A molecular dynamics study of the complexation of tryptophan,phenylalanine and tyrosine amino acids with cucurbit[7]uril

Journal of Inclusion Phenomena and Macrocyclic Chemistry - Molecular dynamics simulations were performed in aqueous solution to elucidate an atomistic level picture of complex formation between...     

Scaled Enflo type is equivalent to Rademacher type

We introduce the notion of the scaled Enflo type of a metricspace, and show that for Banach spaces, scaled Enflo type pis equivalent to Rademacher type p.     

Integrating proteomics with electrochemistry for identifying kinase biomarkers

We present an integrated approach for highly sensitive identification and validation of substrate-specific kinases as cancer biomarkers. Our approach combines phosphoproteomics for high throughput cancer-related biomarker discovery from patient tissues and an impedimetric kinase activity biosensor for sensitive validation. Using non-small-cell lung cancer (NSCLC) as a proof-of-concept study, label-free quantitative phosphoproteomic analysis of a pair of cancerous and its adjacent normal tissues revealed 198 phosphoproteins that are over-phosphorylated in NSCLC. Among the differentially regulated phosphorylation sites, the most significant alteration was in residue S165 in the Hepatoma Derived Growth Factor (HDGF) protein. Hence, HDGF was selected as a model system for the electrochemical studies. Further motif-based analysis of this altered phosphorylation site revealed that extracellular-signal-regulated kinase 1/2 (ERK1/2) are most likely to be the corresponding kinases. For validation of the kinase–substrate pair, densely packed peptide monolayers corresponding to the HDGF phosphorylation site were coupled to a gold electrode. Phosphorylation of the monolayer by ERK2 and dephosphorylation by alkaline phosphatase (AP) were detected by electrochemical impedance spectroscopy (EIS) and surface roughness analysis. Compared to other methods for quantification of kinase concentration, this label-free electrochemical assay offers the advantages of ultra-sensitivity as well as higher specificity for the detection of cancer-related kinase–substrate pair. With implementation of multiple kinase–substrate biomarker pairs, we expect this integrated approach to become a high throughput platform for discovery and validation of phosphorylation-mediated biomarkers.     

Synthesis,Structure, and Optical Properties of New Cadmium Chalcogenide Clusters of the Type [Cd10E4(E'Ph)12(PR3)4], (E,E' = Te,Se, S)

New cadmium chalcogenide cluster molecules [Cd₁₀E₄(E'Ph)₁₂(PⁿPr₃)₄], E = Te, E' = Te ( 1 ) and [Cd₁₀E₄(E'Ph)₁₂ (PⁿPr₂Ph)₄] E = Te, E' = Se ( 2 ); E = Te E' = S ( 3 ); E = Se, E' = S ( 4 ) have been synthesized and structurally characterized by single crystal X‐ray structure analysis. The influence of the variation of the chalcogen atom is investigated by structural means and by optical spectroscopy. All cluster‐molecules have a broad emission in the blue‐visible range at low temperature as indicated by photo luminescence (PL) measurements. A clear classification of the emission peak position can be made based on the E' species suggesting that the emission is assigned to transitions associated with the cluster surface ligands. Photoluminescence excitation and absorption measurements display a systematic shift of the band gap to the higher energies with the variation of E and E' from Te to Se to S, as also occurs in the respective series of the bulk semiconductors.     

Mutual Information between Order Book Layers

The order book is a list of all current buy or sell orders for a given financial security. The rise of electronic stock exchanges introduced a debate about the relevance of the information it encapsulates of the activity of traders. Here, we approach this topic from a theoretical perspective, estimating the amount of mutual information between order book layers, i.e., different buy/sell layers, which are aggregated by buy/sell orders. We show that (i) layers are not independent (in the sense that the mutual information is statistically larger than zero), (ii) the mutual information between layers is small (compared to the joint entropy), and (iii) the mutual information between layers increases when comparing the uppermost layers to the deepest layers analyzed (i.e., further away from the market price). Our findings, and our method for estimating mutual information, are relevant to developing trading strategies that attempt to utilize the information content of the limit order book.     

Constructions of optimal packing designs

Let v and k be positive integers. A (v, k, 1)-packing design is an ordered pair (V, B) where V is a v-set and B is a collection of k-subsets of V (called blocks) such that every 2-subset of V occurs in at most one block of B. The packing problem is mainly to determine the packing number P(k, v), that is, the maximum number of blocks in such a packing design. It is well known that P(k, v) ≤ ⌊v⌊(v − 1)/(k − 1)⌋/k⌋ = J(k, v) where ⌊×⌋ denotes the greatest integer y such that y ≤ x. A (v, k, 1)-packing design having J(k, v) blocks is said to be optimal. In this article, we develop some general constructions to obtain optimal packing designs. As an application, we show that P(5, v) = J(5, v) if v ≡ 7, 11 or 15 (mod 20), with the exception of v ∈ {11, 15} and the possible exception of v ∈ {27, 47, 51, 67, 87, 135, 187, 231, 251, 291}. © 1998 John Wiley & Sons, Inc. J Combin Designs 6: 245–260, 1998     

On the Interactive Capacity of Finite-State Protocols

The interactive capacity of a noisy channel is the highest possible rate at which arbitrary interactive protocols can be simulated reliably over the channel. Determining the interactive capacity is notoriously difficult, and the best known lower bounds are far below the associated Shannon capacity, which serves as a trivial (and also generally the best known) upper bound. This paper considers the more restricted setup of simulating finite-state protocols. It is shown that all two-state protocols, as well as rich families of arbitrary finite-state protocols, can be simulated at the Shannon capacity, establishing the interactive capacity for those families of protocols.     

Targeting an Interaction Between Two Disordered Domains by Using a Designed Peptide

Intrinsically disordered regions in proteins (IDRs) mediate many disease-related protein–protein interactions. However, the unfolded character and continuous conformational changes of IDRs make them difficult to target for therapeutic purposes. Here, we show that a designed peptide based on the disordered p53 linker domain can be used to target a partner IDR from the anti-apoptotic iASPP protein, promoting apoptosis of cancer cells. The p53 linker forms a hairpin-like structure with its two termini in close proximity. We designed a peptide derived from the disordered termini without the hairpin, designated as p53 LinkTer. The LinkTer peptide binds the disordered RT loop of iASPP with the same affinity as the parent p53 linker peptide, and inhibits the p53–iASPP interaction in vitro. The LinkTer peptide shows increased stability to proteolysis, penetrates cancer cells, causes nuclei shrinkage, and compromises the viability of cells. We conclude that a designed peptide comprising only the IDR from a peptide sequence can serve as an improved inhibitor since it binds its target protein without the need for pre-folding, paving the way for therapeutic targeting of IDRs.