Conformations of cyclic octapeptides and the influence of heterocyclic ring constraints upon calcium binding

A comparison is made between the structures and calcium binding properties of four cyclic octapeptides that differ in the number of heterocyclic thiazole and oxazoline ring constraints. The conformations of the naturally occurring cyclic octapeptides ascidiacyclamide 1 and patellamide D 2, which each contain two oxazoline and two thiazole rings, are compared by H-1 NMR spectroscopy with the analogues cyclo(Thr-D-Val(Thz)-Ile)(2) 3 with just two thiazoles, and cyclo(Thr-D-Val-alpha Abu-Ile)(2) 4, with no 5-membered rings. The conformations observed in the solid state for ascidiacyclamide (saddle) and patellamide D (twisted figure of eight) were retained in solution, whilst peptide 3 was found to have a chair shape and peptide 4 displayed a range of conformations. The solid state structure of 4 revealed that the peptide takes a relatively planar conformation with a number of transannular hydrogen bonds, which are apparently retained in solution. Complexation studies utilising H-1 NMR and CD spectroscopy yielded 1∶1 calcium-peptide binding constants (log K) for the four peptides (2.9 (1), 2.8 (2), 4.0 (3) and 5.5 (4)) as well as a 1 : 2 metal-peptide binding constant for 3 (log K = 4.5). The affinity for Ca2+ thus decreases with increasing number of 5-membered ring constraints in the macrocycle (4 > 3 > 2 approximate to 1).

The Ni-II, Hg-II and Cu-II complexes of 12-membered-ring mixed-donor macrocycles

The structures of diaqua(1,7-dioxa-4-thia-10-azacyclododecane)nickel dinitrate, [Ni(C8H17NO2S)(H2O)(2)](NO3)(2), (I), bis(nitrato-O,O')(1,4,7-trioxa-10-azacyclododecane)mercury, [Hg(NO3)(2)(C8H17NO3)], (II), and aqua(nitrato-O)(1-oxa-4,7,10-triazacyclododecane)copper nitrate, [Cu(NO3)(C8H19N3O)(H2O)]NO3, (III), reveal each macrocycle binding in a tetradentate manner. The conformations of the ligands in (I) and (III) are the same and distinct from that identified for (II). These differences are in agreement with molecular-mechanics predictions of ligand conformation as a function of metal-ion size.

Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA - Crystal structure of an oligomeric complex of yeast SmF

Sm and Sm-like proteins are key components of small ribonucleoproteins involved in many RNA and DNA processing pathways. In eukaryotes, these complexes contain seven unique Sm or Sm-like (Lsm) proteins assembled as hetero-heptameric rings, whereas in Archaea and bacteria six or seven-membered rings are made from only a single polypeptide chain. Here we show that single Sm and Lsm proteins from yeast also have the capacity to assemble into homo-oligomeric rings. Formation of homo-oligomers by the spliceosomal small nuclear ribonucleoprotein components SmE and SmF preclude hetero-interactions vital to formation of functional small nuclear RNP complexes in vivo. To better understand these unusual complexes, we have determined the crystal structure of the homomeric assembly of the spliceosomal protein SmF. Like its archaeal/bacterial homologs, the SmF complex forms a homomeric ring but in an entirely novel arrangement whereby two heptameric rings form a co-axially stacked dimer via interactions mediated by the variable loops of the individual SmF protein chains. Furthermore, we demonstrate that the homomeric assemblies of yeast Sm and Lsm proteins are capable of binding not only to oligo(U) RNA but, in the case of SmF, also to oligo(dT) single-stranded DNA.

Effects of Si content on defect band formation in hypoeutectic Al-Si die castings

Al-3-11% Si alloys have been high-pressure die-cast and characterized microstructurally. Alstruc was used to calculate the solidification characteristics and fraction of eutectic. Defect bands were observed at all Si contents, although their constitution, position and distinctiveness were a function of Si content. The defect bands contain a higher fraction Al-Si eutectic than the surroundings in all alloys, and porosity was additionally found in the band in AlSi3. With decreasing Si content, the defect bands formed closer to the casting surface, became more prevalent and also the width of the bands decreased. These differences are discussed by considering the effect of Si content on the distribution of solid in the mushy wall layers and on the feeding potentials of the alloys. The observations are consistent with the mechanism proposed by Gourlay et al. in which bands form due to deformation within the solidifying mushy wall layers. (c) 2005 Elsevier B.V. All rights reserved.

