A probabilistic approach for validating protein NMR chemical shift assignments.
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.
Wang
Bowei
B
Shanghai American School Pudong, 201201, San Jia Gang, Pudong, Shanghai, People's Republic of China.
Wang
Yunjun
Y
Wishart
David S
DS
D000595:Amino Acid Sequence; D015233:Models, Statistical; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software; D014584:User-Computer Interface
D011506:Proteins
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