Pulse Sequences

NMR Pulse Sequences for BRUKER Spectrometers

  1. MQ-(H)CCmHm-TOCSY
  2. MQ-H(C)CmHm-TOCSY
  3. MQ-(H)CCH-nct-TOCSY
  4. diagonal-suppressed 15N-edited NOESY
  5. Interface_RHz
  6. 4D 13C,15N-edited NOESY
  7. Simultaneously 13C,15N-edited NOESY (3D)
  8. CH3_crossJ
  9. CH3 T1
  10. 3D TROSY HNCA ( for fully protonated samples )
  11. 3D TROSY HN(CO)CA ( for fully protonated samples )
  12. 4D time-shared NOESY

 

1 MQ-(H)CCmHm-TOCSY
Description correlates methyl 1H/13C with all aliphatic 13C spins in the same residue through a 13C TOCSY mixing scheme
Reference Yang, Daiwen; Zheng, Yu; Liu, Dingjiang; Wyss, Daniel F. Sequence-specific assignments of methyl groups in high-molecular weight proteins. Journal of the American Chemical Society (2004), 126(12), 3710-3711.
Download hcch3 tocsy with parameters

 

2 MQ-H(C)CmHm-TOCSY
Description correlates methyl 1H/13C with all aliphatic 1H spins in the same residue through a 13C TOCSY mixing scheme
Reference Zheng, Yu; Giovannelli, Janel L.; Ho, Nancy T.; Ho, Chien; Yang, Daiwen. Side-chain assignments of methyl-containing residues in a uniformly 13C-labeled hemoglobin in the carbonmonoxy form. Journal of Biomolecular NMR (2004), 30(4), 423-429.
Download  hcch3 h tocsy with parameters

 

3 MQ-(H)CCH-nct-TOCSY
Description The sequence is used for the assignment of aliphatic side-chain resonances. It can also be used for the assignment of Leu methyl groups with strong coupling effects or methyl assignment in the case where sensitivity is an issue.
Reference

Zheng, Yu; Giovannelli, Janel L.; Ho, Nancy T.; Ho, Chien; Yang, Daiwen. Side-chain assignments of methyl-containing residues in a uniformly 13C-labeled hemoglobin in the carbonmonoxy form. Journal of Biomolecular NMR (2004), 30(4), 423-429.

Xu, Yingqi; Lin, Zhi; Chien, Ho; Yang, Daiwen. A general strategy for the assignment of aliphatic side-chain resonances of uniformly 13C,15N-labeled large proteins, Journal of the American Chemical Society(2005), 127(34): 11920 – 11921.

Download mqtocsy (Sequence, Parameters and NMRpipe Script)

 

4 diagonal-suppressed 15N-edited NOESY
Description 15N-edited NOESY spectra: one with only diagonal peaks and one with both diagonals and cross-peaks. The difference spectrum contains no diagonal peaks. The data sets should be separated and subtracted before processing using the scripts attached here.
Reference Wu, Jihui; Fan, Jing-song; Pascal, Steven M.; Yang, Daiwen. General method for suppression of diagonal peaks in heteronuclear-edited NOESY spectroscopy. Journal of the American Chemical Society (2004), 126(46), 15018-15019.
Download N15 NOESY noD (Sequence, Parameters and NMRpipe Scripts)

 

5 Interface_RHz
Description Measurement of amide proton longitudinal relaxation time with suppression of cross-relaxation between amide and aliphatic protons and NH-H2O exchange effect. Using this experiment, one can map out protein-protein interaction interfaces.
Reference Sui, Xiaogang; Xu, Yingqi; Giovannelli, Janel L.; Ho, Nancy T.; Chien, Ho, Yang, Daiwen. Mapping protein-protein interface on the basis of proton density difference. Angewandte Chemie International Edition (2005), 44(32):5141-5144
Download protein-protein interface (pulse and parameters)

 

6 4D 13C,15N-edited NOESY
Description It is a HMQC-NOESY-HSQC experiment. It is optimized for fully protonated proteins > 20 kDa. One can use it to assign either side-chain resonances based on prior backbone assignment of large proteins. One can also use it to do de nevo resonance assignment of large proteins without deuteration. Of course, the experiment provides NOEs for structure determination.
Reference

Xu, Yingqi; Zheng, Yu; Fan, Jing-song; Yang, Daiwen. A novel strategy for structure determination of large proteins without deuteration, Nature Methods(2006),3(11): 931-937.

