Supramolecular Fullerene Tetramers Concocted with Porphyrin Boxes Enable Efficient Charge Separation and Delocalization.

Herein, we report a novel porphyrin/fullerene supramolecular cocrystal using a shape-persistent zinc-metalated porphyrin box (Zn-PB) and C60/C70. An unprecedented arrangement of a tightly packed square-planar core of four C60 or C70 surrounded by six cube-shaped Zn-PBs was observed. This unique packing promotes strong charge transfer (CT) interactions between the two components in the ground state and formation of charge-separated states with very long lifetimes in the excited state and enables unusually high photoconductivity. Quantum chemical calculations show that these features are enabled by delocalized orbitals that promote the CT, on one hand, and that are spatially separated from each other, on the other hand. This work may open a new avenue to design novel electron donor/acceptor architectures for artificial photosynthesis.

Rational Design and Construction of Hierarchical Superstructures Using Shape-Persistent Organic Cages: Porphyrin Box-Based Metallosupramolecular Assemblies.

We report a new approach to building hierarchical superstructures using a shape-persistent porous organic cage, which acts as a premade secondary building unit, and coordination chemistry. To illustrate the principle, a zinc-metalated porphyrin box (Zn-PB), a corner-truncated cubic porous cage, was connected by suitable dipyridyl terminated bridging ligands to construct PB-based hierarchical superstructures (PSSs). The PSSs were stabilized not only by the coordination bonds between Zn ions and bipyridyl-terminated ligands but also by π-π interactions between the corners of the Zn-PB units. By varying the length of the linker, we identified an optimum range of the linker length for construction of PSSs. The PSSs have large void volumes and an extrinsic surface area compared to the parent PBs, which can be exploited for the selective encapsulation and interior functionalization of the PSSs for various applications, including catalysis. We observed that singlet oxygen induced synthesis of the natural product, juglone, is more efficiently catalyzed by PSS-1 than its constituent component Zn-PB.

Force Measurement for the Interaction between Cucurbit[7]uril and Mica and Self-Assembled Monolayer in the Presence of Zn2+ Studied with Atomic Force Microscopy.

Force spectroscopy with atomic force microscopy (AFM) revealed that cucurbit[7]uril (CB[7]) strongly binds to a mica surface in the presence of cations. Indeed, Zn2+ was observed to facilitate the self-assembly of CB[7] on the mica surface, whereas monocations, such as Na+, were less effective. The progression of the process and the cation-mediated self-assembled monolayer were characterized using AFM, and the observed height of the layer agrees well with the calculated CB[7] value (9.1 Å). We utilized force-based AFM to further study the interaction of CB[7] with guest molecules. To this end, CB[7] was immobilized on a glass substrate, and aminomethylferrocene (am-Fc) was conjugated onto an AFM tip. The single-molecule interaction between CB[7] and am-Fc was monitored by collecting the unbinding force curves. The force histogram showed single ruptures and a unimodal distribution, and the most probable unbinding force value was 101 pN in deionized water and 86 pN in phosphate-buffered saline buffer. The results indicate that the unbinding force was larger than that of streptavidin-biotin measured under the same conditions, whereas the dissociation constant was smaller by 1 order of magnitude (0.012 s-1 vs 0.13 s-1). Furthermore, a high-resolution adhesion force map showed a part of the CB[7] cavities on the surface.

Ferrocene and ferrocenium inclusion compounds with cucurbiturils: a study of metal atom dynamics probed by Mössbauer spectroscopy.

