Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions.
Protein-protein interactions are often studied by chemical shift mapping using solution NMR spectroscopy. When heteronuclear data are available the interaction interface is usually predicted by combining the chemical shift changes of different nuclei to a single quantity, the combined chemical shift perturbation Deltadelta comb In this paper different procedures (published and non-published) to calculate Deltadelta comb are examined that include a variety of different functional forms and weighting factors for each nucleus. The predictive power of all shift mapping methods depends on the magnitude of the overlap of the chemical shift distributions of interacting and non-interacting residues and the cut-off criterion used. In general, the quality of the prediction on the basis of chemical shift changes alone is rather unsatisfactory but the combination of chemical shift changes on the basis of the Hamming or the Euclidian distance can improve the result. The corrected standard deviation to zero of the combined chemical shift changes can provide a reasonable cut-off criterion. As we show combined chemical shifts can also be applied for a more reliable quantitative evaluation of titration data.
Schumann
Frank H
FH
Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany.
Riepl
Hubert
H
Maurer
Till
T
Gronwald
Wolfram
W
Neidig
Klaus-Peter
KP
Kalbitzer
Hans Robert
HR
D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D002417:Cattle; D002918:Chymotrypsin / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular; D010059:Ovomucin / Q000737:chemistry; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D012680:Sensitivity and Specificity
D000596:Amino Acids; D010059:Ovomucin; D002918:Chymotrypsin; C117608:alpha-chymotrypsin