Exploring privileged structures: the combinatorial synthesis of cyclic peptides

Head-to-tail cyclic peptides have been reported to bind to multiple, unrelated classes of receptor with high affinity. They may therefore be considered to be privileged structures. This review outlines the strategies by which both macrocyclic cyclic peptides and cyclic dipeptides or diketopiperazines have been synthesised in combinatorial libraries. It also briefly outlines some of the biological applications of these molecules, thereby justifying their inclusion as privileged structures.

Mixed gas equilibrium adsorption on zeolites and energetic heterogeneity of adsorption volume

A model for binary mixture adsorption accounting for energetic heterogeneity and intermolecular interactions is proposed in this paper. The model is based on statistical thermodynamics, and it is able to describe molecular rearrangement of a mixture in a nonuniform adsorption field inside a cavity. The Helmholtz free energy obtained in the framework of this approach has upper and lower limits, which define a permissible range in which all possible solutions will be found. One limit corresponds to a completely chaotic distribution of molecules within a cavity, while the other corresponds to a maximum ordered molecular structure. Comparison of the nearly ideal O-2-N-2-zeolite NaX system at ambient temperature with the system Of O-2-N-2-zeolite CaX at 144 K has shown that a decrease of temperature leads to a molecular rearrangement in the cavity volume, which results from the difference in the fluid-solid interactions. The model is able to describe this behavior and therefore allows predicting mixture adsorption more accurately compared to those assuming energetic uniformity of the adsorption volume. Another feature of the model is its ability to correctly describe the negative deviations from Raoult's law exhibited by the O-2-N-2-CaX system at 144 K. Analysis of the highly nonideal CO2-C2H6-zeolite NaX system has shown that the spatial molecular rearrangement in separate cavities is induced by not only the ion-quadrupole interaction of the CO2 molecule but also the significant difference in molecular size and the difference between the intermolecular interactions of molecules of the same species and those of molecules of different species. This leads to the highly ordered structure of this system.

Is Cadinella ornatissima a chomodorid? Sperm ultra structure in an enigmatic nudibranch (Opisthobranchia Mollusca)

Sperm ultrastructure is described for the nudibranch gastropod Cadlinella ornatissima, type species of the genus Cadlinella (Thiele). Although C. ornatissima exhibits most of the sperm features characteristic of other Opisthobranchia and the Pulmonata (a small, rounded acrosomal vesicle, a complex, helical, mitochondrial derivative - partially paracrystalline, coarse fibres associated with the axoneme), it also possesses a number of previously undescribed and possibly unique features (a longitudinally inrolled acrosomal pedestal, an axial structure within the cavity of the acrosomal pedestal, an electron-dense collar at the anterior region of the acrosomal pedestal, the presence of crystalloid bodies within the glycogen helices of the mitochondrial derivative). To our knowledge this is the first report of crystalloid bodies in mature sperm of any mollusc. Collectively this evidence raises questions concerning the affinities and systematic position of Cadlinella within the Nudibranchia. The peculiar nature of the sperm differences, in comparison with other investigated nudibranchs, suggest that Cadlinella is not easily linked to either the Cadlinidae or Chromodorididae, and should be considered incertae sedis.

The synthesis and structure of an n-terminal dodecanoic acid conjugate of a-conotoxin MII

The alpha-conotoxin MII is a 16 amino acid long peptide toxin isolated from the marine snail, Conus magus. This toxin has been found to be a highly selective and potent inhibitor of neuronal nicotinic acetylcholine receptors of the subtype alpha3beta2. To improve the bioavailability of this peptide, we have coupled to the N-terminus of conotoxin MII, 2-amino-D,L-dodecanoic acid (Laa) creating a lipidic linear peptide which was then successfully oxidised to produce the correctly folded conotoxin MII construct.