Temperature-dependent 57Fe Mössbauer effect (ME) spectroscopic studies were carried out on ferrocene (Fc), 1,1'-dimethylferrocene (1,1'(CH3)2Fc) and ferrocenium hexafluorophosphate (FcPF6) guest species in cucurbit[n]uril (n = 7, 8) inclusion complexes. The solid inclusion complexes were isolated by freeze-drying of dilute aqueous solutions and/or microwave-assisted precipitation from concentrated mixtures. The presence of genuine 1 : 1 (host : guest) inclusion complexes in the isolated solids was supported by liquid-state 1H and solid-state 13C{1H} MAS NMR, elemental and thermogravimetric analyses, powder X-ray diffraction, FTIR spectroscopy, and diffuse reflectance UV-Vis spectroscopy. The ME spectra of the complexes CB7·Fc and CB7·1,1'(CH3)2Fc consist of well-resolved doublets with hyperfine parameters (isomer shift and quadrupole splitting at 90 K) and temperature-dependent recoil-free fraction data that are very similar to those for the neat parent compounds, Fc and 1,1'(CH3)2Fc, suggesting that the organometallic guest molecules do not interact significantly with the host environment over the experimental temperature range. The ME spectra for CB7·FcPF6 and CB8·FcPF6 consist of a major broad line resonance attributed to a paramagnetic FeIII site. From the temperature-dependence of the recoil-free fraction it is evident that the charged guest species in these systems interact with the host environment significantly more strongly than was observed in the case of the neutral guest species, Fc and 1,1'(CH3)2Fc. Moreover, the ME data indicate that the vibrational amplitude of the ferrocenium guest molecule is significantly larger in the CB8 host molecule than in the CB7 homologue, as expected on the basis of the different cavity sizes.

High-throughput analysis of in vivo protein stability.

Determining the half-life of proteins is critical for an understanding of virtually all cellular processes. Current methods for measuring in vivo protein stability, including large-scale approaches, are limited in their throughput or in their ability to discriminate among small differences in stability. We developed a new method, Stable-seq, which uses a simple genetic selection combined with high-throughput DNA sequencing to assess the in vivo stability of a large number of variants of a protein. The variants are fused to a metabolic enzyme, which here is the yeast Leu2 protein. Plasmids encoding these Leu2 fusion proteins are transformed into yeast, with the resultant fusion proteins accumulating to different levels based on their stability and leading to different doubling times when the yeast are grown in the absence of leucine. Sequencing of an input population of variants of a protein and the population of variants after leucine selection allows the stability of tens of thousands of variants to be scored in parallel. By applying the Stable-seq method to variants of the protein degradation signal Deg1 from the yeast Matα2 protein, we generated a high-resolution map that reveals the effect of ∼30,000 mutations on protein stability. We identified mutations that likely affect stability by changing the activity of the degron, by leading to translation from new start codons, or by affecting N-terminal processing. Stable-seq should be applicable to other organisms via the use of suitable reporter proteins, as well as to the analysis of complex mixtures of fusion proteins.

The Cdc48 ATPase modulates the interaction between two proteolytic factors Ufd2 and Rad23.

Rad23 and cell division cycle protein 48 (Cdc48), two key regulators of postubiquitylation events, act on distinct and overlapping sets of substrates. The principle underlying their division of labor and cooperation in proteolysis remains elusive. Both Rad23 and Cdc48 bind a ubiquitin protein ligase ubiquitin fusion degradation-2 (Ufd2), and regulate the degradation of Ufd2 substrates. With its ability to bind ubiquitin chains directly and the proteasome via different domains, Rad23 serves as a bridge linking ubiquitylated substrates to the proteasome. The significance and specific role of the Ufd2-Cdc48 interaction are unclear. Here, we demonstrate that mutations in Ufd2 alter its interaction with Cdc48 and impair its function in substrate proteolysis but not in ubiquitylation. Furthermore, Cdc48 promotes the disassembly of the Ufd2-Rad23 complex in an manner that is dependent on ATP and Ufd2 binding, revealing a biochemical role for Cdc48. Rad23 was shown to bind separately to Ufd2 and to the proteasome subunit Rpn1, which define two distinct steps in proteolysis. The action of Cdc48 could free Rad23 from Ufd2 to allow its subsequent association with Rpn1, which in turn may facilitate the orderly transfer of the substrate from the ubiquitylation apparatus to the proteasome.

The Cdc48 protein and its cofactor Vms1 are involved in Cdc13 protein degradation.

