Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome.

Phosphorylation sites are hyperabundant in the eukaryotic disordered proteome, suggesting that conformational fluctuations play a major role in determining to what extent a kinase interacts with a particular substrate. In biophysical terms, substrate selectivity may be determined not just by the structural-chemical complementarity between the kinase and its protein substrates but also by the free energy difference between the conformational ensembles that are, or are not, recognized by the kinase. To test this hypothesis, we developed a statistical-thermodynamics-based informatics framework, which allows us to probe for the contribution of equilibrium fluctuations to phosphorylation, as evaluated by the ability to predict Ser/Thr/Tyr phosphorylation sites in the disordered proteome. Essential to this framework is a decomposition of substrate sequence information into two types: vertical information encoding conserved kinase specificity motifs and horizontal information encoding substrate conformational equilibrium that is embedded, but often not apparent, within position-specific conservation patterns. We find not only that conformational fluctuations play a major role but also that they are the dominant contribution to substrate selectivity. In fact, the main substrate classifier distinguishing selectivity is the magnitude of change in local compaction of the disordered chain upon phosphorylation of these mostly singly phosphorylated sites. In addition to providing fundamental insights into the consequences of phosphorylation across the proteome, our approach provides a statistical-thermodynamic strategy for partitioning any sequence-based search into contributions from structural-chemical complementarity and those from changes in conformational equilibrium.

Extra adsorption and adsorbate superlattice formation in metal-organic frameworks.

Metal-organic frameworks (MOFs) have a high internal surface area and widely tunable composition, which make them useful for applications involving adsorption, such as hydrogen, methane or carbon dioxide storage. The selectivity and uptake capacity of the adsorption process are determined by interactions involving the adsorbates and their porous host materials. But, although the interactions of adsorbate molecules with the internal MOF surface and also amongst themselves within individual pores have been extensively studied, adsorbate-adsorbate interactions across pore walls have not been explored. Here we show that local strain in the MOF, induced by pore filling, can give rise to collective and long-range adsorbate-adsorbate interactions and the formation of adsorbate superlattices that extend beyond an original MOF unit cell. Specifically, we use in situ small-angle X-ray scattering to track and map the distribution and ordering of adsorbate molecules in five members of the mesoporous MOF-74 series along entire adsorption-desorption isotherms. We find in all cases that the capillary condensation that fills the pores gives rise to the formation of 'extra adsorption domains'-that is, domains spanning several neighbouring pores, which have a higher adsorbate density than non-domain pores. In the case of one MOF, IRMOF-74-V-hex, these domains form a superlattice structure that is difficult to reconcile with the prevailing view of pore-filling as a stochastic process. The visualization of the adsorption process provided by our data, with clear evidence for initial adsorbate aggregation in distinct domains and ordering before an even distribution is finally reached, should help to improve our understanding of this process and may thereby improve our ability to exploit it practically.

Aggregation-free gold nanoparticles in ordered mesoporous carbons: toward highly active and stable heterogeneous catalysts.

A coordination-assisted synthetic approach is reported here for the synthesis of highly active and stable gold nanoparticle catalysts in ordered mesoporous carbon materials using triblock copolymer F127 as a structure-directing agent, thiol-containing silane as a coordination agent, HAuCl4 as a gold source, and phenolic resin as a carbon source. Upon carbonization, the gold precursor becomes reduced to form monodispersed Au nanoparticles of ca. 9.0 nm, which are entrapped or confined by the "rigid" mesoporous carbonaceous framework. Nanoparticle aggregation is inhibited even at a high temperature of 600 °C. After removal of the silica component, the materials possess the ordered mesostructure, high surface area (~1800 m(2)/g), large pore volume (~1.19 cm(3)/g), and uniform bimodal mesopore size (<2.0 and 4.0 nm). The monodispersed gold nanoparticles are highly exposed because of the interpenetrated bimodal pores in the carbon framework, which exhibit excellent catalytic performance. A completely selective conversion of benzyl alcohol in water to benzoic acid can be achieved at 90 °C and 1 MPa oxygen. Benzyl alcohol can also be quantitatively converted to benzoic acid at 60 °C even under an atmospheric pressure, showing great advantages in green chemistry. The catalysts are stable, poison resistant, and reusable with little activity loss due to metal leaching. The silane coupling agent played several functions in this approach: (1) coordinating with gold species by the thiol group to benefit formation of monodispersed Au nanoparticles; (2) reacting with phenolic resins by silanol groups to form relatively "rigid" composite framework; (3) pore-forming agent to generate secondary pores in carbon pore walls, which lead to higher surface area, larger pore volumes, and higher accessibility to to the gold nanoparticles. Complete removal of the silica component proves to have little effect on the catalytic performance of entrapped Au nanoparticles.

