Modelling and mutation studies on the histamine H1-receptor agonist binding site reveal different binding modes for H1-agonists: Asp116 (TM3) has a constitutive role in receptor stimulation

Summary A modelling study has been carried out, investigating the binding of histamine (Hist), 2-methylhistamine (2-MeHist) and 2-phenylhistamine (2-PhHist) at two postulated agonistic binding sites on transmembrane domain 5 (TM5) of the histamine H₁-receptor. For this purpose a conformational analysis study was performed on three particular residues of TM5, i.e., Lys²⁰⁰, Thr²⁰³ and Asn²⁰⁷, for which a functional role in binding has been proposed. The most favourable results were obtained for the interaction between Hist and the Lys²⁰⁰/Asn²⁰⁷ pair. Therefore, Lys²⁰⁰ was subsequently mutated and converted to an alanine, resulting in a 50-fold decrease of H₁-receptor stimulation by histamine. Altogether, the data suggest that the Lys²⁰⁰/Asn²⁰⁷ pair is important for activation of the H₁-receptor by histamine. In contrast, analogues of 2-PhHist seem to belong to a distinct subclass of histamine agonists and an alternative mode of binding is proposed in which the 2-phenyl ring binds to the same receptor location as one of the aromatic rings of classical histamine H₁-antagonists. Subsequently, the binding modes of the agonists Hist, 2-MeHist and 2-PhHist and the H₁-antagonist cyproheptadine were evaluated in three different seven--helical models of the H₁-receptor built in homology with bacteriorhodopsin, but using three different alignments. Our findings suggest that the position of the carboxylate group of Asp¹¹⁶ (TM3) within the receptor pocket depends on whether an agonist or an antagonist binds to the protein; a conformational change of this aspartate residue upon agonist binding is expected to play an essential role in receptor stimulation.Abbreviations 2-MeHist 2-methylhistamine - 2-PEA 2-pyridyl-ethylamine - 2-PhHist 2-phenylhistamine - CHO Chinese hamster ovary - E_int interaction energy - E_str strain energy - GES global energy structure - gpH₁R guinea pig H₁-receptor - GPCR G-protein coupled receptor - Hist histamine - N proximal nitrogen - N tele nitrogen - TM transmembrane domain - WT wild type     

Heme-protein active site models via self-assembly in water

[structure: see text] Water-soluble models of heme-protein active sites are obtained via the self-assembly of cationic porphyrins 1 and tetrasulfonato calix[4]arene 2 (K(1.2)() = 10(5) M(-)(1)). Selective binding of ligands either outside or inside the cavity of assemblies 1.2 via coordination to the zinc center has been observed. Small ligands such as 4-methylpyridine and 1-methylimidazole are encapsulated, while the bulkier caffeine is bound outside. Assemblies Co-1.2, in which the Zn porphyrin moiety has been replaced by a Co(II) porphyrin, can act as O(2) carriers.     

Amplification of chirality: the "sergeants and soldiers" principle applied to dynamic hydrogen-bonded assemblies

The amplification of supramolecular chirality has been studied in dynamic chiral hydrogen-bonded assemblies 1(3).(CA)(6) using "Sergeants and Soldiers" experiments. Previously, we have shown that chiral centers present in either the dimelamine component 1 or the cyanurate component CA quantitatively induce one handedness (M or P) in the assembly. This offers the possibility to study the amplification of chirality under two different kinetic regimes. When chiral dimelamines 1 are used, the exchange of chiral components and (M/P)-interconversion, i.e., interconversion between the (M)- and (P)-isomers of assembly 1(3).(CA)(6), take place via identical pathways (condition A). When chiral cyanurates CA are used, the exchange of chiral components occurs much faster than (M/P)-interconversion (condition B). Experimentally, a much stronger chiral amplification is observed under condition B. For example, the observed chiral amplification for a mixture of chiral and achiral components (40:60) is 46% under condition B and 32% under condition A. Kinetic models were developed to fit the experimental data and to simulate chiral amplification in dynamic systems in general. These simulations show that it is theoretically possible that the diastereomeric excess in a dynamic system is more than 99% with less than 1% chiral component present!     

Ag+ labeling: a convenient new tool for the characterization of hydrogen-bonded supramolecular assemblies by MALDI-TOF mass spectrometry

Herein we describe our results on the characterization of a wide variety of different hydrogen-bonded assemblies by means of a novel matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique with Ag+ labeling. The labeling technique with Ag+ ions is extremely mild and provides a nondestructive way to generate charged assemblies that can be detected by mass spectrometry. Up to now more than 25 different single (1(3).2(3)), double (3(3).2(6)), and tetrarosettes (4(3).2(12)) have been successfully characterized by the use of this method. The success of the method entirely depends on the presence of a suitable binding site for the Ag+ ion. A variety of functionalities has been identified that provide strong binding sites for Ag+, either acting in a cooperative way (pi-arene and pi-alkene donor functionalities) or individually (cyano and crown ether functionalities). The method works well for assemblies with molecular weights between 2,000 and 8,000 Da, and most likely far beyond this limit.     