Vms1 is a newly identified Cdc48-binding protein. The biological function of Vms1 remains obscure. Here, we show that both Cdc48 and Vms1, but not Cdc48 cofactors Ufd1 and Ufd2, are crucial for the degradation of Cdc13, a telomere regulator. Interestingly, both autophagy and the proteasome are involved in Cdc13 turnover. Toxicity associated with accumulation of large amounts of Cdc13 in vms1Δ or autophagy mutants underscores the significance of the proteolytic regulation of Cdc13. Because few ubiquitylated yeast proteins are known to be degraded by autophagy under non-stress conditions, the identification of Cdc13 as a target of autophagy provides a valuable tool to unravel the mechanism of autophagy-mediated selective protein degradation.

Large-Area Synthesis of Ultrathin, Flexible, and Transparent Conductive Metal-Organic Framework Thin Films via a Microfluidic-Based Solution Shearing Process.

Iminosemiquinone-linker-based conductive metal-organic frameworks (c-MOFs) have attracted much attention as next-generation electronic materials due to their high electrical conductivity combined with high porosity. However, the utility of such c-MOFs in high-performance devices has been limited to date by the lack of high-quality MOF thin-film processing. Herein, a technique known as the microfluidic-assisted solution shearing combined with post-synthetic rapid crystallization (MASS-PRC) process is introduced to generate a high-quality, flexible, and transparent thin-film of Ni3 (hexaiminotriphenylene)2 (Ni3 (HITP)2 ) uniformly over a large-area in a high-throughput manner with thickness controllability down to tens of nanometers. The MASS-PRC process utilizes: 1) a micromixer-embedded blade to simultaneously mix and continuously supply the metal-ligand solution toward the drying front during solution shearing to generate an amorphous thin-film, followed by: 2) immersion in amine solution for rapid directional crystal growth. The as-synthesized c-MOF film has transparency of up to 88.8% and conductivity as high as 37.1 S cm-1 . The high uniformity in conductivity is confirmed over a 3500 mm2 area with an arithmetic mean roughness (Ra ) of 4.78 nm. The flexible thin-film demonstrates the highest level of transparency for Ni3 (HITP)2 and the highest hydrogen sulfide (H2 S) sensing performance (2,085% at 5 ppm) among c-MOFs-based H2 S sensors, enabling wearable gas-sensing applications.

Identification of an Htm1 (EDEM)-dependent, Mns1-independent Endoplasmic Reticulum-associated Degradation (ERAD) pathway in Saccharomyces cerevisiae: application of a novel assay for glycoprotein ERAD.

Endoplasmic reticulum (ER)-associated degradation (ERAD) is a quality control system for newly synthesized proteins in the ER; nonfunctional proteins, which fail to form their correct folding state, are then degraded. The cytoplasmic peptide:N-glycanase is a deglycosylating enzyme that is involved in the ERAD and releases N-glycans from misfolded glycoproteins/glycopeptides. We have previously identified a mutant plant toxin protein, RTA (ricin A-chain nontoxic mutant), as the first in vivo Png1 (the cytoplasmic peptide:N-glycanase in Saccharomyces cerevisiae)-dependent ERAD substrate. Here, we report a new genetic device to assay the Png1-dependent ERAD pathway using the new model protein designated RTL (RTA-transmembrane-Leu2). Our extensive studies using different yeast mutants identified various factors involved in RTL degradation. The degradation of RTA/RTL was independent of functional Sec61 but was dependent on Der1. Interestingly, ER-mannosidase Mns1 was not involved in RTA degradation, but it was dependent on Htm1 (ERAD-related alpha-mannosidase in yeast) and Yos9 (a putative degradation lectin), indicating that mannose trimming by Mns1 is not essential for efficient ERAD of RTA/RTL. The newly established RTL assay will allow us to gain further insight into the mechanisms involved in the Png1-dependent ERAD-L pathway.

The Png1-Rad23 complex regulates glycoprotein turnover.