Structure-based design and biochemical evaluation of sulfanilamide derivatives as hepatitis B virus capsid assembly inhibitors.

Virus capsid structure is essential in virion maturation and durability, so disrupting capsid assembly could be an effective way to reduce virion count and cure viral diseases. However, currently there is no known antiviral which affects capsid inhibition, and only a small number of assembly inhibitors were experimentally successful. In this present study, we aimed to find hepatitis B virus (HBV) capsid assembly inhibitor which binds to the HBV core protein and changes protein conformation. Several candidate molecules were found to bind to certain structure in core protein with high specificity. Furthermore, these molecules significantly changed the protein conformation and reduced assembly affinity of core protein, leading to decrease of the number of assembled capsid or virion, both in vitro and in vivo. In addition, prediction also suggests that improvements in inhibition efficiency could be possible by changing functional groups and ring structures.

Silver Nanowire/Carbon Sheet Composites for Electrochemical Syngas Generation with Tunable H2/CO Ratios.

Generating syngas (H2 and CO mixture) from electrochemically reduced CO2 in an aqueous solution is one of the sustainable strategies utilizing atmospheric CO2 in value-added products. However, a conventional single-component metal catalyst, such as Ag, Au, or Zn, exhibits potential-dependent CO2 reduction selectivity, which could result in temporal variation of syngas composition and limit its use in large-scale electrochemical syngas production. Herein, we demonstrate the use of Ag nanowire (NW)/porous carbon sheet composite catalysts in the generation of syngas with tunable H2/CO ratios having a large potential window to resist power fluctuation. These Ag NW/carbon sheet composite catalysts have a potential window increased by 10 times for generating syngas with the proper H2/CO ratio (1.7-2.15) for the Fischer-Tropsch process and an increased syngas production rate of about 19 times compared to that of a Ag foil. Additionally, we tuned the H2/CO ratio from ∼2 to ∼10 by adjusting only the quantity of the Ag NWs under the given electrode potential. We believe that our Ag NW/carbon sheet composite provides new possibilities for designing electrode structures with a large potential window and controlled CO2 reduction products in aqueous solutions.

Tailoring Photoelectrochemical Performance and Stability of Cu(In,Ga)Se2 Photocathode via TiO2-Coupled Buffer Layers.

We report on the photoelectrochemical (PEC) performance and stability of Cu(In,Ga)Se2 (CIGS)-based photocathodes for photocatalytic hydrogen evolution from water. Various functional overlayers, such as CdS, TiO2, ZnxSnyOz, and a combination of the aforementioned, were applied on the CIGS to improve the performance and stability. We identified that the insertion of TiO2 overlayer on p-CIGS/n-buffer layers significantly improves the PEC performance. A multilayered photocathode consisting of CIGS/CdS/TiO2/Pt exhibited the best current-potential characteristics among the tested photocathodes, which demonstrates a power-saved efficiency of 2.63%. However, repeated linear sweep voltammetry resulted in degradation of performance. In this regard, we focused on the PEC durability issues through in-depth chemical characterization that revealed the degradation was attributed to atomic redistribution of elements constituting the photocathode, namely, in-diffusion of Pt catalysts, out-diffusion of elements from the CIGS, and removal of the metal-oxide layers; the best-performing CIGS/CdS/TiO2/Pt photocathode retained its initial performance until the TiO2 overlayer was removed. It was also found that the durability of CIGS photocathodes with a TiO2-coated metal-oxide buffer layer such as ZnxSnyOz was better than those with a TiO2-coated CdS, and the degradation mechanism was different, suggesting that the stability of a CIGS-based photocathode can be improved by careful design of the structure.