Metastable chaos in the ammonia ring laser

We report experimental studies of metastable chaos in the far-infrared ammonia ring: laser. When the laser pump power is switched from above chaos threshold to slightly below, chaotic intensity pulsations continue for a varying time afterward before decaying to either periodic or cw emission. The behavior is in good qualitative agreement with that predicted by the Lorenz equations, previously used to describe this laser. The statistical distribution of the duration of the chaotic transient is measured and shown to be in excellent agreement with the Lorenz equations in showing a modified exponential distribution. We also give a brief numerical analysis and graphical visualization of the Lorenz equations in phase space illustrating the boundary between the metastable chaotic and the stable fixed point basins of attraction. This provides an intuitive understanding of the metastable dynamics of the Lorenz equations and the experimental system.

Strong Grobner bases for polynomials over a principal ideal ring

Grobner bases have been generalised to polynomials over a commutative ring A in several ways. Here we focus on strong Grobner bases, also known as D-bases. Several authors have shown that strong Grobner bases can be effectively constructed over a principal ideal domain. We show that this extends to any principal ideal ring. We characterise Grobner bases and strong Grobner bases when A is a principal ideal ring. We also give algorithms for computing Grobner bases and strong Grobner bases which generalise known algorithms to principal ideal rings. In particular, we give an algorithm for computing a strong Grobner basis over a finite-chain ring, for example a Galois ring.

The strain-driven pyrochlore to "defect fluorite" phase transition in rare earth sesquioxide stabilized cubic zirconias

The relationship between the ordering characteristic of the pyrochlore structure type and that characteristic of the defect fluorite structure type (immediately on either side of two phase regions separating the two structure types) in a range of rare eath sesquioxide stabilized cubic zirconias is investigated via electron diffraction and imaging. Systematic structural change as a function of composition and relative size of the constituent metal ions is highlighted and a multi-q to single-q = 1/2 [111]* model proposed for the observed pyrochlore to defect fluorite phase transition. Strain introduced into the close-packed {111} metal ion planes of the defect fluorite average structure by the local cation and oxygen vacancy distribution is pointed to as the likely origin of the observed behavior. (C) 2001 Academic Press

Pharmacotherapy of the ion transport defect in cystic fibrosis

1. More than 1300 different mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) cause cystic fibrosis (CF), a disease characterized by deficient epithelial Cl- secretion and enhanced Na+ absorption. The clinical course of the disease is determined by the progressive lung disease. Thus, novel approaches in pharmacotherapy are based primarily on correction of the ion transport defect in the airways. 2. The current therapeutic strategies try to counteract the deficiency in Cl- secretion and the enhanced Na+ absorption. A number of compounds have been identified, such as genistein and xanthine derivatives, which directly activate mutant CFTR. Other compounds may activate alternative Ca2+-activated Cl- channels or basolateral K+ channels, which supply the driving force for Cl- secretion. Apart from that, Na+ channel blockers, such as phenamil and benzamil, are being explored, which counteract the hyperabsorption of NaCl in CF airways. 3. Clinical trials are under way using purinergic compounds such as the P2Y(2) receptor agonist INS365. Activation of P2Y(2) receptors has been found to both activate Cl- secretion and inhibit Na+ absorption. 4. The ultimate goal is to recover Cl- channel activity of mutant CFTR by either enhancing synthesis and expression of the protein or by activating silent CFTR Cl- channels. Strategies combining these drugs with compounds facilitating Cl- secretion and inhibiting Na+ absorption in vivo may have the best chance to counteract the ion transport defect in cystic fibrosis.

Ring flexibility within tricyclic antidepressant drugs

The internal flexibility of the central seven-membered ring of a series of tricyclic antidepressant drugs (TCAs), imipramine {l}, amitriptyline {2}, doxepin {3}, and dothiepin {4}, has been investigated by H-1 and C-13 nuclear magnetic (NMR) techniques. Two dynamic processes were examined: ring inversion and bridge flexing. H-1 NMR lineshape analysis was used to obtain ring inversion barriers for 2-4. These studies yielded energy barriers of 14.3, 16.7, and 15.7 +/- 0.6 kcal/mol for the hydrochloride salts of doxepin, dothiepin, and amitriptyline, respectively. The barriers for the corresponding free bases were lower by 0.6 kcal/mol on average. (CT1)-C-13 relaxation measurements were used to determine the degree of bridge flexing associated with the central seven-membered ring for all four compounds. By fitting the T-1 data to a two-state jump model, lifetimes and amplitudes of rapid bridge flexing motions were determined. The results show that imipramine has the fastest rate of bridge flexing, followed by amitriptyline, doxepin, and dothiepin. The pharmacological profiles of the TCAs are complex and they interact with many receptor sites, resulting in numerous side effects and a general lack of understanding of their precise mode of action in different anxiety-related disorders. They all have similar three-dimensional structures, which makes it difficult to rationalize their differing relative potency in different assays/clinical settings. However, the clear finding here that there are significantly different degrees of internal mobility suggests that molecular dynamics should be an additional factor considered when trying to understand the mode of action of this clinically important family of molecules. (C) 2001 Wiley-Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 90:713-721, 2001.