Use of very long-distance NOEs in a fully deuterated protein: an approach for rapid protein fold determination.
The high sensitivity of modern NMR instrumentation, in combination with full deuteration, enabled the measurement of long-range NOEs between amide protons in a fully deuterated protein corresponding to distances up to 8A. These are beyond the limit normally observed in protonated samples. Such long-distance NOEs could be observed using long mixing times, which became possible due to reduced spin diffusion and T1 relaxation of the amide protons in the fully deuterated sample. This information was used in combination with secondary structure restraints derived from secondary chemical shifts for structure calculations. With these backbone amide proton NOEs only, a unique fold could be obtained with positional root mean square deviations from the average of 1.30 and 2.25 A for backbone and heavy atoms, respectively. Despite the low density of restraints, no mirror image problems were observed. Addition of sidechain NOE information increased the precision of the ensemble and in particular of the core packing. The structures obtained in this way were close to the published crystal structure. NOE completeness analysis revealed that the cumulative completeness is still more than 80% for an 8.0 A cut-off distance.
Koharudin
Leonardus M I
LM
Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
Bonvin
Alexandre M J J
AM
Kaptein
Robert
R
Boelens
Rolf
R
D000577:Amides / Q000737:chemistry*; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D003903:Deuterium / Q000737:chemistry; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D010940:Plant Proteins; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry; D011522:Protons; D012996:Solutions
D000577:Amides; D010455:Peptides; D010940:Plant Proteins; D011506:Proteins; D011522:Protons; D012996:Solutions; C093336:chymotrypsin inhibitor 2; D003903:Deuterium