 1H H2O selective flip-back pulse, as well as 1H, 13C, and 15N 90° pulse widths using the "Optimization" tab of BioTop. Alternatively, 1H 90° pulse width and offset can be calibrated using other methods, such as pulsecal or calibo1p1. Additional parameters, like 15N and 13C offsets and spectral width can be either optimized or manually entered in the "Optimization" tab of BioTop. Note that since BioTop optimizations are saved in the dataset folder, all experiments should be created under the same dataset name when using BioTop for acquisition setup.

Refer to protocols
  1. Acquisition Setup Workflow, Solution NMR Structural Biology
  2. PRESAT_bio.nan
  3. HSQC_13C.nan
  4. HNCO_3D.nan
  5. Biotop-Calibration and Acquisition setup

Create C_CACO_IPAP experiment file
Create C_CACO_IPAP experiment file
Start with existing dataset containing 1D proton or 13C-HSQC, or 15N-HSQC data for this sample.
Open create dataset window with edc command or through menu.
Edit text in Title box.
To select starting parameter set, check 'Read parameterset' box, and click Select.
For standard NAN parameter sets, change the Source directory at upper right corner of the window:
Source = /opt/NAN_SB/par
Click 'Select' to bring up list of parameter sets.
Select C_CACO_IPAP_xxx.par, where xxx=900,800 or 600.
Click OK at bottom of window to create the new EXPNO directory.
If not previously done, tune Nitrogen and Carbon channels.
Return to the 'Acquire' menu and click 'Tune' ( or type atma on command line).
Calibrate pulses and adjust parameters
Calibrate pulses and adjust parameters
Note
Loading the C_CACO_IPAP_xxx.par parameter set enters the default parameters into the experiment directory. While they represent a good starting point, they may not be fully optimal or accurate for your particular sample or spectrometer hardware. The probe- and solvent-specific parameters, specifically the 1H 90° pulse length, and possibly the 13C and 15N 90° pulse lengths, along with other dependent pulse widths and powers may need to be updated.

There are two ways of automatically updating experimental parameters:
1) Use getprosol command, which typically only updates proton pulse widths and power levels. It is most useful for running routine experiments using the default parameters.
2) Or use bioTop module that organizes calibrated and defined parameters for a dataset.

Loading pulse widths and power levels with getprosol:

Use the calibrated proton P1 value obtained from the proton experiment ( protocol PRESAT_bio.nan) and note the standard power level attenuation in dB for P1 (PLW1); otherwise type calibo1p1 and wait till finished.

Then execute the getprosol command:
getprosol 1H [ calibrated P1 value] [power level for P1]
e.g. getprosol 1H 9.9 -13.14.
Where for example, the calibrated P1=9.9 at power level -13.14 dB attenuation
This also loads 15N and 13C pulse widths and power levels from the PROSOL table, and are assumed to be sufficiently accurate.

Go togo to step #2.3 If not using BioTop
Loading experimental parameters from BioTop:

If you previously performed parameter calibrations using the "Optimizations" tab of the BioTop GUI, or entered parameters manually in the "Optimizations" tab, you can type btprep at the command line.

See protocol 'BioTop: calibration and acquisition setup' and attached Bruker manual 'biotop.pdf' for details.
Inspect and adjust parameters
Inspect and adjust parameters
Examine parameters by typing 'eda', or select the 'Acqpars' tab and get the 'eda' window by clicking on the 'A' icon. This view shows the two dimensions, F2 (13CO) and F1 (13CA) in columns.
Parameters to check:

  • FnTYPE - 'traditional planes' or 'non-uniform sampling' ( see step 2.5 below )
  • NS - Multiple of 4; increase for for higher signal to noise ( S/N increases as square root of NS )
  • DS - 32-128 'dummy' scans that are not recorded (multiple of 32); allows system to reach steady state equilibration.
  • 2 TD - Number of 13CO time domain real points (~512-2048, preferably 2N, keep 2 AQ at ~50-200 ms)
  • 1 TD - Number of 13CA time domain real points, 1 AQ ~12 ms (TopSpin 4.x) or ~24 ms (TopSpin 3.x). Limited by JCA,CB coupling, semi-CT dimension. Note that in TopSpin 3.x the inner IPAP loop counts toward the TD points.
  • 2 SW - 13CO spectral width (~20 ppm, defined in BioTop)
  • 1 SW - 13CA spectral width (~40 ppm, defined in BioTop)
  • O1P - 13CO offset (~173 ppm, defined in BioTop)
  • O2P - 1H offset (~4.7 ppm, defined in BioTop)
  • O3P - 15N amide offset (~122 ppm, defined in bioTop)


Then examine the parameters in Acqpars 'ased' window (click 'pulse' icon), or type ased.
Most of the default parameters should be appropriate, however it is recommended to compare values in the fields against those proposed by the original parameter file and the pulseprogram comments.
  • CNST21 - 13CO offset (~173 ppm, same as O1P, defined in BioTop)
  • CNST22 - 13CA offset (~48 ppm, defined in BioTop)
  • P3 - 1H 90º high power pulse (calibrated with calibo1p1 or BioTop)
  • CPDPRG2 - 1H decoupling (garp)
  • P21 - 15N 90º high power pulse (calibrated with BioTop)
  • CPDPRG3 - 15N decoupling (garp or garp4)
Acquire and Process Data
Acquire and Process Data
Type 'expt' to calculate the expected run time
Go togo to step #2.3 If necessary to re-adjust parameters

Type 'rga' or click on 'Gain' in Topspin Acquire menu to execute automatic gain adjustment.
Type 'zg' or click on 'Run' in Topspin Acquire menu to begin acquisition.
You can always check the first FID by typing 'efp' to execute an exponential multiplied Fourier transform. It will ask for a FID #, choose the default #1. You can evaluate the 1D spectrum for amide proton signal to noise and water suppression.
2D planes with NUS or uniformly sampled can be processed with Topspin: xfb
Protocol references
J.Cavanaugh, W.Fairbrother, A.Palmer, N.Skelton: Protein NMR Spectroscopy: Principles and Practice.
Academic Press 2006 ; Hardback ISBN: 97801216449189, eBook ISBN: 9780080471037

R.T. Clubb, V. Thanabal & G. Wagner, J. Magn. Reson. 97, 213-217 (1992)
L.E. Kay, G.Y. Xu & T. Yamazaki, J. Magn. Reson. A109, 129-133 (1994)

'nusPGSv8' written by Scott Anthony Robson 2013