Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design

The human genome codes only a few thousand druggable proteins, mainly receptors and enzymes. While this pool of available drug targets is limited, there is an untapped potential for discovering new drug-binding mechanisms and modes. For example, enzymes with long binding cavities offer numerous prerequisite binding sites that may be visited by an inhibitor during migration from a bulk solution to the destination site. Drug design can use these prerequisite sites as new structural targets. However, identifying these ephemeral sites is challenging. Here, we introduce a new method called NetBinder for the systematic identification and classification of prerequisite binding sites at atomic resolution. NetBinder is based on atomistic simulations of the full inhibitor binding process and provides a networking framework on which to select the most important binding modes and uncover the entire binding mechanism, including previously undiscovered events. NetBinder was validated by a study of the binding mechanism of blebbistatin (a potent inhibitor) to myosin 2 (a promising target for cancer chemotherapy). Myosin 2 is a good test enzyme because, like other potential targets, it has a long internal binding cavity that provides blebbistatin with numerous potential prerequisite binding sites. The mechanism proposed by NetBinder of myosin 2 structural changes during blebbistatin binding shows excellent agreement with experimentally determined binding sites and structural changes. While NetBinder was tested on myosin 2, it may easily be adopted to other proteins with long internal cavities, such as G-protein-coupled receptors or ion channels, the most popular current drug targets. NetBinder provides a new paradigm for drug design by a network-based elucidation of binding mechanisms at an atomic resolution.     

Correlation of Immunological and Histopathological Features with Gene Expression-Based Classifiers in Colon Cancer Patients

The purpose of this study was to evaluate the association between four distinct histopathological features: (1) tumor infiltrating lymphocytes, (2) mucinous differentiation, (3) tumor-stroma ratio, plus (4) tumor budding and two gene expression-based classifiers—(1) consensus molecular subtypes (CMS) plus (2) colorectal cancer intrinsic subtypes (CRIS). All four histopathological features were retrospectively scored on hematoxylin and eosin sections of the most invasive part of the primary tumor in 218 stage II and III colon cancer patients from two independent cohorts (AMC-AJCC-90 and AC-ICAM). RNA-based CMS and CRIS assignments were independently obtained for all patients. Contingency tables were constructed and a χ2 test was used to test for statistical significance. Odds ratios with 95% confidence intervals were calculated. The presence of tumor infiltrating lymphocytes and a mucinous phenotype (>50% mucinous surface area) were strongly correlated with CMS1 (p < 0.001 and p = 0.008) and CRIS-A (p = 0.006 and p < 0.001). The presence of mucus (≥ 10%) was associated with CMS3: mucus was present in 64.1% of all CMS3 tumors (p < 0.001). Although a clear association between tumor-stroma ratio and CMS4 was established in this study (p = 0.006), still 32 out of 61 (52.5%) CMS4 tumors were scored as stroma-low, indicating that CMS4 tumors cannot be identified solely based on stromal content. Higher budding counts were seen in CMS4 and CRIS-B tumors (p = 0.045 and p = 0.046). No other associations of the measured parameters were seen for any of the other CRIS subtypes. Our analysis revealed clear associations between histopathologic features and CMS or CRIS subtypes. However, identification of distinct molecular subtypes solely based on histopathology proved to be infeasible. Combining both molecular and morphologic features could potentially improve patient stratification.     

New aspects in cationization of lignocellulose materials. IX. Flame retardancy effect of modification with nitrogen and sulfur containing groups

Lignocellulose materials were modified with 3-chlor-2-hydroxypropyltrimethylammoniumchloride, 1,3-bis(3-chlor-2-hydroxypropyl)imidazoliumhydrogensulphate, and 2-chlorethyl-sodiumsulphonate and the flame-retardant properties of materials obtained were studied. The flame-retardant effect was proved using the limited oxygen index (LOI) method and values up to 32.8 vol % of oxygen were determined. The LOI values were higher when the modification was done without using NaOH for activation, but in that case the alkylating groups were not chemically bonded to the material. The NaOH activation was necessary to obtain material with flame-retardant properties stable against washing. No synergistic effects were observed when the material was modified with both nitrogen- and sulfur-containing groups.     