Stress correlation function evolution in lattice solid elasto-dynamic models of shear and fracture zones and earthquake prediction

It has been argued that power-law time-to-failure fits for cumulative Benioff strain and an evolution in size-frequency statistics in the lead-up to large earthquakes are evidence that the crust behaves as a Critical Point (CP) system. If so, intermediate-term earthquake prediction is possible. However, this hypothesis has not been proven. If the crust does behave as a CP system, stress correlation lengths should grow in the lead-up to large events through the action of small to moderate ruptures and drop sharply once a large event occurs. However this evolution in stress correlation lengths cannot be observed directly. Here we show, using the lattice solid model to describe discontinuous elasto-dynamic systems subjected to shear and compression, that it is for possible correlation lengths to exhibit CP-type evolution. In the case of a granular system subjected to shear, this evolution occurs in the lead-up to the largest event and is accompanied by an increasing rate of moderate-sized events and power-law acceleration of Benioff strain release. In the case of an intact sample system subjected to compression, the evolution occurs only after a mature fracture system has developed. The results support the existence of a physical mechanism for intermediate-term earthquake forecasting and suggest this mechanism is fault-system dependent. This offers an explanation of why accelerating Benioff strain release is not observed prior to all large earthquakes. The results prove the existence of an underlying evolution in discontinuous elasto-dynamic, systems which is capable of providing a basis for forecasting catastrophic failure and earthquakes.

Simulation of the load-unload response ratio and critical sensitivity in the lattice solid model

The Load-Unload Response Ratio (LURR) method is an intermediate-term earthquake prediction approach that has shown considerable promise. It involves calculating the ratio of a specified energy release measure during loading and unloading where loading and unloading periods are determined from the earth tide induced perturbations in the Coulomb Failure Stress on optimally oriented faults. In the lead-up to large earthquakes, high LURR values are frequently observed a few months or years prior to the event. These signals may have a similar origin to the observed accelerating seismic moment release (AMR) prior to many large earthquakes or may be due to critical sensitivity of the crust when a large earthquake is imminent. As a first step towards studying the underlying physical mechanism for the LURR observations, numerical studies are conducted using the particle based lattice solid model (LSM) to determine whether LURR observations can be reproduced. The model is initialized as a heterogeneous 2-D block made up of random-sized particles bonded by elastic-brittle links. The system is subjected to uniaxial compression from rigid driving plates on the upper and lower edges of the model. Experiments are conducted using both strain and stress control to load the plates. A sinusoidal stress perturbation is added to the gradual compressional loading to simulate loading and unloading cycles and LURR is calculated. The results reproduce signals similar to those observed in earthquake prediction practice with a high LURR value followed by a sudden drop prior to macroscopic failure of the sample. The results suggest that LURR provides a good predictor for catastrophic failure in elastic-brittle systems and motivate further research to study the underlying physical mechanisms and statistical properties of high LURR values. The results provide encouragement for earthquake prediction research and the use of advanced simulation models to probe the physics of earthquakes.

Simulation of the influence of rate- and state-dependent friction on the macroscopic behavior of complex fault zones with the lattice solid model

In order to understand the earthquake nucleation process, we need to understand the effective frictional behavior of faults with complex geometry and fault gouge zones. One important aspect of this is the interaction between the friction law governing the behavior of the fault on the microscopic level and the resulting macroscopic behavior of the fault zone. Numerical simulations offer a possibility to investigate the behavior of faults on many different scales and thus provide a means to gain insight into fault zone dynamics on scales which are not accessible to laboratory experiments. Numerical experiments have been performed to investigate the influence of the geometric configuration of faults with a rate- and state-dependent friction at the particle contacts on the effective frictional behavior of these faults. The numerical experiments are designed to be similar to laboratory experiments by DIETERICH and KILGORE (1994) in which a slide-hold-slide cycle was performed between two blocks of material and the resulting peak friction was plotted vs. holding time. Simulations with a flat fault without a fault gouge have been performed to verify the implementation. These have shown close agreement with comparable laboratory experiments. The simulations performed with a fault containing fault gouge have demonstrated a strong dependence of the critical slip distance D-c on the roughness of the fault surfaces and are in qualitative agreement with laboratory experiments.

