Computer-assisted assignment of 2D 1H NMR spectra of proteins: basic algorithms and application to phoratoxin B.
A suite of computer programs (CLAIRE) is described which can be of assistance in the process of assigning 2D 1H NMR spectra of proteins. The programs embody a software implementation of the sequential assignment approach first developed by Wüthrich and co-workers (K. Wüthrich, G. Wider, G. Wagner and W. Braun (1982) J. Mol. Biol. 155, 311). After data-abstraction (peakpicking), the software can be used to detect patterns (spin systems), to find cross peaks between patterns in 2D NOE data sets and to generate assignments that are consistent with all available data and which satisfy a number of constraints imposed by the user. An interactive graphics program called CONPAT is used to control the entire assignment process as well as to provide the essential feedback from the experimental NMR spectra. The algorithms are described in detail and the approach is demonstrated on a set of spectra from the mistletoe protein phoratoxin B, a homolog of crambin. The results obtained compare well with those reported earlier based entirely on a manual assignment process.
Kleywegt
G J
GJ
Department of Chemistry, University of Utrecht, The Netherlands.
Boelens
R
R
Cox
M
M
Llinás
M
M
Kaptein
R
R
D000465:Algorithms; D000595:Amino Acid Sequence; D003196:Computer Graphics; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry; D011487:Protein Conformation; D012984:Software
D010940:Plant Proteins; C008873:phoratoxin protein, Phoradendron tomentosum