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posted Dec 03 '11 at 11:34

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sekhar Talluri
621

To generate a 2D 1H-15N HSQC spectrum you need information regarding chemical shifts of 1H and attached 15N nuclei, 1H-15N coupling constants and relaxation rates. You can generate a model 1H-15N HSQC spectrum from BMRB chemical shifts, if the chemical shifts of 15N nuclei in the proton and the attached protons have been assigned for the molecular (protein?) of interest. If information, regarding relaxation times is also available for the same protein in BMRB then you can calculate the linewidths. The 1J(1H-15N) coupling constant is fairly uniform for most backbone amides, and most peaks in the protein 1H-15N HSQC spectrum are from backbone amides. If information regarding relaxation times is not available in BMRB for the protein of interest and if you have a globular protein, and if its molecular weight is known, then you can predict T2's for backbone amides. As an initial approximation, you may neglect the effects of chemical exchange. For proteins, the molecular weight of the monomer can be easily calculated from knowledge of the amino-acid sequence (this information should be present in the BMRB data files) - the number of monomers in a molecule of the protein has to be determined experimentally. A number of spectral simulation programs are available, e.g., GAMMA from ETH group.
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posted Dec 03 '11 at 11:43

sekhar%20Talluri's gravatar image

sekhar Talluri
621

To generate simulate a 2D 1H-15N HSQC spectrum you will need information regarding chemical shifts of 1H and attached 15N nuclei, 1H-15N coupling constants and relaxation rates.rates/line-widths.

You can generate a model 1H-15N HSQC spectrum from BMRB chemical shifts, if the chemical shifts of ALL the 15N nuclei in the proton protein and the attached protons have been assigned for the molecular (protein?) of interest. If information, regarding relaxation times rates is also available for the same protein in BMRB then you can calculate the linewidths. You may find that for many BMRB data sets the 15N relaxation rates are available, but the corresponding relaxation rates for 1H are not available. The 1J(1H-15N) coupling constant is fairly uniform for most backbone amides, and the literature value should be fine for most peaks in the protein 1H-15N HSQC spectrum are from backbone amides.applications.

If information regarding relaxation times rates is not available in BMRB for the protein of interest and if you have a globular protein, and if its molecular weight is known, then you can predict T2's for backbone amides. As an initial approximation, you may neglect the effects of chemical exchange. For proteins, the molecular weight of the monomer can be easily calculated from knowledge of the amino-acid sequence (this information should be present in the BMRB data files) - the number of monomers in a molecule of the protein has to be determined experimentally.

A number of spectral simulation programs capable of generating 1H-15N HSQC spectra from chemical shifts, coupling constants and relaxation rates are available, e.g., GAMMA from ETH group.

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