Crystal structures and melting points of unsaturated triacylglycerols in theβ phase

Theβ-phase crystal structures of unsaturated triacyl-glycerols (TAGs) have been analyzed. Long spacings and melting points of monounsaturated TAGs such as16· O· 16 and16· O ·18 indicate aβ-3C packing mode with a methyl terrace that differs from that of the saturatedβ- 3 TAGs. In addition to the hydrocarbon chain subcell packing and the methyl terrace structure, the conformation of the oleoyl chain also has to be considered. This conformation is analyzed in connection with the symmetry relation between the two half-layers on either side of the plane through the double bonds. Geometric analysis shows four possibilities, which have been explored further by means of energy minimization computations. In these calculations the structure of the oleoyl chain, in its crystalline environment, has been optimized while taking all relevant intramolecular and intermolecular forces into account. Though the calculations reveal relatively small energy differences between the four possibilities, the most likely structure can still be identified. On the basis of the results obtained for the monounsaturated TAGs, proposals for the crystal structures of diunsaturated (e.g., O · 18 · O) and triunsaturatede.g., O· O · O TAGs are briefly outlined.     

Interfacial tension of demixed polymer solutions near the critical temperature: polystyrene + methylcyclohexane

Interfacial tension between demixed solutions of polystyrene + methylcyclohexane has been measured near the critical temperature as a function of temperature using polystyrenes with molecular weights 9000 ～ 1.26 × 10⁶. The critical exponent for the interfacial tension was determined to be about 1.30 for the lower molecular weight systems. However, for higher molecular weights the exponent could not be obtained because the system departed from critical behaviour. Magnitudes of the interfacial tension were proportional to about N^?0.44, where N is the polymerization index. Experimental results were compared with the recently-proposed theories and found to be in qualitative agreement. The tricritical theory of polymer solutions was also compared with the experimental results.     

Solid state 13C-NMR of cellulose. A relaxation study

Summary The ¹³C spin-lattice relaxation times T₁ of hydrolysed cotton cellulose have been determined in the solid state. T₁ is between 202 and 266 seconds in the crystalline regions of the sample for all the carbons in the anhydroglucose unit and less than 15 seconds in the amorphous part. Based on the relaxation data, spectral assignment of the C2-C3-C5 region is proposed.     

Role of the alpha-glucanase Agn2p in ascus-wall endolysis following sporulation in fission yeast

During sporulation in the ascomyceteous fungus Schizosaccharomyces pombe, diploid cells undergo differentiation into asci containing four haploid ascospores, which are highly resistant to environmental stresses. Although the morphogenetic processes involved in ascospore formation have been studied extensively, little is known about the molecular mechanism that ensures the release of mature ascospores from the ascus, allowing their dispersal into the environment. Recently, we identified Agn2p as the paralogue of the characterized endo-(1,3)-alpha-glucanase Agn1p, and observed that asci deleted for agn2 are defective in ascospore dispersal. Here, we focus on the cellular and biochemical functions of Agn2p. By placing agn2 under the control of an inducible promoter, we show that expression of agn2 is required for the efficient release of ascospores from their asci. Furthermore, we characterize the enzyme activity of purified recombinant Agn2p and show that Agn2p, like Agn1p, is an endo-(1,3)-alpha-glucanase that produces predominantly (1,3)-alpha-glucan pentasaccharides. Finally, we demonstrate that exogenous addition of purified Agn2p liberated the ascospores from asci deleted for agn2. We propose that Agn2p participates in the endolysis of the ascus wall by hydrolysing its (1,3)-alpha-glucan, thereby assisting in the release of ascospores.