Floating stereospecific assignment revisited: application to an 18 kDa protein and comparison with J-coupling data.
We report a floating chirality procedure to treat nonstereospecifically assigned methylene or isopropyl groups in the calculation of protein structures from NMR data using restrained molecular dynamics and simulated annealing. The protocol makes use of two strategies to induce the proper conformation of the prochiral centres: explicit atom 'swapping' following an evaluation of the NOE energy term, and atom 'floating' by reducing the angle and improper force constants that enforce a defined chirality at the prochiral centre. The individual contributions of both approaches have been investigated. In addition, the effects of accuracy and precision of the interproton distance restraints were studied. The model system employed is the 18 kDa single-stranded DNA binding protein encoded by Pseudomonas bacteriophage Pf3. Floating chirality was applied to all methylene and isopropyl groups that give rise to non-degenerate NMR signals, and the results for 34 of these groups were compared to J-coupling data. We conclude that floating stereospecific assignment is a reliable tool in protein structure calculation. Its use is beneficial because it allows the distance restraints to be extracted directly from the measured peak volumes without the need for averaging or adding pseudoatom corrections. As a result, the calculated structures are of a quality almost comparable to that obtained with stereospecific assignments. As floating chirality furthermore is the only approach treating prochiral centres that ensures a consistent assignment of the two proton frequencies in a single structure, it seems to be preferable over using pseudoatoms or (R(-6)) averaging.
Folmer
R H
RH
Nijmegen SON Research Centeer, University of Nijmegen, The Netherlands.
Hilbers
C W
CW
Konings
R N
RN
Nilges
M
M
D000595:Amino Acid Sequence; D001435:Bacteriophages / Q000378:metabolism; D002151:Calorimetry; D004268:DNA-Binding Proteins / Q000096:biosynthesis / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011549:Pseudomonas / Q000821:virology
D004268:DNA-Binding Proteins