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

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

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07-14-2012, 01:53 PM

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

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

Publication year: 2012
Source:Journal of Magnetic Resonance

Yi-Jan Lin, Donata K. Kirchner, Peter Güntert

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 1H 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 1H 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.
Graphical abstract

Graphical abstract Highlights

? Impact of interface assignment completeness on homodimer structure determination. ? CYANA can calculate homodimer structures with automated NOE assignment. ? About 80–90% complete shift assignment in the interface needed for homodimers. ? Target function and RMSD values are not sufficient to judge homodimer structures.

Source: Journal of Magnetic Resonance

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