Enantioselective formation of a dynamic hydrogen-bonded assembly based on the chiral memory concept

In this paper, we report the enantioselective formation of a dynamic noncovalent double rosette assembly 1a(3).(CYA)(6) composed of three 2-pyridylcalix[4]arene dimelamines (1a) and six butylcyanuric acid molecules (BuCYA). The six 2-pyridyl functionalities of the assembly interact stereoselectively with chiral dicarboxylic acids 3a-e via two-point hydrogen-bonding interactions. One of the two enantiomeric assemblies (P- or M-) 1a(3).(CYA)(6) is formed in excess as the result of the complexation of the chiral diacids, resulting in formation of optically active assemblies. The complexations with dibenzoly tartaric acids D-3a and L-3a (3 equivalent), respectively, leading to the formation of diastereomeric assemblies (P)-1a(3).(BuCYA)(6).(D-3a)(3) and (M)-1a(3).(BuCYA)(6).(L-3a)(3) with 90% diastereomeric excess. The diastereomeric excess in (M)-1a(3).(BuCYA)(6).(L-3a)(3) is "memorized" when L-3a is removed by precipitation with ethlylenediamine (EDA). The assembly (M)-1a(3).(BuCYA)(6) is still optically active (90% enantiomeric excess), although none of its individual components are chiral. (M)-1a(3).(BuCYA)(6) has a high kinetic stability toward racemization (E(a) = 119 kJ mol(-)(1), half-life of (M)-1a(3).(BuCYA)(6) is ca. 1 week at 20 degrees C).     

Covariances Simultaneous Component Analysis: a new method within a framework for modeling covariances

In modern omics research, it is more rule than exception that multiple data sets are collected in a study pertaining to the same biological organism. In such cases, it is worthwhile to analyze all data tables simultaneously to arrive at global information of the biological system. This is the area of data fusion or multi‐set analysis, which is a lively research topic in chemometrics, bioinformatics, and biostatistics. Most methods of analyzing such complex data focus on group means, treatment effects, or time courses. There is also information present in the covariances among variables within a group, because this relates directly to individual differences, heterogeneity of responses, and changes of regulation in the biological system. We present a framework for analyzing covariance matrices and a new method that fits nicely in this framework. This new method is based on combining covariance prototypes using simultaneous components and is, therefore, coined Covariances Simultaneous Component Analysis (COVSCA). We present the framework and our new method in mathematical terms, thereby explaining the (dis)similarities of the methods. Systems biology models based on differential equations illustrate the type of variation generated in real‐life biological systems and how this type of variation can be modeled within the framework and with COVSCA. The method is subsequently applied to two real‐life data sets from human and plant metabolomics studies showing biologically meaningful results. Copyright © 2015 John Wiley & Sons, Ltd.     

Complexation of phenolic guests by endo- and exo-hydrogen-bonded receptors

This article describes the complexation of phenol derivatives by hydrogen-bonded receptors. These phenol receptors are formed by self-assembly of calix[4]arene dimelamine or tetramelamine derivatives with 5,5-diethylbarbiturate (DEB) or cyanurate derivatives (CYA). The double rosette assemblies 3(3).(DEB)6/(CYA)6 have their phenol-binding functionalities (ureido groups) at the top and at the bottom of the double rosette (exo-receptors). The tetrarosette assemblies 4(3).(DEB)12/(CYA)12 form a cavity with binding sites between the two double rosettes for guest encapsulation (endo-receptors). An intrinsic binding constant Ka of 202 M-1 and 286 M-1 for the binding of 4-nitrophenol to the ureido functionalized exo- and endo-receptors, respectively, was observed. For the exo-receptor a 1:6 stoichiometry was observed while for the endo-receptor 1:4 binding stoichiometry was determined by Job plot and MALDI-TOF MS. The important role that the hydroxy group's acidity plays in the complexation of 4-nitrophenol is clarified by binding studies with different phenol derivatives. The hydrogen-bonded receptors showed a much smaller response towards less acidic phenol derivatives.     

Making Connections: Elementary Teachers' Construction of Division Word Problems and Representations

If teachers make few connections among multiple representations of division, supporting students in using representations to develop operation sense demanded by national standards will not occur. Studies have investigated how prospective and practicing teachers use representations to develop knowledge of fraction division. However, few studies examined primary (K‐3) teachers' learning of contextual division problems, making connections among representations of division, and resolving the ambiguity of representing quotients with remainders. A written post‐course assessment provided evidence that most teachers created partitive division word problems, used a set model without splitting the remainder, and wrote equations with limited success. Post‐course written reflections demonstrated that many teachers developed pedagogical knowledge for helping students make connections among multiple representations, and mathematical knowledge of unit fractions. These findings suggest two areas that have implications for mathematics teacher educators who design professional development courses to facilitate teachers' learning of mathematical content and pedagogical knowledge of division and fraction relationships.     

Direct bandgap optical transitions in Si nanocrystals

JETP Letters - The effect of quantum confinement on the direct bandgap of spherical Si nanocrystals has been modelled theoretically. We conclude that the energy of the direct bandgap at the...