Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1

Retinoblastoma-binding protein 1 (RBBP1) is involved in gene regulation, epigenetic regulation, and disease processes. RBBP1 contains five domains with DNA-binding or histone-binding activities, but how RBBP1 specifically recognizes chromatin is still unknown. An AT-rich interaction domain (ARID) in RBBP1 was proposed to be the key region for DNA-binding and gene suppression. Here, we first determined the solution structure of a tandem PWWP-ARID domain mutant of RBBP1 after deletion of a long flexible acidic loop L12 in the ARID domain. NMR titration results indicated that the ARID domain interacts with DNA with no GC- or AT-rich preference. Surprisingly, we found that the loop L12 binds to the DNA-binding region of the ARID domain as a DNA mimic and inhibits DNA binding. The loop L12 can also bind weakly to the Tudor and chromobarrel domains of RBBP1, but binds more strongly to the DNA-binding region of the histone H2A-H2B heterodimer. Furthermore, both the loop L12 and DNA can enhance the binding of the chromobarrel domain to H3K4me3 and H4K20me3. Based on these results, we propose a model of chromatin recognition by RBBP1, which highlights the unexpected multiple key roles of the disordered acidic loop L12 in the specific binding of RBBP1 to chromatin.     

Crystal structure of yeast V1‐ATPase in the autoinhibited state

Vacuolar ATPases (V‐ATPases) are essential proton pumps that acidify the lumen of subcellular organelles in all eukaryotic cells and the extracellular space in some tissues. V‐ATPase activity is regulated by a unique mechanism referred to as reversible disassembly, wherein the soluble catalytic sector, V₁, is released from the membrane and its MgATPase activity silenced. The crystal structure of yeast V₁ presented here shows that activity silencing involves a large conformational change of subunit H, with its C‐terminal domain rotating ~150° from a position near the membrane in holo V‐ATPase to a position at the bottom of V₁ near an open catalytic site. Together with biochemical data, the structure supports a mechanistic model wherein subunit H inhibits ATPase activity by stabilizing an open catalytic site that results in tight binding of inhibitory ADP at another site.     

NMR reveals novel mechanisms of protein activity regulation

NMR spectroscopy is one of the most powerful tools for the characterization of biomolecular systems. A unique aspect of NMR is its capacity to provide an integrated insight into both the structure and intrinsic dynamics of biomolecules. In addition, NMR can provide site-resolved information about the conformation entropy of binding, as well as about energetically excited conformational states. Recent advances have enabled the application of NMR for the characterization of supramolecular systems. A summary of mechanisms underpinning protein activity regulation revealed by the application of NMR spectroscopy in a number of biological systems studied in the lab is provided.     

Structures of the Gasdermin D C-Terminal Domains Reveal Mechanisms of Autoinhibition

1. Download high-res image (212KB)
2. Download full-size image

     

Regulation of the Activity in the p53 Family Depends on the Organization of the Transactivation Domain

1. Download high-res image (164KB)
2. Download full-size image

     

The D3 dopamine receptor inhibits dopamine release in PC-12/hD3 cells by autoreceptor signaling via PP-2B, CK1, and Cdk-5

The function of the D₃ dopamine (DA) receptor remains ambiguous largely because of the lack of selective D₃ receptor ligands. To investigate the function and intracellular signaling of D₃ receptors, we established a PC‐12/hD3 clone, which expresses the human D₃ DA receptor in a DA producing cell line. In this model, we find that the D₃ receptor functions as an autoreceptor controlling neurotransmitter secretion. Pre‐treatment with 3,6a,11, 14‐tetrahydro‐9‐methoxy‐2 methyl‐(12H)‐isoquino[1,2‐b] pyrrolo[3,2‐f][1,3] benzoxanzine‐1‐carboxylic acid, a D₃ receptor preferring agonist, dose‐dependently suppressed K⁺‐evoked [³H]DA release in PC‐12/hD3 cells but not in the control cell line. This effect was prevented by D₃ receptor preferring antagonists GR103691 and SB277011‐A. Furthermore, activation of D₃ receptors significantly inhibits forskolin‐induced cAMP accumulation and leads to transient increases in phosphorylation of cyclin‐dependent kinase 5 (Cdk5), dopamine and cAMP‐regulated phosphoprotein of M_r 32 000 and Akt. Because we observed differences in Cdk5 phosphorylation as well as Akt phosphorylation after DA stimulation, we probed the ability of Cdk5 and phosphatidylinositol‐3 kinase (PI3K) to influence DA release. Cdk5 inhibitors, roscovitine, or olomoucine, but not the PI3K inhibitor wortmannin, blocked the D₃ receptor inhibition of DA release. In a complimentary experiment, over‐expression of Cdk5 potentiated D₃ receptor suppression of DA release. Pertussis toxin, 3‐[(2,4,6‐trimethoxyphenyl)methylidenyl]‐indolin‐2‐one and cyclosporine A also attenuated D₃ receptor‐mediated inhibition of DA release indicating that this phenomenon acts through Gi/oα and casein kinase 1, and phosphatase protein phosphatase 2B (calcineurin), respectively. In support of previous data that D₃ DA receptors reduce transmitter release from nerve terminals, the current results demonstrate that D₃ DA receptors function as autoreceptors to inhibit DA release and that a signaling pathway involving Cdk5 is essential to this regulation.     

Regulation of the Yeast Formin Bni1p by the Actin‐Regulating Kinase Prk1p

The formin family of proteins promotes the assembly of linear actin filaments in the cells of diverse eukaryotic organisms. The predominant formins in mammalian cells are self‐inhibited by an intramolecular interaction between two terminal domains and are activated by the binding of the Rho GTPases and other factors. In this study, we show that Bni1p, a formin required for the assembly of actin cables in budding yeast, is also regulated by an autoinhibitory mechanism and phosphorylation by the actin regulatory kinase Prk1p, and possibly Ark1p as well, plays a key role in unlocking the inhibition. Bni1p is phosphorylated by Prk1p at three [L/V/I]xxxxTG motifs in vitro, and the phosphorylation is sufficient to activate Bni1p by disrupting its intramolecular interaction. This finding extends the roles of Prk1p in the regulation of actin dynamics to be associated with both anterograde and retrograde transport pathways, i.e. exocytosis and endocytosis, in yeast.