Article

Crystal structure of the PB1 domain of NBR1.

EMBL-Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.
FEBS Letters (Impact Factor: 3.34). 02/2006; 580(1):341-4. DOI: 10.1016/j.febslet.2005.12.021
Source: PubMed

ABSTRACT The scaffold protein NBR1 is involved in signal transmission downstream of the serine/protein kinase from the giant muscle protein titin. Its N-terminal Phox and Bem1p (PB1) domain plays a critical role in mediating protein-protein interactions with both titin kinase and with another scaffold protein, p62. We have determined the crystal structure of the PB1 domain of NBR1 at 1.55A resolution. It reveals a type-A PB1 domain with two negatively charged residue clusters. We provide a structural perspective on the involvement of NBR1 in the titin kinase signalling pathway.

1 Bookmark
 · 
92 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: Bem1 and Cdc24 of the budding yeast Saccharomyces cerevisiae interact with each other through PB1-PB1 heterodimer formation to regulate the establishment of cell polarity. Here we present the tertiary structure of the heterodimer of Bem1 and Cdc24 PB1 domains determined by NMR spectroscopy. To avoid ambiguity in the NMR spectral analysis, we first prepared a mutant of the Cdc24 PB1 domain that had truncated loops. The mutant provided well dispersed spectra without spectral overlapping, thus allowing unambiguous spectral assignments for structure determination. We confirmed that the loop deletion-mutant was quite similar to the wild-type in both 3D structure and binding affinity. The NMR structure of the heterodimer of the deletion-mutant of Cdc24 PB1 and Bem1 PB1 was determined using a variety of isotope labelled samples including perdeuteration. The interface between the Bem1/Cdc24 PB1 heterodimer was analysed at atomic resolution. Through a comparison with the tertiary structures of other PB1-PB1 heterodimers, we found that conserved electrostatic properties on the molecular surface were commonly used for PB1-PB1 interaction, but hydrophobic interactions were important for cognate interaction in Bem1/Cdc24 PB1 heterodimer formation.
    Journal of Biochemistry 06/2009; 146(3):317-25. · 3.07 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The dynamics of the Phox and Bem1p (PB1) domain, which adopts an ubiquitin-like β-grasp fold, have been simulated using two implicit solvent models (GBSW and EEF1.1) and two force fields (CHARMM19 and 22). The protein undergoes a large re-orientation using EEF1.1 with the CHARMM19 force field. This computational model is often applied in folding simulations. However, the conformational dynamics generated using EEF1.1 with the CHARMM22 force field are similar to those in the GBSW simulations and do not show any large re-orientation. These findings underscore the care needed in the selection of, not only the implicit solvent model, but also an appropriate protein force field.
    Chemical Physics Letters 10/2011; 515(s 4–6):283–289. · 1.99 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The PB1 domain of NBR1 folds via a single pathway mechanism involving two sequential energy barriers separated by a high-energy intermediate. The structural ensemble representing each of the two transition states (TS1 and TS2) has been calculated using experimental Φ values and biased molecular dynamics simulations. Both TS1 and TS2 represent compact states (β(TS1) = 0.71, and β(TS2) = 0.93) but are defined by quite different distributions of Φ values, degrees of structural heterogeneity, and nativelike secondary structure. TS1 forms a heterogeneous ensemble of dynamic structures, representing a global collapse of the polypeptide chain around a set of weak nativelike contacts. In contrast, TS2 has a high proportion of nativelike secondary structure, which is reflected in an extensive distribution of high Φ values. Two snapshots along the folding pathway of the PB1 domain reveal insights into the malleability, the solvent accessibility, and the timing of nativelike core packing that stabilizes the folded state.
    Biochemistry 12/2010; 50(1):125-35. · 3.38 Impact Factor