In many cases of protein structure determination by NMR a high-quality structure is required. An important contribution to structural precision is stereospecific assignment of magnetically nonequivalent prochiral methylene and methyl groups, eliminating the need for introducing pseudoatoms and pseudoatom corrections in distance restraint lists. Here, we introduce the stereospecific assignment program that uses the resonance assignment, a preliminary 3D structure and 2D and/or 3D nuclear Overhauser effect spectroscopy peak lists for stereospecific assignment. For each prochiral group the algorithm automatically calculates a score for the two different stereospecific assignment possibilities, taking into account the presence and intensity of the nuclear Overhauser effect (NOE) peaks that are expected from the local environment of each prochiral group (i.e., the close neighbors). The performance of the algorithm has been tested and used on NMR data of -helical and -sheet proteins using homology models and/or X-ray structures. The program produced no erroneus stereospecific assignments provided the NOEs were carefully picked and the 3D model was sufficiently accurate. The set of NOE distance restraints produced by nmr2st using the results of the SSA module was superior in generating good-quality ensembles of NMR structures (low deviations from upper limits in conjunction with low root-mean-square-deviation values) in the first round of structure calculations. The program uses a novel approach that employs the entire 3D structure of the protein to obtain stereospecific assignment; it can be used to speed up the NMR structure refinement and to increase the quality of the final NMR ensemble even when no scalar or residual dipolar coupling information is available.
Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data / Pristovsek, P.; Franzoni, Lorella. - In: JOURNAL OF COMPUTATIONAL CHEMISTRY. - ISSN 0192-8651. - 27 (6):(2006), pp. 791-797. [10.1002/jcc.20389]
Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data
FRANZONI, Lorella
2006-01-01
Abstract
In many cases of protein structure determination by NMR a high-quality structure is required. An important contribution to structural precision is stereospecific assignment of magnetically nonequivalent prochiral methylene and methyl groups, eliminating the need for introducing pseudoatoms and pseudoatom corrections in distance restraint lists. Here, we introduce the stereospecific assignment program that uses the resonance assignment, a preliminary 3D structure and 2D and/or 3D nuclear Overhauser effect spectroscopy peak lists for stereospecific assignment. For each prochiral group the algorithm automatically calculates a score for the two different stereospecific assignment possibilities, taking into account the presence and intensity of the nuclear Overhauser effect (NOE) peaks that are expected from the local environment of each prochiral group (i.e., the close neighbors). The performance of the algorithm has been tested and used on NMR data of -helical and -sheet proteins using homology models and/or X-ray structures. The program produced no erroneus stereospecific assignments provided the NOEs were carefully picked and the 3D model was sufficiently accurate. The set of NOE distance restraints produced by nmr2st using the results of the SSA module was superior in generating good-quality ensembles of NMR structures (low deviations from upper limits in conjunction with low root-mean-square-deviation values) in the first round of structure calculations. The program uses a novel approach that employs the entire 3D structure of the protein to obtain stereospecific assignment; it can be used to speed up the NMR structure refinement and to increase the quality of the final NMR ensemble even when no scalar or residual dipolar coupling information is available.File | Dimensione | Formato | |
---|---|---|---|
Pristovsek J Comp Chem 2006 27 791-797.pdf
non disponibili
Tipologia:
Documento in Post-print
Licenza:
Creative commons
Dimensione
237.07 kB
Formato
Adobe PDF
|
237.07 kB | Adobe PDF | Visualizza/Apri Richiedi una copia |
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.