Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar couplings--an assessment of the interrelation of NMR restraints.
We have examined how the hydrogen bond geometry in three different proteins is affected when structural restraints based on measurements of residual dipolar couplings are included in the structure calculations. The study shows, that including restraints based solely on (1)H(N)-(15)N residual dipolar couplings has pronounced impact on the backbone rmsd and Ramachandran plot but does not improve the hydrogen bond geometry. In the case of chymotrypsin inhibitor 2 the addition of (13)CO-(13)C(alpha) and (15)N-(13)CO one bond dipolar couplings as restraints in the structure calculations improved the hydrogen bond geometry to a quality comparable to that obtained in the 1.8 A resolution X-ray structure of this protein. A systematic restraint study was performed, in which four types of restraints, residual dipolar couplings, hydrogen bonds, TALOS angles and NOEs, were allowed in two states. This study revealed the importance of using several types of residual dipolar couplings to get good hydrogen bond geometry. The study also showed that using a small set of NOEs derived only from the amide protons, together with a full set of residual dipolar couplings resulted in structures of very high quality. When reducing the NOE set, it is mainly the side-chain to side-chain NOEs that are removed. Despite of this the effect on the side-chain packing is very small when a reduced NOE set is used, which implies that the over all fold of a protein structure is mainly determined by correct folding of the backbone.
Jensen
Pernille Rose
PR
Institute of Molecular Biology, University of Copenhagen, Øster Farimagsgade 2A, DK-1353 Copenhagen K, Denmark.
Axelsen
Jacob Bock
JB
Lerche
Mathilde Hauge
MH
Poulsen
Flemming M
FM
D026261:Diazepam Binding Inhibitor / Q000737:chemistry; D006860:Hydrogen Bonding; D015394:Molecular Structure; D019006:Neural Cell Adhesion Molecules / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010455:Peptides / Q000737:chemistry; D010940:Plant Proteins; D011506:Proteins / Q000737:chemistry*
D026261:Diazepam Binding Inhibitor; D019006:Neural Cell Adhesion Molecules; D010455:Peptides; D010940:Plant Proteins; D011506:Proteins; C093336:chymotrypsin inhibitor 2