Article

Journal of Biomolecular NMR

, Volume 47, Issue 2, pp 85-99

First online:

A probabilistic approach for validating protein NMR chemical shift assignments

  • Bowei WangAffiliated withShanghai American School Pudong
  • , Yunjun WangAffiliated with
  • , David S. WishartAffiliated withDepartments of Computing Science and Biological Sciences, University of Alberta Email author 

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Abstract

It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3–6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called “Probabilistic Approach for protein Nmr Assignment Validation (PANAV)” and as a web server (http://​redpoll.​pharmacy.​ualberta.​ca/​PANAV) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.

Keywords

NMR Protein chemical shift Chemical shift assignment Chemical shift assignment validation BioMagResBank (BMRB)