Xu, Yingqi; Lin, Zhi; Chien, Ho; Yang, Daiwen. A general strategy for the assignment of aliphatic side-chain resonances of uniformly 13C,15N-labeled large proteins, J. Am. Chem. Soc(2005), 127(34):11920 – 11921.

Download  noesy-nc-4d

 

7 Simultaneously 13C,15N-edited NOESY (3D)
Description Using this experiment, one can obtain two 3D spectra: 13C-edited NOESY and 15N-edited NOESY.� These two spectra are obtained from the addition and subtruction of two data sets recorded in an interleaved manner. Aromatic resonances can be assigned with this experiment.
Reference Lin, Zhi; Xu, Yingqi; Yang, Shuai; Yang, Daiwen. Sequence-Specific Assignment of Aromatic Resonances of Uniformly 13C,15N-Labeled Proteins with Use of 13C- and 15N-edited NOESY Spectra, Angew. Chem. Int. Ed. Engl(2006), 45:1960-1963
Download nc 3d noesy

 

8 CH3_crossJ
Description Measurement of methyl C-H/C-H cross-correlated relaxation. It is a 2D 1H-13C HSQC-type experiment.
Reference Zhang, Xu; Sui, Xiaogang; Yang, Daiwen. Probing methyl dynamics from 13C auto- and cross-correlated relaxation, Journal of the American Chemical Society(2006), 128(15):5073- 5081
Download  ch3_crossj

 

9 CH3 T1
Description Measurement of methyl 13C T1. It is a 2D 1H-13C HSQC-type experiment.
Reference Zhang, Xu; Sui, Xiaogang; Yang, Daiwen. Probing methyl dynamics from 13C auto- and cross-correlated relaxation, Journal of the American Chemical Society(2006), 128(15):5073- 5081
Download  CH3C T1

 

10 3D TROSY HNCA ( for fully protonated samples )
Description Using 3D TROSY-HNCA, 3D MQ-(H)CCH-TOCSY & 4D 13C,15N-edited NOESY, one can assign backbone & sidechain resonances of large proteins without deuteration.
Reference Xu, Yingqi; Zheng, Yu; Fan, Jing-song; Yang, Daiwen. A novel strategy for structure determination of large proteins without deuteration, Nature Methods(2006),3(11): 931-937.
Download  trosy hnca h

 

11 3D TROSY HN(CO)CA ( for fully protonated samples )
Description Using 3D TROSY-HN(CO)CA together with TROSY-HNCA, 3D MQ-(H)CCH-TOCSY & 4D 13C,15N-edited NOESY, one can assign backbone & sidechain resonances of large proteins without deuteration
Reference Xu, Yingqi; Zheng, Yu; Fan, Jing-song; Yang, Daiwen. A novel strategy for structure determination of large proteins without deuteration, Nature Methods(2006),3(11): 931-937
Download  trosyhncoca_h

 

12 4D time-shared NOESY
Description Four 4D NOESY spectra: 15N,15N-edited, 15N,13C-edited, 13C-15N-edited and 13C,13C-edited NOESY are recorded simultaneously in a single experiment. It can be applied to small and large 13C,15N-labeled proteins.
Reference Xu, Yingqi; Long, Dong; Yang, Daiwen. Rapid data collection for protein structure determination by NMR spectroscopy, Journal of the American Chemical Society (2007), 129(25): 7722-7723.
Download  noesy4d