Mapping of protein structural ensembles by chemical shifts.
Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift prediction methods are optimized to predict the lowest energy ground state structure that is only weakly populated at physiological temperatures. An analysis of the data shows that a chemical shift prediction can be used as measure to define the minimum size of the structural bundle required for a faithful description of the structural ensemble.
Baskaran
Kumaran
K
Department of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Federal Republic of Germany.
Brunner
Konrad
K
Munte
Claudia E
CE
Kalbitzer
Hans Robert
HR
D000465:Algorithms; D002244:Carbon / Q000737:chemistry; D006859:Hydrogen / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D015203:Reproducibility of Results; D013696:Temperature
D011506:Proteins; D002244:Carbon; D006859:Hydrogen