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J Magn Reson. 2012 Sep;222:96-104. doi: 10.1016/j.jmr.2012.07.001. Epub 2012 Jul 14.

Influence of ¹H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins.

Author information

1
Graduate Institute of Natural Products and Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan. yjlin@kmu.edu.tw

Abstract

Homodimeric proteins pose a difficulty for NMR structure determination because the degeneracy of the chemical shifts in the two identical monomers implies an ambiguity in all assignments of distance restraints. For homodimeric proteins, residues involved in the interface between two monomers provide essential intermolecular NOEs. The structure determination of homodimeric proteins hence relies strongly on chemical shift assignments of these interface residues. Our paper discusses the influence of the extent of (1)H chemical shift assignments of interface residues on the structure determinations of homodimeric proteins using the CYANA program. The results reveal that successful structure determinations of homodimeric proteins with automated NOE assignment depend on the percentage of assigned interface residues and that a high completeness of around 80-90% of the (1)H chemical shift assignment in the interface is needed for reliable NMR structure determinations of homodimeric proteins for which no experimental distinction between intra- and intermolecular NOEs, e.g. by filtered NOESY experiments, is available. Our results also show that RMSD and target function values are insufficient to judge the quality of homodimeric structures determined using automated NOE assignment. Structure determinations of homodimeric proteins by NMR using conventional NOESY experiments are thus possible but more challenging than for monomeric proteins.

PMID:
22858667
DOI:
10.1016/j.jmr.2012.07.001
[Indexed for MEDLINE]

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