Some NMR experiments and a structure determination employing a [15N,2H] enriched protein.
We present the results of studies of an aqueous sample of a highly [15N,2H] enriched protein, the SH3 domain from Fyn. Measurements of 1H relaxation and interactions between H2O solvent and exchangeable protons are given, as well as a method for increasing the effective longitudinal relaxation of solvent exchangeable proton resonances. The long-range isotope shifts are measured, for 1H and 15N, which arise due to perdeuteration. Simulations, which employed a 7 or 8 spin relaxation matrix analysis, were compared to the experimental data from a time series of 2D NOESY datasets for some resonances. The agreement between experiment and simulation suggest that, with this 1H dilute sample, relatively long mixing times (up to 1.2 s) can be used to detect specific dipolar interactions between amide protons up to about 7A apart. A set of 155 inter-amide NOEs and 7 side chain NOEs were thus identified in a series of 3D HSQC-NOESY-HSQC experiments. These data, alone and in combination with previously collected restraints, were used to calculate sets of structures using X-PLOR. These results are compared to the available X-ray and NMR structures of the Fyn SH3 domain.
Mal
T K
TK
Oxford Centre for Molecular Sciences, University of Oxford, UK.
Matthews
S J
SJ
Kovacs
H
H
Campbell
I D
ID
Boyd
J
J
D000577:Amides / Q000737:chemistry; D000595:Amino Acid Sequence; D003903:Deuterium; D004926:Escherichia coli / Q000235:genetics; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008969:Molecular Sequence Data; D009587:Nitrogen Isotopes; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011505:Protein-Tyrosine Kinases / Q000737:chemistry* / Q000235:genetics; D011518:Proto-Oncogene Proteins / Q000737:chemistry* / Q000235:genetics; D051076:Proto-Oncogene Proteins c-fyn; D011522:Protons; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics; D012997:Solvents; D014867:Water; D018909:src Homology Domains
D000577:Amides; D009587:Nitrogen Isotopes; D011518:Proto-Oncogene Proteins; D011522:Protons; D011994:Recombinant Proteins; D012997:Solvents; D014867:Water; D003903:Deuterium; D011505:Protein-Tyrosine Kinases; D051076:Proto-Oncogene Proteins c-fyn