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.

1H
gyromagnetic ratio
carrier frequency (MHz)
carrier shift (ppm)
Values for the gyromagnetic ratios were obtained from the BMRB but may be edited if you wish to use different values.

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.

protein 2H
DNA 13C
RNA 15N

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.

This calcluator will calculate MW given tauM and vice versa.
Molecular weight (kDa)
Correlation time (ns)

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 30oC

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 2015-Feb-2

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