Misfolded proteins in the endoplasmic reticulum (ER) are destroyed by a pathway termed ER-associated protein degradation (ERAD). Glycans are often removed from glycosylated ERAD substrates in the cytosol before substrate degradation, which maintains the efficiency of the proteasome. Png1, a deglycosylating enzyme, has long been suspected, but not proven, to be crucial in this process. We demonstrate that the efficient degradation of glycosylated ricin A chain requires the Png1-Rad23 complex, suggesting that this complex couples protein deglycosylation and degradation. Rad23 is a ubiquitin (Ub) binding protein involved in the transfer of ubiquitylated substrates to the proteasome. How Rad23 achieves its substrate specificity is unknown. We show that Rad23 binds various regulators of proteolysis to facilitate the degradation of distinct substrates. We propose that the substrate specificity of Rad23 and other Ub binding proteins is determined by their interactions with various cofactors involved in specific degradation pathways.

One-pot Synthesis of a Truncated Cone-shaped Porphyrin Macrocycle and Its Self-assembly into Permanent Porous Material.

Here, we report the synthesis of a truncated cone-shaped triangular porphyrinic macrocycle, P3 L3 , via a single step imine condensation of a cis-diaminophenylporphyrin and a bent dialdehyde-based linker as building units. X-ray diffraction analysis reveals that the truncated cone-shaped P3 L3 molecules are stacked on top of each other by π⋯π and CH⋯π interactions, to form 1.7 nm wide hollow columns in the solid state. The formation of the triangular macrocycle is corroborated by quantum chemical calculations. The permanent porosity of the P3 L3 crystals is demonstrated by several gas sorption experiments and powder X-ray diffraction analysis.

What's Ub chain linkage got to do with it?

Ubiquitination-the covalent conjugation of ubiquitin (Ub) to other cellular proteins-regulates a wide range of cellular processes. Often, multiple Ub molecules are added to the substrate to form a Ub chain. Distinct outcomes have been observed for substrates modified with multi-Ub chains linked through particular lysine residues. However, recent studies suggest that Ub chain linkages may not be the key determinant for substrate fate. Here, we review evidence suggesting that Ub-binding proteins play a pivotal role in determining the outcome of substrate ubiquitination. In fulfilling their functions in proteasome-mediated proteolysis or signaling, Ub receptors link ubiquitinated proteins to downstream molecules through protein-protein interactions. Studies of Ub-binding factors may therefore hold the key to understanding the diverse functions of the Ub molecule.

Multiple interactions of rad23 suggest a mechanism for ubiquitylated substrate delivery important in proteolysis.

The mechanism underlying the delivery of ubiquitylated substrates to the proteasome is poorly understood. Rad23 is a putative adaptor molecule for this process because it interacts with ubiquitin chains through its ubiquitin-associated motifs (UBA) and with the proteasome through a ubiquitin-like element (UBL). Here, we demonstrate that the UBL motif of Rad23 also binds Ufd2, an E4 enzyme essential for ubiquitin chain assembly onto its substrates. Mutations in the UBL of Rad23 alter its interactions with Ufd2 and the proteasome, and impair its function in the UFD proteolytic pathway. Furthermore, Ufd2 and the proteasome subunit Rpn1 compete for the binding of Rad23, suggesting that Rad23 forms separate complexes with them. Importantly, we also find that the ability of other UBL/UBA proteins to associate with Ufd2 correlates with their differential involvement in the UFD pathway, suggesting that UBL-mediated interactions may contribute to the substrate specificity of these adaptors. We propose that the UBL motif, a protein-protein interaction module, may be used to facilitate coupling between substrate ubiquitylation and delivery, and to ensure the orderly handoff of the substrate from the ubiquitylation machinery to the proteasome.

Analysis of ubiquitin chain-binding proteins by two-hybrid methods.

