The solution structure of an N-terminally truncated version of the yeast CDC24p PB1 domain shows a different beta-sheet topology.

Phox and Bem1 (PB1) domains mediate protein-protein interactions via the formation of homo- or hetero-dimers. The C-terminal PB1 domain of yeast cell division cycle 24 (CDC24p), a guanine-nucleotide exchange factor involved in cell polarity establishment, is known to interact with the PB1 domain occurring in bud emergence MSB1 interacting 1 (BEM1p) during the regulation of the yeast budding process via its OPR/PC/AID (OPCA) motif. Here, we present the structure of an N-terminally truncated version of the Sc CDC24p PB1 domain.

Quantitative study of the effects of chemical shift tolerances and rates of SA cooling on structure calculation from automatically assigned NOE data.

The calculation of protein structures from nuclear magnetic resonance (NMR) data has been greatly facilitated by improvements in software for the automatic assignment of NOESY spectra. Nevertheless, for larger proteins, resonance overlap may lead to an overwhelming number of assignment options per peak. Although most software for automatic NOESY assignment can deal with a certain level of assignment ambiguity, structure calculations fail when this becomes too high.

Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data.

Large-scale protein structure determination by NMR via automatic assignment of NOESY spectra requires the adjustment of several parameters for optimal performance. Among those are the chemical shift tolerance windows (delta), which allow for the compensation of badly matching chemical shifts in the assignment-list and peak-lists, and the maximum number of assignment possibilities allowed per peak (n(max)). Here, we test the influence of different values for Delta and n(max) on the performance of automated assignment of NOESY spectra by ARIA.