Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data

Journal of Computational Chemistry
Primoz Pristovsek, Lorella Franzoni

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 alpha-helical and beta-sheet proteins using homology models and/or X-ray structures. The program produced no erroneous stereospecific assignments provided the NOEs were carefully picked and the 3D model was sufficiently accurate. The set of NOE distance restraints produced by nmr2st ...Continue Reading

References

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Mar 23, 2002·Journal of Computational Chemistry·Primoz PristovsekRoman Jerala
Apr 6, 2002·The Journal of Biological Chemistry·Lorella FranzoniHeinz Rüterjans
May 13, 2003·The Journal of Biological Chemistry·Primoz PristovsekFrank Bernhard
Dec 5, 2003·European Journal of Biochemistry·Vladimir V RogovHeinz Rüterjans
Feb 3, 2005·The Journal of Biological Chemistry·Bostjan JapeljRoman Jerala

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Citations

Oct 19, 2013·Journal of Biomolecular NMR·Julien OrtsPeter Güntert
Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Richard JangMing Li
Feb 18, 2011·Journal of Bioinformatics and Computational Biology·Babak AlipanahiMing Li
Dec 22, 2009·Journal of Biomolecular NMR·Dirk StratmannCarine van Heijenoort
Nov 29, 2015·Journal of Biomolecular NMR·Rafal AugustyniakFabien Ferrage
Jun 11, 2020·Journal of Natural Products·Kyoung Jin ParkKang Ro Lee

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