Ubiquitin (Ub) regulates important cellular processes through covalent attachment to its substrates. Distinct fates are bestowed on multi-Ub chains linked through different lysine residues. Ub contains seven conserved lysines, all of which could be used for multi-Ub chain formation. K29 and K48 are the signals for proteasome-mediated proteolysis. Multi-Ub chains linked through K63 have nonproteolytic functions. Studies of Ub-binding factors are likely the key to understanding diverse functions of the Ub molecule. Yeast two-hybrid assay can be a powerful approach to dissect the interaction between Ub and its binding proteins and also the function of these Ub-chain binding proteins in vivo.

Rad4 regulates protein turnover at a postubiquitylation step.

The ubiquitin (Ub)-binding protein Rad23 plays an important role in facilitating the transfer of substrates to the proteasome. However, the mechanism underlying Rad23's function in proteolysis remains unknown. Here, we demonstrate that Rad4, a Rad23-binding protein, also regulates ubiquitylated substrate turnover. Rad4 was known previously only as a key repair factor that directly recognizes DNA damage and initiates DNA repair. Our results, however, reveal a novel function of Rad4. We found that Rad4 and Rad23 share several common substrates. Substrates in rad4Delta cells are ubiquitylated, indicating that Rad4 regulates a postubiquitylation event. Moreover, we found that Rad4 participates in the Rad23-Ufd2 pathway, but not the Rad23-Png1 pathway, consistent with previous findings that Png1 and Rad4 or Ufd2 form separate Rad23 complexes. The Rad4-binding domain is crucial for the functioning of Rad23 in degradation, suggesting that Rad4 and Rad23 work together in proteolysis. It is interesting to note that upon DNA damage, Rad4 becomes concentrated in the nucleus and degradation of the nonnuclear protein Pex29 is compromised, further suggesting that Rad4 may influence the coordination of various cellular processes. Our findings will help to unravel the detailed mechanisms underlying the roles of Rad23 and Rad4 in proteolysis and also the interplay between DNA repair and proteolysis.

Usa1 protein facilitates substrate ubiquitylation through two separate domains.

BACKGROUND: Defects in protein folding are recognized as the root of many neurodegenerative disorders. In the endoplasmic reticulum (ER), secretory proteins are subjected to a stringent quality control process to eliminate misfolded proteins by the ER-associated degradation (ERAD) pathway. A novel ERAD component Usa1 was recently identified. However, the specific role of Usa1 in ERAD remains obscure. METHODOLOGY/PRINCIPAL FINDINGS: Here, we demonstrate that Usa1 is important for substrate ubiquitylation. Furthermore, we defined key cis-elements of Usa1 essential for its degradation function. Interestingly, a putative proteasome-binding motif is dispensable for the functioning of Usa1 in ERAD. We identify two separate cytosolic domains critical for Usa1 activity in ERAD, one of which is involved in binding to the Ub-protein ligase Hrd1/Hrd3. Usa1 may have another novel role in substrate ubiquitylation that is separate from the Hrd1 association. CONCLUSIONS/SIGNIFICANCE: We conclude that Usa1 has two important roles in ERAD substrate ubiquitylation.

Cellular tolerance of prion protein PrP in yeast involves proteolysis and the unfolded protein response.

Secretory proteins undergo a stringent quality control process in the endoplasmic reticulum (ER). Misfolded ER proteins are returned to the cytosol and destroyed by the proteasome. Prion protein PrP is degraded by the proteasome in mammalian cells. However, the significance of proteolysis on PrP-induced cell death is controversial. Moreover, the specific pathway involved in PrP degradation remains unknown. Here, we demonstrate that the unglycosylated form of human PrP is subjected to the ER-associated protein degradation (ERAD) process in the yeast Saccharomyces cerevisiae. We also show that unglycosylated PrP is degraded by the Hrd1-Hrd3 pathway. Accumulation of misfolded proteins triggers the unfolded protein response (UPR), which promotes substrate refolding. Interestingly, we find that the expression of PrP leads to growth impairment in cells deficient in UPR and ERAD. These findings raise the possibility that decreased UPR activity and proteolysis may contribute to the pathogenesis of some prion-related diseases.