The Three-dimensional Solution Structure of NaD1, a New Floral Defensin from Nicotiana alata and its Application to a Homology Model of the Crop Defense Protein alfAFP

NMR spectroscopy and simulated annealing calculations have been used to determine the three-dimensional structure of NaD1, a novel antifungal and insecticidal protein isolated from the flowers of Nicotiana alata. NaD1 is a basic, cysteine-rich protein of 47 residues and is the first example of a plant defensin from flowers to be characterized structurally. Its three-dimensional structure consists of an a-helix and a triple-stranded anti-parallel beta-sheet that are stabilized by four intramolecular disulfide bonds. NaD1 features all the characteristics of the cysteine-stabilized up motif that has been described for a variety of proteins of differing functions ranging from antibacterial insect defensins and ion channel-perturbing scorpion toxins to an elicitor of the sweet taste response. The protein is biologically active against insect pests, which makes it a potential candidate for use in crop protection. NaD1 shares 31% sequence identity with alfAFP, an antifungal protein from alfalfa that confers resistance to a fungal pathogen in transgenic potatoes. The structure of NaD1 was used to obtain a homology model of alfAFP, since NaD1 has the highest level of sequence identity with alfAFP of any structurally characterized antifungal defensin. The structures of NaD1 and alfAFP were used in conjunction with structure - activity data for the radish defensin Rs-AFP2 to provide an insight into structure-function relationships. In particular, a putative effector site was identified in the structure of NaD1 and in the corresponding homology model of alfAFP. (C) 2002 Elsevier Science Ltd. All rights reserved.

Synthesis and structural analysis of the N-terminal domain of the thyroid hormone-binding protein transthyretin

Transthyretin (TTR) is a 55 kDa protein responsible for the transport of thyroid hormones and retinol in human serum. Misfolded forms of the protein are implicated in the amyloid diseases familial amyloidotic polyneuropathy and senile systemic amyloidosis. Its folding properties and stabilization by ligands are of current interest due to their importance in understanding and combating these diseases. To assist in such studies we developed a method for the solid phase synthesis of the monomeric unit of a TTR analogue and its folding to form a functional 55 kDa tetramer. The monomeric unit of the protein was chemically synthesized in three parts, comprising amino acid residues 151, 5499 and 102127, and ligated using chemoselective thioether ligation chemistry. The synthetic protein was folded and assembled to a tetrameric structure in the presence of the TTRs native ligand, thyroxine, as shown by gel filtration chromatography, native gel electrophoresis, TTR antibody recognition and thyroid hormone binding. In the current study the solution structure of the first of these fragment peptides, TTR(151) is examined to determine its intrinsic propensity to form beta-sheet structure, potentially involved in amyloid fibril formation by TTR. Despite the presence of extensive beta-structure in the native form of the protein, the Nterminal fragment adopts an essentially random coil conformation in solution.

Secondary structure of the third extracellular loop responsible for ligand selectivity of a mammalian gonadotropin-releasing hormone receptor

The extracellular loop 3 (ECL3) of the mammalian gonadotropin-releasing hormone receptor (GnRH-R) contains an acidic amino acid (Glu(301) in the mouse GnRH-R,) that confers agonist selectivity for Are in mammalian GnRH. It is proposed that a specific conformation of ECL3 is necessary to orientate the carboxyl side chain of the acidic residue for interaction with Arg(8) of GnRH, which is supported by decreased affinity for Arg(8) GnRH but not Gln(8) GnRH when an adjacent Pro is mutated to Ala. To probe the structural contribution of the loop domain to the proposed presentation of the carboxyl side chain, we synthesized a model peptide (CGPEMLNRVSEPGC) representing residues 293-302 of mouse ECL3, where Cys and Gly residues are added symmetrically at the N and C termini, respectively, allowing the introduction of a disulfide bridge to simulate the distances at which the ECL3 is tethered to the transmembrane domains 6 and 7 of the receptor. The ability of the ECL3 peptide to bind GnRH with low affinity was demonstrated by its inhibition of GnRH stimulation of inositol phosphate production in cells expressing the GnRH-R. The CD bands of the ECL3 peptides exhibited a superposition of predominantly unordered structure and partial contributions from beta-sheet structure. Likewise, the analysis of the amide I and amide III bands from micro-Raman and FT Raman experiments revealed mainly unordered conformations of the cyclic and of the linear peptide. NMR data demonstrated the presence of a beta-hairpin among an ensemble of largely disordered structures in the cyclic peptide. The location of the turn linking the two strands of the hairpin was assigned to the three central residues L-296, N-297, and R-298. A small population of structured species among an ensemble of predominantly random coil conformation suggests that the unliganded receptor represents a variety of structural conformers, some of which have the potential to make contacts with the ligand. We propose a mechanism of receptor activation whereby binding of the agonist to the inactive receptor state induces and stabilizes a particular structural state of the loop domain, leading to further conformational rearrangements across the transmembrane domain and signal propagating interaction with G proteins. Interaction of the Glu(301) of the receptor with Arg(8) of GnRH induces a folded configuration of the ligand. Our proposal thus suggests that conformational changes of both ligand and receptor result from this interaction.