DOT1L cooperates with the c-Myc-p300 complex to epigenetically derepress CDH1 transcription factors in breast cancer progression.

DOT1L has emerged as an anticancer target for MLL-associated leukaemias; however, its functional role in solid tumours is largely unknown. Here we identify that DOT1L cooperates with c-Myc and p300 acetyltransferase to epigenetically activate epithelial-mesenchymal transition (EMT) regulators in breast cancer progression. DOT1L recognizes SNAIL, ZEB1 and ZEB2 promoters via interacting with the c-Myc-p300 complex and facilitates lysine-79 methylation and acetylation towards histone H3, leading to the dissociation of HDAC1 and DNMT1 in the regions. The upregulation of these EMT regulators by the DOT1L-c-Myc-p300 complex enhances EMT-induced breast cancer stem cell (CSC)-like properties. Furthermore, in vivo orthotopic xenograft models show that DOT1L is required for malignant transformation of breast epithelial cells and breast tumour initiation and metastasis. Clinically, DOT1L expression is associated with poorer survival and aggressiveness of breast cancers. Collectively, we suggest that cooperative effect of DOT1L and c-Myc-p300 is critical for acquisition of aggressive phenotype of breast cancer by promoting EMT/CSC.

Interaction between nucleophosmin and HBV core protein increases HBV capsid assembly.

Host factors are involved in Hepatitis B virus (HBV) genome replication and capsid formation during the viral life cycle. A host factor, nucleophosmin (B23), was found to bind to HBV core protein dimers, but its functional role has not been studied. This interaction promoted HBV capsid assembly and decreased the degree of capsid dissociation when subjected to denaturant treatments in vitro. In addition, inhibition of B23 reduced intracellular capsid formation resulting in a decrease of HBV production in HepG2.2.15 cells. These results provide important evidence that B23 acts on core capsid assembly via its interaction with HBV core dimers.

Myoplasmic [ca], crossbridge phosphorylation and latch in rabbit bladder smooth muscle.

TONIC SMOOTH MUSCLE EXHIBIT THE LATCH PHENOMENON: high force at low myosin regulatory light chains (MRLC) phosphorylation, shortening velocity (Vo), and energy consumption. However, the kinetics of MRLC phosphorylation and cellular activation in phasic smooth muscle are unknown. The present study was to determine whether Ca(2+)-stimulated MRLC phosphorylation could suffice to explain the agonist- or high K(+)-induced contraction in a fast, phasic smooth muscle. We measured myoplasmic [Ca(2+)], MRLC phosphorylation, half-time after step-shortening (a measure of Vo) and contractile stress in rabbit urinary bladder strips. High K(+)-induced contractions were phasic at both 22℃ and 37℃: myoplasmic [Ca(2+)], MRLC phosphorylation, 1/half-time, and contractile stress increased transiently and then all decreased to intermediate values. Carbachol (CCh)-induced contractions exhibited latch at 37℃: stress was maintained at high levels despite decreasing myoplasmic [Ca(2+)], MRLC phosphorylation, and 1/half-time. At 22℃ CCh induced sustained elevations in all parameters. 1/half-time depended on both myoplasmic [Ca(2+)] and MRLC phosphorylation. The steady-state dependence of stress on MRLC phosphorylation was very steep at 37℃ in the CCh- or K(+)-depolarized tissue and reduced temperature flattend the dependence of stress on MRLC phosphorylation compared to 37℃. These data suggest that phasic smooth muscle also exhibits latch behavior and latch is less prominent at lower temperature.