Biomolecular NMR tools

Here are some tools to help with common biomolecular NMR chores.

Indirect referencing

Referencing of heteronuclear dimensions can be done indirectly by using the ratio of the gyromagnetic ratios of the heteronucleus and of ¹H and the frequency of the DSS resonance. You need to record a ¹H spectrum of a sample containing DSS so that you can obtain the chemical shift of the ¹H carrier frequency.

In the form below edit the ¹H carrier frequency and the ¹H chemical shift at this frequency. Next, select the heteronucleus to obtain its gyromagnetic ratio, enter the carrier frequency used for this heteronucleus, then click on the "Calculate carrier shift" button.

Isotopic labelling

To check that isotopic labelling has worked mass spectrometry is often used. To calculate the expected molecular weight with different labelling schemes use the calculator below.

Enter your sequence in the text box. It must be in single letter code and any non-standard letters will be ignored. Do not inculde a header or ID line. Define the nature of the sequence as protein, DNA or RNA. Select the isotopic labelling scheme. More than one can be selected. The calculator assumes 100% labelling of a selected nucleus. Unselected nuclei will use the natural abundance average atomic mass. Click on "Calculate MW" to run the calculation. The molecular formula and the mass will be reported. Note that the calculation assumes all cysteines are reduced.

Molecular weight vs correlation time

Measuring ¹⁵N relaxation rates of backbone amide N-H bonds enables the determination of the molecular correlation time (tauM), the rate at which a molecule tumbles within solution. Correlation time is related to the size of a molecule so by detemining tauM one can determine if a protein is monomeric or aggregated, folded or unfolded.

The calculator uses the relationship tauM = MW x 0.433859 + 0.775137 which was determined by fitting a straight line to 16 literature cases where correlation times were determined from model free analysis of NMR relaxation data.

The data used for the graph are tabulated below.

Protein	MW (kDa)	tauM (ns)	Reference
Xfin-31	2.9	1.88 ±0 .02	Palmer et al 1991 JACS
SH3 folded 30^oC	6.0	4.2	Farrow et al 1997 Biochemistry
Ubiquitin	8.5	4.03	Lienin et al 1998 JACS
Ubiquitin	8.5	4.1	Schneider et al 1992 Biochemistry
Calbindin D9K	8.5	4.25 ± 0.04	Kordel et al 1992 Biochemistry
SH2 domain bound	13.72	6.6 ± 0.3	Farrow et al 1994 Biochemistry
Interleukin 3	17.2	6.50 ± 0.04	Feng et al 1996 J Mol Biol
Glucose permease IIA	11.2	6.24 ± 0.01	Stone et al 1992 Biochemistry
Ribonuclease A	13.7	6.61 ± 0.01	Kovrigin et al 2003
Cellular RBP II	15.6	8.1	Lu et al 2003
Interleukin 1b	17.4	8.3 ± 0.05	Clore et al 1990 Biochemistry
Staphylococcal nuclease	18	9.1 ± 0.5	Kay et al 1989 Biochemistry
Leukemia Inhibitory Factor	20	9.75 ± 0.46	Yao et al 1998 J Magn Reson
Antibody NpN43C9	25	12.3	Kroon et al 2003
Maltose Binding protein	42	18.6	Tugarinov et al 2002 JACS
Malate Synthase G	81	36	Tugarinov et al 2002 JACS

Written by Brendan Duggan. Last modified 2022-Jul-22

Section 'Sub' Navigation:

	¹H
gyromagnetic ratio
carrier frequency (MHz)
carrier shift (ppm)

	protein	2H
	DNA	13C
	RNA	15N