Preservation of three-dimensional capillary structure in frog muscle during aestivation

In mammals, prolonged immobilization of the limbs can result in a loss of capillary tortuosity, resulting in skeletal muscle haemorrhaging if rapid remobilization is permitted. In this study, we examined the effect of 4 months' immobilization on semimembranosus capillary structure in the Green-striped burrowing frog, Cyclorana alboguttata. C alboguttata routinely aestivates as part of a physiological strategy to avoid desiccation in semi-arid environments and, in this capacity, the hindlimbs of C alboguttata are immobilized in a cocoon for months at a time. We found that 4 months' aestivation had no effect on three-dimensional capillary structure in the semimembranosus muscle and that capillary tortuosity is preserved in immobilized C. alboguttata. The preservation of capillary structure in the hindlimb muscles of C alboguttata in part accounts for their remarkable ability to emerge with a fully competent locomotor system after prolonged immobilization.

Structure of the gut contents of Trichogramma australicum Girault (Hymenoptera : Trichogrammatidae) larvae fixed in situ in eggs of its host Helicoverpa armigera (Hubner) (Lepidoptera : Noctuidae)

Trichogramma australicum larvae develop most rapidly in younger eggs of its host, the pest lepidopteran Helicoverpa armigera . To establish how the developmental stage of the host affects the diet of T. australicum , larvae were fixed in situ in eggs of H. armigera of different ages and the structure of the egg contents and parasitoid gut contents examined histologically. Larvae feeding on newly laid host eggs contain primarily yolk particles in their gut, while larvae feeding on older hosts contain necrotic cells and yolk particles. The gut of T. australicum larvae does not contain organised tissue remnants, indicating that larvae feed primarily by sucking food into their pharynx and feed best on a mixture of particulate semisolids in a liquid matrix. Secretory structures of T. australicum larvae that could be involved in modifying the host environment were examined. The hindgut is modified to form an anal vesicle with a number of attributes suggesting that it may be a specialised secretory structure. The paired salivary glands open to the exterior via a common duct.

A suite of novel allenes from Australian melolonthine scarab beetles. Structure, synthesis, and stereochemistry

A suite of allenic hydrocarbons, previously unknown as a molecular class from insects, has been characterized from several Australian melolonthine scarab beetles. The allenes are represented by the formula CH3(CH2)nCH=.=CH(CH2)(7)CH3 with n being 11-15, 17 and 19, and thus, all have Delta(9,10)-unsaturation. These structures have been confirmed by syntheses and comparisons of spectral and chromatographic properties with those of the natural components. The enantiomers of (+/-)-Delta(9,10)-tricosadiene and Delta(9,10)-pentacosadiene were separable on a modified beta-cyclodextrin column (gas chromatography), and the natural Delta(9,10)-tricosadiene (n = 11) and Delta(9,10)-pentacosadiene (n = 13) were shown to be of >85% ee. Syntheses of nonracemic allenes of known predominating chirality were acquired using both organotin chemistry and sulfonylhydrazine intermediates, and comparisons then demonstrated that the natural allenes were predominantly (R)-configured.